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A

AA - Static variable in interface apollo.datamodel.SequenceI
AAMultiSequenceAlignerPanel - Class in apollo.gui.detailviewers.sequencealigner.AAPanel: The main class for the Amino Acid view.
AAMultiSequenceAlignerPanel(GuiCurationState, Strand, ReadingFrame) - Constructor for class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel: Constructor
AB_INITIO_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
ABINITIO - Static variable in class apollo.dataadapter.ensj.model.TypesModel
AbstractApolloAdapter - Class in apollo.dataadapter: All the dataadapters now subclass AbstractApolloAdapter, which new data adapters should do as well.
AbstractApolloAdapter() - Constructor for class apollo.dataadapter.AbstractApolloAdapter
AbstractLazySequence - Class in apollo.datamodel.seq: i wonder if this should move to dataadapter package as its a sequence loader basically - so it loads stuff just like a data adapter
AbstractLazySequence(String, Controller) - Constructor for class apollo.datamodel.seq.AbstractLazySequence
AbstractLazySequence.LazyLoadControlledObject - Class in apollo.datamodel.seq
AbstractLazySequence.LazyLoadControlledObject(Controller) - Constructor for class apollo.datamodel.seq.AbstractLazySequence.LazyLoadControlledObject
AbstractParser - Class in apollo.dataadapter.analysis
AbstractParser() - Constructor for class apollo.dataadapter.analysis.AbstractParser
AbstractScrollablePanel - Class in apollo.gui.detailviewers.sequencealigner
AbstractScrollablePanel() - Constructor for class apollo.gui.detailviewers.sequencealigner.AbstractScrollablePanel
AbstractSequence - Class in apollo.datamodel
AbstractSequence(String) - Constructor for class apollo.datamodel.AbstractSequence
AbstractTierPanel - Class in apollo.gui.detailviewers.sequencealigner
AbstractTierPanel() - Constructor for class apollo.gui.detailviewers.sequencealigner.AbstractTierPanel
accept(Visitor) - Method in class apollo.datamodel.AnnotatedFeature: General implementation of Visitor pattern.
accept(Visitor) - Method in class apollo.datamodel.AssemblyFeature
accept(Visitor) - Method in class apollo.datamodel.CurationSet: General implementation of Visitor pattern.
accept(Visitor) - Method in class apollo.datamodel.Evidence: General implementation of Visitor pattern.
accept(Visitor) - Method in class apollo.datamodel.FeatureSet: General implementation of Visitor pattern.
accept(Visitor) - Method in class apollo.datamodel.SeqFeature: General implementation of Visitor pattern.
accept(Visitor) - Method in interface apollo.datamodel.SeqFeatureI: A general utility method to accept Visitors.
accept(Visitor) - Method in class apollo.datamodel.StrandedFeatureSet: General implementation of Visitor pattern.
accept(Visitor) - Method in class apollo.gui.drawable.DrawableSeqFeature: General implementation of Visitor pattern.
accept(File) - Method in class apollo.gui.GenericFileFilter: Whether the given file is accepted by this filter
accept(File) - Method in class apollo.util.ExampleFileFilter: Return true if this file should be shown in the directory pane, false if it shouldn't.
ACCESSION - Static variable in class apollo.dataadapter.otter.parser.TagHandler
ActionEventRouter - Class in apollo.dataadapter.ensj.controller: Generic class to forward action events onto central handler.
ActionEventRouter(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ActionEventRouter
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI.HistoryListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI.ProxyListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das2.DAS2AdapterGUI.HistoryListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das2.DAS2AdapterGUI.ProxyListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.EnsCGIAdapterGUI.ChrStartEndListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj.controller.ActionEventRouter
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj.view.AnnotationsPanel
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowTypesActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser.FindDataSetsListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.ChooserActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.DatabaseFindListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.EnsemblDBSelectionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.HostListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DriverDialog
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataSourceChangeListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.GbrowseAdapterGUI.ChrStartEndListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.graph.GraphAdapterGUI.ColorActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.AlignBlockChooser.OKButtonListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI.ModelChangeListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.DnaAlignTypesButtonActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.FullPanelListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.ShowDataSourceConfigurationActionListener
actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.AddFilterAction
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.CreateExonAction: Performs the insertion
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.CreateIntronAction: Performs the insertion
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.DeleteExonAction: Performs the deletion
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.DisplaySequenceAction: Brings up the display sequence window
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.FrameShiftAction: Performs the insertion
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.MergeExonAction: Performs the merge
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SequenceEditAction: Performs the sequence edit
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SetEndAction: Performs the update
actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SetTranslationStartAction: Performs the update
actionPerformed(ActionEvent) - Method in class apollo.gui.event.MethodRunnerActionListener: Runs the method named in the constructor.
actionPerformed(ActionEvent) - Method in class apollo.gui.FindPanel: Handles all buttons and fields, does name, position, and sequence searching
actionPerformed(ActionEvent) - Method in class apollo.gui.FullSyntenyPanel
actionPerformed(ActionEvent) - Method in class apollo.gui.genomemap.NavigationBar
actionPerformed(ActionEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel: Action event listener
actionPerformed(ActionEvent) - Method in class apollo.gui.GlyphChooser
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.AnalysisMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.AnnotationMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.EditMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.FileMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.GraphMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.HelpMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.LinksMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.PeptideMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.PropertyMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ShowMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.SyntenyLinkMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.SyntenyViewMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ThresholdMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TierPopupMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TiersMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TreeMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TypesMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ViewMenu
actionPerformed(ActionEvent) - Method in class apollo.gui.PropertyPanel
actionPerformed(ActionEvent) - Method in class apollo.gui.ProxyDialog
actionPerformed(ActionEvent) - Method in class apollo.gui.TableColumnChooser
actionPerformed(ActionEvent) - Method in class apollo.gui.tweeker.Tweeker
actionPerformed(ActionEvent) - Method in class apollo.gui.TypePanel
adapter - Variable in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
ADAPTER - Static variable in class apollo.dataadapter.synteny.builder.Model
adapter - Variable in class apollo.gui.ProgressFrame
ADAPTER_CLASSES - Static variable in class apollo.dataadapter.synteny.builder.Model
ADAPTER_SET - Static variable in class apollo.dataadapter.synteny.builder.Model
ADAPTER_TYPES - Static variable in class apollo.dataadapter.synteny.builder.Model
adapterClassName - Variable in class apollo.dataadapter.chado.ChadoDatabase: Fully-qualified name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter; used to implement DBMS-specific features or optimizations.
AdapterModel - Class in apollo.dataadapter.synteny.builder
AdapterModel(String, String, String) - Constructor for class apollo.dataadapter.synteny.builder.AdapterModel
adaptorName - Variable in class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataTypeButton
ADD - Static variable in class apollo.editor.FeatureChangeEvent: Replace these with TransactionOperation!
ADD - Static variable in class apollo.editor.TransactionOperation
add(Comparator<T>) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.MultiComparatorArrayList
add(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
add(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
add(ViewI, Object) - Method in class apollo.gui.genomemap.ApolloPanel: Add a View to the views.
add(ViewI) - Method in class apollo.gui.genomemap.ApolloPanel
add(ViewI, Object) - Method in class apollo.gui.genomemap.LaidoutViewContainer
add(SelectionItem) - Method in class apollo.gui.Selection: I took out the boolean force, add is always an add and if its already it does nothing, in other words have it always be force == true, i dont think force==false was used at all Took out the return value of SelectionItem - dont think it was used.
add(SelectionItem, boolean) - Method in class apollo.gui.Selection
add(FeatureList, Object, boolean) - Method in class apollo.gui.Selection
add(FeatureList, Object) - Method in class apollo.gui.Selection
add(Selection, boolean) - Method in class apollo.gui.Selection
add(Selection) - Method in class apollo.gui.Selection
add(Object) - Method in class apollo.util.FeatureIterator
add(Object) - Method in class apollo.util.FeatureList: addFeature should be used in lieu of add.
ADD_RESULT_GENES_AS_ANNOTATIONS - Static variable in class apollo.dataadapter.StateInformation
ADD_RESULT_GENES_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel
ADD_TRANSCRIPT_SUPPORT - Static variable in class apollo.dataadapter.StateInformation
ADD_TRANSCRIPT_SUPPORT_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel
addActionListener(ActionListener) - Method in class apollo.dataadapter.synteny.builder.Controller
addActionListener(ActionListener) - Method in class apollo.gui.ChromosomeField
addActionRouter(JButton, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addActionRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addActionRouter(JButton, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addActionRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addAdapterModel(String, AdapterModel) - Method in class apollo.dataadapter.synteny.builder.Model
addAdapterSet(String) - Method in class apollo.dataadapter.synteny.builder.Model
addAlignable(SeqFeatureI) - Method in class apollo.util.FeatureList
addAlignFeature(SequenceI, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,
addAlignFeature(SequenceI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Adds feature to an existing SeqWrapper if it doesn't overlap with it, otherwise creates a new SeqWrapper for it,
addAlignPair(FeaturePairI, FeatureSetI) - Method in class apollo.dataadapter.analysis.AlignmentParser
addAll(Collection<? extends SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
addAll(int, Collection<? extends SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
addAll(FeatureList) - Method in class apollo.util.FeatureList: Adds all feats that are new, that it doesnt already have.
addAllFeatures(FeatureList) - Method in class apollo.util.FeatureList
addAnalysisType(String) - Method in class apollo.config.FeatureProperty
addAnalysisType(FeatureProperty, String) - Method in class apollo.config.TierProperty
addAnnot(Vector, boolean) - Method in class apollo.editor.AnnotationEditor: This method is a complete edit for adding a new gene.
addAnnotation(Vector, boolean, String) - Method in class apollo.editor.AnnotationEditor
addAnnotationComment(String) - Method in class apollo.config.Style: Add a canned annotation comment.
addAnnotationEditor(AnnotationEditor, boolean) - Method in class apollo.dataadapter.CurationState
addAnnotationEditor(AnnotationEditor, boolean) - Method in class apollo.gui.synteny.GuiCurationState
addAnnotations(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Adds a collection of annotations to the list of annotations (but not the annotation panel)
addAttributeValue(String, String) - Method in class apollo.dataadapter.gff3.GFF3Entry: Add an attribute
addCapability(String, String) - Method in class apollo.dataadapter.das.simple.SimpleDASDsn: e.g.
addCellEditorListener(CellEditorListener) - Method in class apollo.gui.DisabledEditor
addChange(AnnotationChangeEvent) - Method in class apollo.editor.ChangeList: Add change to end of changes list
addChangeList(ChangeList) - Method in class apollo.editor.ChangeList
addCheckbox(JCheckBox) - Method in class apollo.dataadapter.FileTabPanel
addChildren(SeqFeatureI) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: Find all children of this parent and add them to the parent seqfeature
addColumn(ColumnProperty) - Method in class apollo.config.FeatureProperty
addComment(String) - Method in class apollo.config.FeatureProperty
addComment(String) - Method in class apollo.config.TierProperty
addComment(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Comment strings look like this: Only one EST supports this alternative transcript::DATE:Mon Feb 26 18:08:49 CET 2007::TS:1172509728919 With the author in the pub table
addComment(long, Comment) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add a comment to the database
addComment(Comment) - Method in class apollo.datamodel.AnnotatedFeature
addComment(int, Comment) - Method in class apollo.datamodel.AnnotatedFeature
addComment(Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI
addComment(int, Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI
addComments(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add all comments from an AnnotatedFeatureI object
addContigFeatures(CurationSet, List, Location) - Method in class apollo.dataadapter.ensj.DataFetcher
addController(Controller) - Method in class apollo.gui.MultiController
addCurationSet(Object, CurationSet) - Method in class apollo.datamodel.CurationSet
addCutSites(Vector, Vector, Color) - Method in class apollo.gui.genomemap.ScaleView
addDataChangeListenerToDataSourceConfigPanels() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI
addDataListener(DataListener) - Method in class apollo.dataadapter.DummySequenceAdapter
addDataListener(DataListener) - Method in class apollo.dataadapter.EfetchSequenceAdapter
addDbXref(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
addDbXref(long, DbXref) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
addDbXref(String, String) - Method in class apollo.datamodel.AbstractSequence
addDbXref(String, String, int) - Method in class apollo.datamodel.AbstractSequence
addDbXref(DbXref) - Method in class apollo.datamodel.AbstractSequence
addDbXref(DbXref) - Method in class apollo.datamodel.Identifier
addDbXref(DbXref) - Method in class apollo.datamodel.SeqFeature
addDbXref(DbXref) - Method in interface apollo.datamodel.SeqFeatureI
addDbXref(String, String, int) - Method in interface apollo.datamodel.SequenceI
addDbXref(String, String) - Method in interface apollo.datamodel.SequenceI
addDbXref(DbXref) - Method in interface apollo.datamodel.SequenceI
addDbxrefs(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add all dbxrefs from an AnnotatedFeatureI object
addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableGeneSeqFeature: Draws in translated sequence if feature is an ExonI, its zoomed in, seq is available, and it is in a coding region
addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableResultSeqFeature
addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature: draw in label and codons
addDisplayComponents() - Method in class apollo.dataadapter.analysis.AnalysisPanel: Default display type entry component is JComboBox
addDitagFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addDnaAlignFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableFeatureSet
addDrawable(Drawable) - Method in interface apollo.gui.drawable.DrawableSetI
addEditRegion() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: puts up vertical lines in szap(main window) indicating what region that is currently displayed
addEvidence(String, String, int) - Method in class apollo.datamodel.AnnotatedFeature
addEvidence(String) - Method in class apollo.datamodel.AnnotatedFeature
addEvidence(String, int) - Method in class apollo.datamodel.AnnotatedFeature
addEvidence(Evidence) - Method in class apollo.datamodel.AnnotatedFeature
addEvidence(String) - Method in interface apollo.datamodel.AnnotatedFeatureI
addEvidence(String, int) - Method in interface apollo.datamodel.AnnotatedFeatureI
addEvidence(Evidence) - Method in interface apollo.datamodel.AnnotatedFeatureI
addEvidence(Evidence) - Method in class apollo.datamodel.EvidenceSet
addEvidenceExons() - Method in class apollo.editor.AnnotationEditor: The default method to add evidence to exons.
addEvidenceExonsAllowed() - Method in class apollo.editor.AnnotationEditor: Determine if the current selection sets are compatible with the the default adding evidence to exons method.
addEvidencePanel(EvidencePanel) - Method in class apollo.gui.evidencepanel.EvidencePanelContainer
addExon(SeqFeatureI, String, Date, Long, int, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: Add an exon to the database.
addExon(SeqFeatureI, String, Date, Long, int, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add an exon to a transcript, inserting the exon into the database if it does not already exist.
addExon(ExonI) - Method in class apollo.datamodel.Transcript: If exon overlaps with other exons then it merges them, otherwise adds exon to transcript
addExons() - Method in class apollo.editor.AnnotationEditor: The default addExons which adds exons to a transcript.
addExons(Transcript, Vector) - Method in class apollo.editor.AnnotationEditor: The version of addExons which actually does the work.
addExonsAllowed() - Method in class apollo.editor.AnnotationEditor
addExtension(String) - Method in class apollo.gui.GenericFileFilter: Adds a file extension for filtering
addExtension(String) - Method in class apollo.util.ExampleFileFilter: Adds a filetype "dot" extension to filter against.
addExternalDataChangeListener(ActionListener) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel: Sometimes we want to know when the user has started modifying the datasource, from _outside_ this panel.
addExternalDataSourceChangeListener(ActionListener) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel: The input listener is added to each data source config panel.
addFeature() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser
addFeature(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet: Add feature to end of features list, recalc low and high
addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.FeatureSet
addFeature(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature: no-op.
addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.SeqFeature: no-op - overridden by FeatureSet
addFeature(SeqFeatureI) - Method in interface apollo.datamodel.SeqFeatureI: Add child feature
addFeature(SeqFeatureI, boolean) - Method in interface apollo.datamodel.SeqFeatureI: Add feature at sorted position
addFeature(SeqFeatureI) - Method in class apollo.datamodel.StrandedFeatureSet: Features must be added in sort order, if this turns out to be too slow, then we will need to figure out another way to keep them all sorted (5prime to 3prime that is)
addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.StrandedFeatureSet
addFeature(SeqFeatureI) - Method in class apollo.datamodel.Transcript
addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel: Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,
addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,
addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel
addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Adds the feature to this Tier
addFeature(SeqFeatureI) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
addFeature(Drawable, Transformer) - Method in class apollo.gui.genomemap.FeatureTier: Calls addFeature on its FeatureSet with the DrawableSeqFeature and the sort flag set to true, this will cause the DSFs to be sorted Since it only allows DrawableSeqFeatures to be added shouldnt the fset be a DrawableFeatureSet instead of just a FeatureSet? Then getFeatureSet could return a DrawableFeatureSet and we wouldnt have to cast it There doesnt seem to be a reason at the moment to let it other features than dsfs - am i right about this?
addFeature(SeqFeatureI) - Method in class apollo.util.FeatureList: Adds SeqFeatureI if not already in list
addFeatureDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableFeatureSet: Create a drawable for sf(createDrawable) and add it as a child (addDrawable).
addFeatureDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableGeneFeatureSet
addFeatureDrawable(SeqFeatureI) - Method in interface apollo.gui.drawable.DrawableSetI
addFeaturePair(FeaturePairI) - Method in class apollo.util.FeatureList
addFeatureProperty(FeatureProperty) - Method in class apollo.config.TierProperty
addFeatures(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Adds a collection of features to this tier
addFeatures(Collection<SeqFeatureI>) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
addFeatureToPanel(SeqFeatureI, MultiTierPanel) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
addField(String, Component) - Method in class apollo.gui.annotinfo.FeatureEditPanel
addField(JComponent, Component) - Method in class apollo.gui.annotinfo.FeatureEditPanel
addFieldName(String) - Method in class apollo.dataadapter.mysql.Table
addFieldsPanelBottomGlue() - Method in class apollo.gui.annotinfo.FeatureEditPanel: pad out bottom of fields panel, for layout - otherwise syns can get huge
AddFilterAction - Class in apollo.gui.detailviewers.sequencealigner.actions
AddFilterAction(MultiSequenceAlignerPanel, AddFilterPanel.TYPES) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.AddFilterAction
AddFilterPanel - Class in apollo.gui.detailviewers.sequencealigner.menus
AddFilterPanel(MultiSequenceAlignerPanel, AddFilterPanel.TYPES) - Constructor for class apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel
AddFilterPanel.TYPES - Enum in apollo.gui.detailviewers.sequencealigner.menus
addFirst(ViewI, Object) - Method in class apollo.gui.genomemap.LaidoutViewContainer
addGene(FeatureSetI, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GeneFinderParser
addGene(SeqFeatureI, String, Date, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add a gene to the chado database.
addGeneOrTranscript() - Method in class apollo.editor.AnnotationEditor: The default addGeneOrTranscript.
addGeneOrTranscript(boolean) - Method in class apollo.editor.AnnotationEditor
addGeneOrTranscriptAllowed() - Method in class apollo.editor.AnnotationEditor: Determine whether it's OK to do an add gene or transcript.
addGenePredictionResults(Connection, String[], StrandedFeatureSet, FeatureLocImplementation, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Deprecated. use chadoProgram array instead of string array
addGenePredictionResults(Connection, ChadoProgram[], StrandedFeatureSet, FeatureLocImplementation, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve gene predictions and add them to parentFeatSet as SeqFeatures.
addGenePredictionResults(Connection, ChadoProgram[], StrandedFeatureSet, FeatureLocImplementation, SequenceI, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve gene predictions and add them to parentFeatSet as SeqFeatures.
addGenes(StrandedFeatureSet, Location, List, boolean, String) - Method in class apollo.dataadapter.ensj.DataFetcher: Retrieves ensJ genes/transcripts/exons, converts them into seq features and adds them to the curation set.
addGraph(ScoreCalculator, boolean, Color) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
addHighlightRegion(BaseScrollable, Color, boolean) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableFeatureSet
addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature: highlights edges and box around if isHighlighted
addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Triangle
addIsProblematicCheckbox() - Method in class apollo.gui.annotinfo.FeatureEditPanel
addItemListener(ItemListener) - Method in class apollo.dataadapter.ensj19.SourceChooserWithHistory
addKaryotype(Karyotype) - Method in class apollo.dataadapter.KaryotypeAdapter
addKeyRouter(JTextField, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addKeyRouter(Component, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addKeyRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addKeyRouter(JTextField, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addKeyRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addKeyRouter(Component, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addKeyword(String) - Method in class apollo.datamodel.AssemblyFeature
addLayoutComponent(Component, Object) - Method in class apollo.gui.genomemap.ApolloLayoutManager
addLayoutComponent(String, Component) - Method in class apollo.gui.synteny.SyntenyLayout
addLayoutView(ViewI, Object) - Method in class apollo.gui.genomemap.ApolloLayoutManager
addLink(FeaturePairI) - Method in class apollo.datamodel.LinkSet
addLink(Link) - Method in class apollo.datamodel.LinkSet
addLinkPanel(SyntenyLinkPanel) - Method in class apollo.gui.synteny.SyntenyPanel
addLinks(LinkSet) - Method in class apollo.datamodel.LinkSet
addListener(EventListener) - Method in class apollo.gui.Controller
addListener(RubberbandListener) - Method in class apollo.gui.genomemap.Rubberband
addMessage(String, String) - Method in class apollo.gui.PrefsPanel
addNewAnnot(String) - Method in class apollo.editor.AnnotationEditor
addNote(String, PeptideNote) - Method in class apollo.dataadapter.genbank.GenbankValidator
addNotify() - Method in class apollo.gui.annotinfo.FeatureEditorDialog
addNotify() - Method in class apollo.gui.ControlledPanel: override Component.addNotify, called when added to parent.
addNotify() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
addNotify() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel.DefaultRowHeader: This is where the row numbers JLabels get created
addNotify() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
addNotify() - Method in class apollo.gui.featuretree.FeatureTreeFrame
addNotify() - Method in class apollo.gui.FindPanel
addOccurance() - Method in class apollo.analysis.filter.HuffNode
addOneLevelAnnotations(Connection, SequenceI, StrandedFeatureSet, FeatureLocImplementation, boolean, boolean, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: add annotations with only one level, like transposons (for now) and annotated tiling paths, promoters & what not.
addOverlappingAllowed() - Method in class apollo.editor.AnnotationEditor
addOverlappingGene(Vector) - Method in class apollo.editor.AnnotationEditor: This method creates a new gene from the features, whether or not they overlap an existing gene.
addPanel(AbstractTierPanel) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel: Adds a new
addPanel(StrandedZoomableApolloPanel) - Method in class apollo.gui.synteny.SyntenyPanel
addParameter(String, String) - Method in class apollo.config.Style: Whenever we add a new parameter to the style file, we've been adding methods in Style.java to set/get some variable--it's getting annoying.
addPopupRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller
addPopupRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
addPredictionTranscripts(StrandedFeatureSet, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addPrimaryKeyColumnValue(String, HashMap) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
addPropertiesWithPrefix(Properties, String, Properties) - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI
addProperty(String, String) - Method in class apollo.analysis.SeqAnalysisBase
addProperty(String, String) - Method in interface apollo.analysis.SeqAnalysisI: set the value of a property
addProperty(String, String) - Method in class apollo.dataadapter.chado.ChadoTransaction
addProperty(String, String) - Method in class apollo.dataadapter.synteny.builder.AdapterModel
addProperty(String, String) - Method in class apollo.datamodel.FeaturePair
addProperty(String, String) - Method in class apollo.datamodel.seq.GenbankSequence
addProperty(String, String) - Method in class apollo.datamodel.SeqFeature
addProperty(String, String) - Method in interface apollo.datamodel.SeqFeatureI
addProperty(String, String) - Method in class apollo.datamodel.Synonym
addProperty(String, String, int) - Method in class apollo.editor.Transaction: Add a new value to the Vector for this property name.
addPropSchemeChangeListener(PropSchemeChangeListener) - Method in class apollo.config.PropertyScheme
addProteinAlignFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addProteinAlignments(Connection, String, StrandedFeatureSet, FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve a set of protein alignments from Chado and convert them into instances of apollo.datmodel.FeaturePair.
addProteinAnnotations(CurationSet, List, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addRefFeature(String, SeqFeatureI) - Method in class apollo.datamodel.SeqFeature
addRemark(String) - Method in class apollo.datamodel.AssemblyFeature
addRepeatFeatures(CurationSet, List, Location) - Method in class apollo.dataadapter.ensj.DataFetcher: Add all repeat features into the input set.
addResult(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: Adds a result to this panel so that it can be displayed.
AddResultFilterAction - Class in apollo.gui.detailviewers.sequencealigner.actions
AddResultFilterAction(MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction
addResultGenesAsAnnotations() - Method in class apollo.dataadapter.ensj.model.OptionsModel
addResults(Set<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: Adds all results in a set to this panel so that they can be displayed.
addResults(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Adds a collection of results to the list of results (but not to the result panel)
addReturnedObject(Object) - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
addScore(Score) - Method in class apollo.datamodel.FeaturePair
addScore(double) - Method in class apollo.datamodel.FeaturePair
addScore(String, double) - Method in class apollo.datamodel.FeaturePair
addScore(String, String) - Method in class apollo.datamodel.FeaturePair
addScore(Score) - Method in class apollo.datamodel.SeqFeature
addScore(double) - Method in class apollo.datamodel.SeqFeature
addScore(String, double) - Method in class apollo.datamodel.SeqFeature
addScore(String, String) - Method in class apollo.datamodel.SeqFeature
addScore(Score) - Method in interface apollo.datamodel.SeqFeatureI
addScore(double) - Method in interface apollo.datamodel.SeqFeatureI
addScore(String, double) - Method in interface apollo.datamodel.SeqFeatureI
addScore(String, String) - Method in interface apollo.datamodel.SeqFeatureI
addScrollBar() - Method in class apollo.gui.genomemap.TierView
addSearchHits(Connection, ChadoProgram[], boolean, boolean, boolean, boolean, boolean, SequenceI, StrandedFeatureSet, String, boolean, FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve a set of search hits (e.g.
addSelectedToHistory() - Method in class apollo.dataadapter.GuiTabPanel: Puts currently selected item at top of history list
addSelectionListener(SelectableI) - Method in class apollo.gui.SelectionItem
addSequence(SequenceI) - Method in class apollo.datamodel.CurationSet
addSequence(SequenceI, int, String, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
addSequenceEdit(SequenceEdit, String, Date) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: Add a sequence edit to the database.
addSequenceEdit(SequenceEdit, String, Date) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
addSequenceEdit(SequenceEdit) - Method in class apollo.datamodel.AbstractSequence
addSequenceEdit(SequenceEdit) - Method in interface apollo.datamodel.SequenceI
addSequencingErrorPosition(String, int, String) - Method in class apollo.datamodel.AbstractSequence: The position of the genomic sequencing error is in genomic coordinates.
addSequencingErrorPosition(String, int, String) - Method in interface apollo.datamodel.SequenceI
addSimpleFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher
addSite(int) - Method in class apollo.gui.genomemap.Sites
addSpeciesComparison(SpeciesComparison) - Method in class apollo.datamodel.CompositeDataHolder
addSubject(String, String, String) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: Add the subject id and range to the feature as properties.
addSupportToTranscripts() - Method in class apollo.dataadapter.ensj.model.OptionsModel
addSynonym(AnnotatedFeatureI, String) - Method in class apollo.config.DefaultNameAdapter: returns an add transaction for adding synonym to annot.
addSynonym(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
addSynonym(long, String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add a synonym to the database
addSynonym(String) - Method in class apollo.datamodel.AnnotatedFeature: addSynonym used to refuse (quite reasonably) to add synonyms that are the same as the name of the feature, but Chado XML is rather fond of those reflexive synonyms, so go ahead and add them, what the heck.
addSynonym(int, String) - Method in class apollo.datamodel.AnnotatedFeature
addSynonym(Synonym) - Method in class apollo.datamodel.AnnotatedFeature
addSynonym(String) - Method in interface apollo.datamodel.AnnotatedFeatureI
addSynonym(int, String) - Method in interface apollo.datamodel.AnnotatedFeatureI
addSynonym(Synonym) - Method in interface apollo.datamodel.AnnotatedFeatureI
addSynonym(String) - Method in class apollo.datamodel.Identifier
addSynonym(int, String) - Method in class apollo.datamodel.Identifier
addSynonym(Synonym) - Method in class apollo.datamodel.Identifier
addSynonym(int, Synonym) - Method in class apollo.datamodel.Identifier
addSynonymGui() - Method in class apollo.gui.annotinfo.FeatureEditPanel
addSynonyms(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add all synonyms from an AnnotatedFeatureI object
addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in class apollo.dataadapter.GFFSyntenyAdapter
addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in class apollo.dataadapter.SyntenyAdapter
addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in interface apollo.dataadapter.SyntenyAdapterI
addSyntenyRegionsForChromosome(String, Vector) - Method in class apollo.dataadapter.SyntenyAdapter
addSyntenyResultMenuItem() - Method in class apollo.config.Style: Whether to add a menu item to the result popup menu that will bring up the selected feature as the other species in synteny
addSyntenySpeciesNumDropdown() - Method in class apollo.config.Style: Whether to add link query radio buttons to synteny adap gui
addTable(Table) - Method in class apollo.dataadapter.mysql.Database
addTier(SequenceI, int, String, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Adds a new tier to the panel.
addTierManagerListener(TierManagerListener) - Method in class apollo.gui.TierManager
addTierType(TierProperty) - Method in class apollo.config.PropertyScheme
addToCurationSet() - Method in class apollo.dataadapter.AbstractApolloAdapter
addToCurationSet() - Method in class apollo.dataadapter.analysis.AnalysisAdapter: from ApolloDataAdapterI interface.
addToCurationSet() - Method in interface apollo.dataadapter.ApolloDataAdapterI
addToCurationSet() - Method in class apollo.dataadapter.chado.ChadoAdapter
addToCurationSet() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Like getCurationSet--used for layering new data.
addToCurationSet() - Method in class apollo.dataadapter.ensj.EnsJAdapter
addToCurationSet() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
addToCurationSet() - Method in class apollo.dataadapter.gamexml.GAMEAdapter: Called if user is layering additional GAME data on top of whatever's already been loaded
addToCurationSet() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Add GFF3 data to currently existing CurationSet
addToCurationSet(Color) - Method in class apollo.dataadapter.graph.GraphAdapter: Add graph data
addToCurationSet() - Method in class apollo.main.DataLoader: Layer data onto curationset (if multi species active species cur set)
addToCurrentSelection(Selection) - Method in class apollo.gui.SelectionManager: Just adds newSelection to the current selection.
addToFeature(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature
addToPanel(JComponent) - Method in class apollo.dataadapter.analysis.AnalysisPanel
addTopLevelAnnot(SeqFeatureI, String, Date, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: Add a top level annotation to the database.
addTopLevelAnnot(SeqFeatureI, String, Date, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add a top level annotation to the chado database.
AddTransaction - Class in apollo.editor: Transaction for adding a SeqFeatureI.
AddTransaction() - Constructor for class apollo.editor.AddTransaction
AddTransaction(SeqFeatureI) - Constructor for class apollo.editor.AddTransaction
AddTransaction(SeqFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AddTransaction
AddTransaction(SeqFeatureI, TransactionSubpart, Object) - Constructor for class apollo.editor.AddTransaction
AddTransaction(Object, SeqFeatureI, TransactionSubpart, Object) - Constructor for class apollo.editor.AddTransaction
AddTransaction(SeqFeatureI, TransactionSubpart, Object, int) - Constructor for class apollo.editor.AddTransaction
AddTransaction(Object, SeqFeatureI, TransactionSubpart, Object, int) - Constructor for class apollo.editor.AddTransaction
addTransaction(Transaction) - Method in class apollo.editor.AnnotationChangeEvent: If compound change event, add trans to compound transaction AnnotationCompoundEvent overrides no-op
addTransaction(Transaction) - Method in class apollo.editor.AnnotationChangeLog
addTransaction(Transaction) - Method in class apollo.editor.AnnotationCompoundEvent
addTransaction(CompoundTransaction) - Method in class apollo.editor.AnnotationCompoundEvent
addTransaction(Transaction) - Method in class apollo.editor.CompoundTransaction: Add a child Transaction to this CompoundTransaction object.
addTransaction(CompoundTransaction) - Method in class apollo.editor.CompoundTransaction: Adds the children of the compound trans NOT the CompoundTransaction itself.
addTransaction(Transaction) - Method in class apollo.editor.TransactionManager
addTranscript(Transcript, String, Date, Long, long, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: Add a transcript to the database.
addTranscript(Transcript, String, Date, Long, long, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Add a transcript to the chado database.
addTranscript() - Method in class apollo.editor.AnnotationEditor: If called with no args, addTranscript checks which gene was selected and adds the transcript to that gene.
addTranscriptAllowed() - Method in class apollo.editor.AnnotationEditor: Whether allowed to add transcript, just calls addEvidenceExonsAllowed as conditions are same
addTranscriptComment(String) - Method in class apollo.config.Style: Add a canned transcript comment.
addUpdateProperty(String, String) - Method in class apollo.dataadapter.chado.ChadoUpdateTransaction
addVector(Vector) - Method in class apollo.util.FeatureList
addViewListener(ViewListener) - Method in class apollo.gui.genomemap.LinearView
addViewListener(ViewListener) - Method in interface apollo.gui.genomemap.ViewI: Add a View event listener
addVisibilityListener(VisibilityListener) - Method in class apollo.gui.genomemap.LinearView
addWindowListener(WindowListener) - Method in class apollo.gui.TypePanel
adjustEdges() - Method in class apollo.datamodel.FeatureSet: Set low and high according to lowest and highest coord in kids
adjustEdges(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet: If span has higher high and or lower low than current, reset high/low
adjustEdges() - Method in interface apollo.datamodel.FeatureSetI
adjustEdges(SeqFeatureI) - Method in interface apollo.datamodel.FeatureSetI
adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.detailviewers.sequencealigner.HorizontalScrollBarAdjustmentListener: assumes that the scrollbar adjustment values have the same bounds as the number of pixels in the component in the viewport
adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.detailviewers.sequencealigner.VerticalScrollBarAdjustmentListener: assumes that the scrollbar adjustment values have the same bounds as the number of pixels in the component in the viewport
adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.genomemap.TierView
AFTER_LOAD - Static variable in class apollo.gui.event.LazyLoadEvent
aggregateSizeChange - Variable in class apollo.gui.TierManager
AGGRESSIVE_GENE_NAMING - Static variable in class apollo.dataadapter.StateInformation
AGGRESSIVE_NAMING_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel
aggressiveGeneNaming() - Method in class apollo.dataadapter.ensj.model.OptionsModel
Ala - Static variable in class apollo.seq.ResidueProperties
align_seq - Variable in class apollo.dataadapter.analysis.AlignmentParser
AlignBlockChooser - Class in apollo.dataadapter.synteny: I am popped up by the compara adapter if the user is required to choose between different align blocks that a fixed genomic range is mapped to - for instance, if human chr A:x-y maps to mosquito chr B:l-m, AND mosquito chr C: p-q, then we need the user to choose between these regions before we can display the alignments from human<->mosquito.
AlignBlockChooser(HashMap) - Constructor for class apollo.dataadapter.synteny.AlignBlockChooser
AlignBlockChooser.OKButtonListener - Class in apollo.dataadapter.synteny
AlignBlockChooser.OKButtonListener() - Constructor for class apollo.dataadapter.synteny.AlignBlockChooser.OKButtonListener
alignmentIsPeptide() - Method in class apollo.datamodel.SeqFeature: Returns true if alignment is peptide sequence, false if nucleotide This is for the hit alignment(not query).
alignmentIsPeptide() - Method in interface apollo.datamodel.SeqFeatureI: Sequence of the alignment of hit to query, previously stored in hit features subject_alignment property.
AlignmentParser - Class in apollo.dataadapter.analysis
AlignmentParser() - Constructor for class apollo.dataadapter.analysis.AlignmentParser
allowedSet - Variable in class apollo.dataadapter.StateInformation
allowsMovement - Variable in class apollo.gui.genomemap.ApolloPanel
allowsTierDrags() - Method in class apollo.gui.genomemap.AnnotationView
allowsTierDrags() - Method in class apollo.gui.genomemap.SiteView
allowsTierDrags() - Method in class apollo.gui.genomemap.TierView
allowsTierDrags() - Method in interface apollo.gui.genomemap.TierViewI: Whether this view allows tier dragging
ALLSTOPS - Static variable in interface apollo.gui.drawable.DrawableAnnotationConstants: Show all stop codons which are in phase.
AllTests - Class in apollo.dataadapter.gff3
AllTests() - Constructor for class apollo.dataadapter.gff3.AllTests
AllTests - Class in apollo.util
AllTests() - Constructor for class apollo.util.AllTests
allTypes - Variable in class apollo.config.TiersIO
AlternateEnsJSequence - Class in apollo.dataadapter.ensj
AlternateEnsJSequence(String, Controller, Location, Properties) - Constructor for class apollo.dataadapter.ensj.AlternateEnsJSequence
AlternateEnsJSequence - Class in apollo.dataadapter.ensj19
AlternateEnsJSequence(String, Controller, LinearLocation, Properties) - Constructor for class apollo.dataadapter.ensj19.AlternateEnsJSequence
amend_RNA(StringBuffer) - Method in class apollo.datamodel.SeqFeature
AminoAcidBaseRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers
AminoAcidBaseRenderer(int, Orientation) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidBaseRenderer
AminoAcidRenderer - Class in apollo.gui.detailviewers.exonviewer
AminoAcidRenderer(int, int, int, SeqAlignPanel) - Constructor for class apollo.gui.detailviewers.exonviewer.AminoAcidRenderer
AminoAcidRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers
AminoAcidRenderer(ReadingFrame) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRenderer
AminoAcidRendererOLD - Class in apollo.gui.detailviewers.sequencealigner
AminoAcidRendererOLD(int, int, int, SeqAlignPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD
AminoAcidRendererSpaced - Class in apollo.gui.detailviewers.sequencealigner.renderers
AminoAcidRendererSpaced(int) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRendererSpaced
ANALYSIS - Static variable in class apollo.editor.ResultChangeEvent
analysis_type - Variable in class apollo.analysis.filter.AnalysisInput
analysis_types - Variable in class apollo.config.FeatureProperty
analysis_types - Variable in class apollo.config.TierProperty
AnalysisAdapter - Class in apollo.dataadapter.analysis
AnalysisAdapter() - Constructor for class apollo.dataadapter.analysis.AnalysisAdapter
AnalysisAdapterGUI - Class in apollo.dataadapter.analysis: Most of the smarts here are actually in AnalysisPanel and its subclasses This just holds the game panels in its tabbed pane
AnalysisAdapterGUI(IOOperation, CurationSet) - Constructor for class apollo.dataadapter.analysis.AnalysisAdapterGUI
AnalysisAdaptor - Class in apollo.dataadapter.gbrowse
AnalysisAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.gbrowse.AnalysisAdaptor
AnalysisDataAdapterI - Interface in apollo.analysis: DataAdapterI interface Used to load annotated and non-annotated data from whatever datasource
AnalysisFilter - Class in apollo.analysis.filter
AnalysisFilter() - Constructor for class apollo.analysis.filter.AnalysisFilter
AnalysisFilterI - Interface in apollo.analysis.filter
AnalysisGUI - Class in apollo.analysis: Provides GUI for running different analysis tools and importing the results into Apollo.
AnalysisGUI() - Constructor for class apollo.analysis.AnalysisGUI: Constructor.
AnalysisGUI(int, int) - Constructor for class apollo.analysis.AnalysisGUI: Constructor.
AnalysisGUI(int, int, int) - Constructor for class apollo.analysis.AnalysisGUI: Constructor.
AnalysisGUI(int, int, int, FeatureList) - Constructor for class apollo.analysis.AnalysisGUI: Constructor.
AnalysisInput - Class in apollo.analysis.filter: This contains all of the filtering parameters to use on a set of raw output from a computational analysis of the sequence.
AnalysisInput() - Constructor for class apollo.analysis.filter.AnalysisInput
AnalysisMenu - Class in apollo.gui.menus: has menu items for gc plot and restriction enzyme.
AnalysisMenu() - Constructor for class apollo.gui.menus.AnalysisMenu
AnalysisPanel - Class in apollo.dataadapter.analysis: This is only used by AnalysisAdapterGUI.
AnalysisPanel.displayTierItemListener - Class in apollo.dataadapter.analysis: Where will the blast analysis results appear, name that tier.
AnalysisPanel.displayTierItemListener() - Constructor for class apollo.dataadapter.analysis.AnalysisPanel.displayTierItemListener
AnalysisPanel.fileItemListener - Class in apollo.dataadapter.analysis: Which file contains the analysis results
AnalysisPanel.fileItemListener() - Constructor for class apollo.dataadapter.analysis.AnalysisPanel.fileItemListener
AnalysisParserI - Interface in apollo.dataadapter.analysis
anchor(Point) - Method in class apollo.gui.genomemap.Rubberband
anchorPt - Variable in class apollo.gui.genomemap.Rubberband
annot_columns - Static variable in class apollo.gui.evidencepanel.EvidencePanel
AnnotatedFeature - Class in apollo.datamodel: One thought Im having is that annotation stuff would be a HASA instead of a ISA for SeqFeatureI.
AnnotatedFeature() - Constructor for class apollo.datamodel.AnnotatedFeature
AnnotatedFeature(SeqFeatureI) - Constructor for class apollo.datamodel.AnnotatedFeature
AnnotatedFeature(FeatureSetI, String) - Constructor for class apollo.datamodel.AnnotatedFeature
AnnotatedFeatureI - Interface in apollo.datamodel
ANNOTATION - Static variable in class apollo.editor.TransactionClass
AnnotationAddEvent - Class in apollo.editor: AnnotationChangeEvent for add
AnnotationAddEvent(Object, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationAddEvent: A feature has been added, e.g.
AnnotationAddEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationAddEvent: A subpart has been added, e.g.
AnnotationAddEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationAddEvent
AnnotationChangeEvent - Class in apollo.editor: A controller managed event class which signals when a change is made to a set of annotations and what type of change occurred.
AnnotationChangeEvent(Object) - Constructor for class apollo.editor.AnnotationChangeEvent: Solely for edit session done event
AnnotationChangeEvent(Object, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationChangeEvent: No subpart
AnnotationChangeEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationChangeEvent: With subpart
AnnotationChangeListener - Interface in apollo.editor
AnnotationChangeLog - Class in apollo.editor: DELETE THIS - replace by TransactionManager - i think i got all references - test that it works out and delete! Logs AnnotationChangeEvents which are fired when edits occur.
AnnotationChangeLog() - Constructor for class apollo.editor.AnnotationChangeLog
AnnotationCompoundEvent - Class in apollo.editor
AnnotationCompoundEvent(CompoundTransaction) - Constructor for class apollo.editor.AnnotationCompoundEvent: Constructor It defaults the transaction to not undo
AnnotationDeleteEvent - Class in apollo.editor
AnnotationDeleteEvent(Object, AnnotatedFeatureI, SeqFeatureI) - Constructor for class apollo.editor.AnnotationDeleteEvent: Delete whole feature.
AnnotationDeleteEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationDeleteEvent: Delete subpart (comment, synonym)
AnnotationDeleteEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationDeleteEvent
AnnotationEditor - Class in apollo.editor: A class for performing edits on the annotations.
AnnotationEditor(GuiCurationState, FeatureSetI) - Constructor for class apollo.editor.AnnotationEditor: The AnnotationEditor constructor.
annotationEditor - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
annotationEditor - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
AnnotationEditor.FeatChangeData - Class in apollo.editor: Helper class for keeping track of changed top level annots
AnnotationEditor.FeatChangeData() - Constructor for class apollo.editor.AnnotationEditor.FeatChangeData
AnnotationEditorMouseListener - Class in apollo.gui.detailviewers.sequencealigner: Class to handle mouse interactions for an annotation panel NOTE: It can be hard to keep track of what coordinate system you are working in.
AnnotationEditorMouseListener(MultiTierPanel, GuiCurationState, MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener: Constructor
AnnotationEnsJAdapter - Class in apollo.dataadapter.ensj19
AnnotationEnsJAdapter() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
AnnotationEnsJAdapterGUI - Class in apollo.dataadapter.ensj19
AnnotationEnsJAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI
AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener - Class in apollo.dataadapter.ensj19: If the user chooses a particular ensembl database from the default filechooser, we will update the other databases with our best guess (if we can find one) for the maps and variation databases.
AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener
AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener - Class in apollo.dataadapter.ensj19: Space saver - Toggles the annotation source chooser to be visible/not.
AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener
AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener - Class in apollo.dataadapter.ensj19: Space saver - Toggles the data source chooser to be visible/not.
AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener
AnnotationEnsJAdapterGUI.ShowTypesActionListener - Class in apollo.dataadapter.ensj19: Sets the Include Panel contained in the types panel to visible and re-packs the dialog - this makes it look like the dialog has expanded with those options
AnnotationEnsJAdapterGUI.ShowTypesActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowTypesActionListener
AnnotationFeatureComparator - Class in apollo.gui.detailviewers.sequencealigner
AnnotationFeatureComparator() - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationFeatureComparator
annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: I don't think this is used in any way...
AnnotationHeaderMouseListener - Class in apollo.gui.detailviewers.sequencealigner.listeners
AnnotationHeaderMouseListener(MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.listeners.AnnotationHeaderMouseListener
AnnotationMenu - Class in apollo.gui.menus: Note that this is actually the popup menu you get when you right-click after selecting an annotation.
AnnotationMenu(GuiCurationState, ApolloPanelI, AnnotationView, Selection, Point) - Constructor for class apollo.gui.menus.AnnotationMenu: Selection is the selection for the whole ApolloPanel (not just the AnnotView)
AnnotationRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers
AnnotationRenderer(GuiCurationState) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
AnnotationReplaceEvent - Class in apollo.editor: This class is temporary in theory.
AnnotationReplaceEvent(Object, AnnotatedFeatureI, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationReplaceEvent
AnnotationRighClickMenu - Class in apollo.gui.detailviewers.sequencealigner: This is the popup menu that gets displayed when you right click on an annotation.
AnnotationRighClickMenu(GuiCurationState, MultiTierPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu: Constructor
annotationRoot - Variable in class apollo.datamodel.AnnotatedFeature
AnnotationsModel - Class in apollo.dataadapter.ensj.model
AnnotationsModel() - Constructor for class apollo.dataadapter.ensj.model.AnnotationsModel
AnnotationSourceChooser - Class in apollo.dataadapter.ensj19: Presents the user with a choice of file or server input for the annotation source.
AnnotationSourceChooser() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser
AnnotationSourceChooser(Vector, Vector, Vector) - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser
AnnotationSourceChooser.FindDataSetsListener - Class in apollo.dataadapter.ensj19
AnnotationSourceChooser.FindDataSetsListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.FindDataSetsListener
AnnotationSourceChooser.RemoveDatasetsListenerForPort - Class in apollo.dataadapter.ensj19
AnnotationSourceChooser.RemoveDatasetsListenerForPort() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForPort
AnnotationSourceChooser.RemoveDatasetsListenerForServer - Class in apollo.dataadapter.ensj19
AnnotationSourceChooser.RemoveDatasetsListenerForServer() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForServer
AnnotationsPanel - Class in apollo.dataadapter.ensj.view
AnnotationsPanel(View) - Constructor for class apollo.dataadapter.ensj.view.AnnotationsPanel
AnnotationUpdateEvent - Class in apollo.editor
AnnotationUpdateEvent(UpdateTransaction) - Constructor for class apollo.editor.AnnotationUpdateEvent: New way of doing annotation change events - they are just carriers of transactions.
AnnotationUpdateEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationUpdateEvent
AnnotationUpdateEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationUpdateEvent
AnnotationView - Class in apollo.gui.genomemap: A view to display annotations in
AnnotationView(JComponent, String, SelectionManager, GuiCurationState) - Constructor for class apollo.gui.genomemap.AnnotationView
annotationView - Variable in class apollo.gui.genomemap.ResultView
annotDrag(DragViewI, Vector, boolean, StringBuffer) - Method in class apollo.gui.genomemap.AnnotationView
annotNumber - Static variable in class apollo.config.GmodNameAdapter
AnnotSessionDoneEvent - Class in apollo.editor: This event indicates that the editor is done with a series of edits.
AnnotSessionDoneEvent(Object) - Constructor for class apollo.editor.AnnotSessionDoneEvent: do we need annot top or changed feature?
Apollo - Class in apollo.main
Apollo() - Constructor for class apollo.main.Apollo
apollo.analysis - package apollo.analysis
apollo.analysis.filter - package apollo.analysis.filter
apollo.bop - package apollo.bop
apollo.config - package apollo.config
apollo.dataadapter - package apollo.dataadapter
apollo.dataadapter.analysis - package apollo.dataadapter.analysis
apollo.dataadapter.chado - package apollo.dataadapter.chado
apollo.dataadapter.chado.jdbc - package apollo.dataadapter.chado.jdbc
apollo.dataadapter.chadoxml - package apollo.dataadapter.chadoxml
apollo.dataadapter.das - package apollo.dataadapter.das: Defines the interfaces to support the reading of DAS datasources by Apollo.
apollo.dataadapter.das.simple - package apollo.dataadapter.das.simple: Provides simple implementations of the interfaces defined in the apollo.dataadapter.das package.
apollo.dataadapter.das2 - package apollo.dataadapter.das2
apollo.dataadapter.debug - package apollo.dataadapter.debug
apollo.dataadapter.ensj - package apollo.dataadapter.ensj
apollo.dataadapter.ensj.controller - package apollo.dataadapter.ensj.controller
apollo.dataadapter.ensj.model - package apollo.dataadapter.ensj.model
apollo.dataadapter.ensj.view - package apollo.dataadapter.ensj.view
apollo.dataadapter.ensj19 - package apollo.dataadapter.ensj19
apollo.dataadapter.exception - package apollo.dataadapter.exception
apollo.dataadapter.flychadoxml - package apollo.dataadapter.flychadoxml
apollo.dataadapter.flygamexml - package apollo.dataadapter.flygamexml
apollo.dataadapter.gamexml - package apollo.dataadapter.gamexml
apollo.dataadapter.gbrowse - package apollo.dataadapter.gbrowse
apollo.dataadapter.genbank - package apollo.dataadapter.genbank
apollo.dataadapter.gff3 - package apollo.dataadapter.gff3
apollo.dataadapter.graph - package apollo.dataadapter.graph
apollo.dataadapter.mysql - package apollo.dataadapter.mysql
apollo.dataadapter.otter - package apollo.dataadapter.otter
apollo.dataadapter.otter.parser - package apollo.dataadapter.otter.parser
apollo.dataadapter.sample - package apollo.dataadapter.sample
apollo.dataadapter.synteny - package apollo.dataadapter.synteny
apollo.dataadapter.synteny.builder - package apollo.dataadapter.synteny.builder
apollo.datamodel - package apollo.datamodel
apollo.datamodel.seq - package apollo.datamodel.seq
apollo.editor - package apollo.editor
apollo.external - package apollo.external
apollo.gui - package apollo.gui
apollo.gui.annotinfo - package apollo.gui.annotinfo
apollo.gui.detailviewers - package apollo.gui.detailviewers
apollo.gui.detailviewers.blixem - package apollo.gui.detailviewers.blixem
apollo.gui.detailviewers.exonviewer - package apollo.gui.detailviewers.exonviewer
apollo.gui.detailviewers.seqexport - package apollo.gui.detailviewers.seqexport
apollo.gui.detailviewers.sequencealigner - package apollo.gui.detailviewers.sequencealigner
apollo.gui.detailviewers.sequencealigner.AAPanel - package apollo.gui.detailviewers.sequencealigner.AAPanel
apollo.gui.detailviewers.sequencealigner.actions - package apollo.gui.detailviewers.sequencealigner.actions
apollo.gui.detailviewers.sequencealigner.comparators - package apollo.gui.detailviewers.sequencealigner.comparators
apollo.gui.detailviewers.sequencealigner.DNAPanel - package apollo.gui.detailviewers.sequencealigner.DNAPanel
apollo.gui.detailviewers.sequencealigner.filters - package apollo.gui.detailviewers.sequencealigner.filters
apollo.gui.detailviewers.sequencealigner.listeners - package apollo.gui.detailviewers.sequencealigner.listeners
apollo.gui.detailviewers.sequencealigner.menus - package apollo.gui.detailviewers.sequencealigner.menus
apollo.gui.detailviewers.sequencealigner.overview - package apollo.gui.detailviewers.sequencealigner.overview
apollo.gui.detailviewers.sequencealigner.renderers - package apollo.gui.detailviewers.sequencealigner.renderers
apollo.gui.drawable - package apollo.gui.drawable
apollo.gui.event - package apollo.gui.event
apollo.gui.evidencepanel - package apollo.gui.evidencepanel
apollo.gui.featuretree - package apollo.gui.featuretree
apollo.gui.genomemap - package apollo.gui.genomemap
apollo.gui.menus - package apollo.gui.menus
apollo.gui.synteny - package apollo.gui.synteny
apollo.gui.tweeker - package apollo.gui.tweeker
apollo.io - package apollo.io
apollo.main - package apollo.main
apollo.seq - package apollo.seq
apollo.seq.io - package apollo.seq.io
apollo.test - package apollo.test
apollo.util - package apollo.util
apollo.util.interval - package apollo.util.interval
apollo_panel - Variable in class apollo.gui.genomemap.LinearView
ApolloAdapterException - Exception in apollo.dataadapter
ApolloAdapterException(String) - Constructor for exception apollo.dataadapter.ApolloAdapterException
ApolloAdapterException(String, Exception) - Constructor for exception apollo.dataadapter.ApolloAdapterException
ApolloAdapterException(Exception) - Constructor for exception apollo.dataadapter.ApolloAdapterException
ApolloControlServer - Class in apollo.external: this class kicks off the servlet.
ApolloControlServer() - Constructor for class apollo.external.ApolloControlServer
ApolloControlServlet - Class in apollo.external: take in http request for a location and load it - for now hardwired to game adapter loading fly actually i dont think thats true anymore - i think this just scrolls & zooms to the region if its within range, rather than causing a whole reload as reloading in apollo isnt zippy like igb so it would be too laggy url that it responds to looks something like this http://localhost:8085/ApolloControl?seqid=chr2R&start=10000&end=12000 maybe add ?organism=dmel
ApolloControlServlet() - Constructor for class apollo.external.ApolloControlServlet
ApolloDataAdapterGUI - Interface in apollo.dataadapter
ApolloDataAdapterI - Interface in apollo.dataadapter: DataAdapterI interface Used to load annotated and non-annotated data from whatever datasource Could this implement org.bdgp.io.VisualDataAdapter or are there apollo adapters with no UI?
ApolloDataI - Interface in apollo.datamodel: DataLoader returns an ApolloDataI which can be queried whether its holding a CurationSet or CompositeDataHolder, which can then be retrieved.
ApolloFrame - Class in apollo.gui: CompositeApolloFrame subclass is now the working instantiation of ApolloFrame.
ApolloFrame() - Constructor for class apollo.gui.ApolloFrame: constructor for singleton.
ApolloJalviewEventBridge - Class in apollo.gui: Converts events from apollo to jalview and vice versa
ApolloJalviewEventBridge(Controller, Controller, AlignFrame) - Constructor for class apollo.gui.ApolloJalviewEventBridge
ApolloLaundry - Class in apollo.test
ApolloLaundry() - Constructor for class apollo.test.ApolloLaundry
ApolloLayoutManager - Class in apollo.gui.genomemap: An Abstract base ApolloLayoutManager class
ApolloLayoutManager() - Constructor for class apollo.gui.genomemap.ApolloLayoutManager
ApolloLoaderI - Interface in apollo.gui: Interface for data loader to layer data on to curation set?
ApolloMetalScrollBarUI - Class in apollo.gui
ApolloMetalScrollBarUI() - Constructor for class apollo.gui.ApolloMetalScrollBarUI
ApolloNameAdapterI - Interface in apollo.config
ApolloPanel - Class in apollo.gui.genomemap: This class is a container to hold and manage the various Views which are needed by Apollo.
ApolloPanelHolderI - Interface in apollo.gui.genomemap: An interface that holds ApolloPanels.
ApolloPanelI - Interface in apollo.gui.genomemap: This was invented to eliminate all of the casting that was going on.
ApolloRunner - Class in apollo.gui
ApolloRunner() - Constructor for class apollo.gui.ApolloRunner
ApolloScrollBar - Class in apollo.gui
ApolloScrollBar() - Constructor for class apollo.gui.ApolloScrollBar
ApolloTest - Class in apollo.test
ApolloTest(String) - Constructor for class apollo.test.ApolloTest: This is for test case.
appearsToBeChadoXML(String, BufferedReader) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Check whether the input appears to be chadoXML by looking for the line
appendCharacterBuffer(String) - Method in class apollo.dataadapter.otter.parser.TagHandler
appendElements(Collection<? extends T>, Collection<? super T>) - Static method in class apollo.util.CollectionUtil: Append elements from src to dest.
applyLayout(JIniFile, boolean) - Method in class apollo.gui.ApolloFrame
applyLayout(JIniFile, String, boolean) - Method in class apollo.gui.evidencepanel.EvidencePanel
applyLayout(JIniFile, boolean) - Method in class apollo.gui.evidencepanel.EvidencePanelContainer
applyLayout(JIniFile, String, boolean) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
applyLayout(JIniFile, boolean) - Method in class apollo.gui.synteny.SyntenyPanel
applyVisibilityFromLayout(JIniFile, String) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
areAnnotationViewsVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
areAnyTiersLabeled() - Method in class apollo.gui.genomemap.FeatureTierManager
areAnyTiersLabeled() - Method in interface apollo.gui.genomemap.FeatureTierManagerI
areLimitsSet() - Method in class apollo.gui.genomemap.LinearView
areLimitsSet() - Method in interface apollo.gui.genomemap.ViewI
areLinksShadedByPercId() - Method in class apollo.gui.synteny.SyntenyPanel
areOpaqueLinksUsed() - Method in class apollo.gui.synteny.SyntenyPanel
areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.NoOverlap: Just returns false
areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.ORF_Overlap
areOverlapping(SeqFeatureI, SeqFeatureI) - Method in interface apollo.config.OverlapI
areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.SimpleOverlap: The simple overlap checking function.
areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.editor.AnnotationEditor: areOverlapping determines if two SeqFeatureIs overlap using the currently defined gene definition (from Config.getGeneDefinition().
areResultViewsVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
areSameLocation(SeqFeatureI, SeqFeatureI) - Method in class apollo.dataadapter.genbank.GenbankRead
areYouSure(String) - Static method in class apollo.main.LoadUtil: Puts up a dialog asking user the question provided (which usually is some variant on "Are you sure?").
Arg - Static variable in class apollo.seq.ResidueProperties
ArrayListTransferHandler - Class in apollo.gui
ArrayListTransferHandler() - Constructor for class apollo.gui.ArrayListTransferHandler
ArrayListTransferHandler.ArrayListTransferable - Class in apollo.gui
ArrayListTransferHandler.ArrayListTransferable(ArrayList) - Constructor for class apollo.gui.ArrayListTransferHandler.ArrayListTransferable
askRenameGameConfig(String, String) - Static method in class apollo.config.Style: 7/2005: Special backwards-compatibility hand-holding: game.style and game.tiers were recently renamed fly.style (which imports game.style) and fly.tiers, but some users may still have a private game.style or game.tiers in their .apollo directory.
Asn - Static variable in class apollo.seq.ResidueProperties
Asp - Static variable in class apollo.seq.ResidueProperties
ASSEMBLY_END - Static variable in class apollo.dataadapter.otter.parser.TagHandler
ASSEMBLY_START - Static variable in class apollo.dataadapter.otter.parser.TagHandler
ASSEMBLY_TYPE - Static variable in class apollo.dataadapter.otter.parser.TagHandler
AssemblyFeature - Class in apollo.datamodel: A class to represent SeqFeatures which have been mapped to a static golden path- the usual start/end is assumed to be in chromosome coords, but the assembly start/end specific to this subclass are in coords relative to the feature.
AssemblyFeature() - Constructor for class apollo.datamodel.AssemblyFeature
AssemblyFeature(int, String) - Constructor for class apollo.datamodel.AssemblyFeature
AssemblyFeatureI - Interface in apollo.datamodel
assignAnnotationName() - Method in class apollo.editor.AnnotationEditor
assignAnnotationNameAllowed() - Method in class apollo.editor.AnnotationEditor
atof(String) - Static method in class apollo.util.Format: Converts a string of digits to an double
atoi(String) - Static method in class apollo.util.Format: Converts a string of digits (decimal, octal or hex) to an integer
atol(String) - Static method in class apollo.util.Format: Converts a string of digits (decimal, octal or hex) to a long integer
attachAnnot(AnnotatedFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel: can be transcript or 1 level annot
attachAnnot(AnnotatedFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: can be transcript or 1 level annot
attachEnsemblDatabaseDropdownListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
attachFeatureToSequence(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
attachFeatureToSequence(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
attachListeners() - Method in class apollo.analysis.SeqAnalysisGUI
attachListeners() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
attachListeners() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
attachListeners() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame
attachListeners() - Method in class apollo.gui.GenericFileAdapterGUI
attachRendererToSequence(int, BaseRenderer) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
attachRendererToTier(int, BaseRenderer) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Attaches a new BaseRenderer to the given tier
attachTranscripts(Vector) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel: Expects a vector of Transcripts or 1 level annots.
attachTranscripts(Vector) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: Expects a vector of Transcripts or 1 level annots.
AUTHOR - Static variable in class apollo.dataadapter.otter.parser.TagHandler
AUTHOR - Static variable in class apollo.dataadapter.StateInformation
author - Variable in class apollo.editor.Transaction
AUTHOR_EMAIL - Static variable in class apollo.dataadapter.otter.parser.TagHandler
AUTHOR_EMAIL - Static variable in class apollo.dataadapter.StateInformation
autonomousHSPs(boolean) - Method in class apollo.analysis.filter.AnalysisInput
autopromote - Variable in class apollo.analysis.filter.AnalysisInput
AutoSaveThread - Class in apollo.gui
AutoSaveThread(String, int) - Constructor for class apollo.gui.AutoSaveThread

B

backBuffer - Variable in class apollo.gui.genomemap.ApolloPanel
backBufferHeight - Variable in class apollo.gui.genomemap.ApolloPanel
backBufferWidth - Variable in class apollo.gui.genomemap.ApolloPanel
backgroundColour - Variable in class apollo.gui.genomemap.LinearView
BaseAdaptor - Class in apollo.dataadapter.mysql
BaseAdaptor() - Constructor for class apollo.dataadapter.mysql.BaseAdaptor
BaseAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.mysql.BaseAdaptor
BaseEditorPanel - Class in apollo.gui.detailviewers.exonviewer
BaseEditorPanel(GuiCurationState, BaseFineEditor, boolean, int, int, SeqFeatureI) - Constructor for class apollo.gui.detailviewers.exonviewer.BaseEditorPanel: Need lowestBase for offset of sequence
BaseEditorPanel - Class in apollo.gui.detailviewers.sequencealigner
BaseEditorPanel(GuiCurationState, BaseFineEditor, boolean, int, int, SeqFeatureI) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: Need lowestBase for offset of sequence
BaseFilter<T> - Class in apollo.gui.detailviewers.sequencealigner.filters
BaseFilter() - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.BaseFilter
BaseFilter(boolean) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.BaseFilter
baseFineEditor - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
BaseFineEditor - Class in apollo.gui.detailviewers.exonviewer
baseFineEditor - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
BaseFineEditor - Class in apollo.gui.detailviewers.sequencealigner
BaseFineEditorHorizontalColHeader - Class in apollo.gui.detailviewers.sequencealigner: Draws the horizontal header at the top of the EDE which displays the base number which is currently in view.
BaseFineEditorHorizontalColHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseFineEditorHorizontalColHeader
BaseFineEditorRowHeader - Class in apollo.gui.detailviewers.exonviewer
BaseFineEditorRowHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.exonviewer.BaseFineEditorRowHeader
BaseFineEditorRowHeader - Class in apollo.gui.detailviewers.sequencealigner
BaseFineEditorRowHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseFineEditorRowHeader
BaseFocusEvent - Class in apollo.gui.event
BaseFocusEvent(Object, int, SeqFeatureI) - Constructor for class apollo.gui.event.BaseFocusEvent: Constructor for position focus event, request to center on focus
BaseFocusEvent(Object, Region) - Constructor for class apollo.gui.event.BaseFocusEvent
BaseFocusListener - Interface in apollo.gui.event
BaseGFFAdapter - Class in apollo.dataadapter: I'm a variant of a GFFAdapter that does NO translation of the features I read into sets of features (ie no post-processing of the data).
BaseGFFAdapter(String) - Constructor for class apollo.dataadapter.BaseGFFAdapter
BaseGFFAdapter() - Constructor for class apollo.dataadapter.BaseGFFAdapter
BASEPAIR_RANGE - Static variable in class apollo.dataadapter.DataInputType
basepairRangeToPixelRange(RangeI) - Method in class apollo.gui.Transformer: This takes care of doing the inclusion at the end of base pair ranges and compensates for xOrientation.
basePairToPos(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
basePairToPos(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
basePairToTierPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel: Converts from base pair to tier position
BaseRenderer - Interface in apollo.gui.detailviewers.exonviewer
BaseRenderer - Interface in apollo.gui.detailviewers.sequencealigner.renderers
BaseRendererFactory - Class in apollo.gui.detailviewers.sequencealigner
BaseRendererFactory() - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseRendererFactory
BaseRendererI - Interface in apollo.gui.detailviewers.sequencealigner.renderers
BaseScrollable - Interface in apollo.gui
BasicWindowListener - Class in apollo.gui.event
BasicWindowListener() - Constructor for class apollo.gui.event.BasicWindowListener
BEFORE_LOAD - Static variable in class apollo.gui.event.LazyLoadEvent
beforeFivePrimeEnd(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet: Returns true if the feature passed in has a 3 prime end that is more 5prime than this feature.
beginTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.FeatureView
beginTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.TierView
beginTierDrag(MouseEvent) - Method in interface apollo.gui.genomemap.TierViewI: Start a tier drag
beginTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Begin a transaction using the current JDBC Connection.
bgColor - Static variable in class apollo.gui.annotinfo.FeatureEditorDialog
bgColor - Static variable in class apollo.gui.detailviewers.seqexport.SeqExport
binarySearch(Vector, Comparator, Object, boolean) - Static method in class apollo.util.SeqFeatureUtil
biotype - Variable in class apollo.datamodel.SeqFeature
BIOTYPE - Static variable in class apollo.gui.DetailInfo
BLACK - Static variable in class apollo.util.interval.RbNode
blankLine(String) - Method in class apollo.config.TiersIO
BlastFilterPanel - Class in apollo.analysis.filter
BlastFilterPanel(Color) - Constructor for class apollo.analysis.filter.BlastFilterPanel
BlastHandler - Class in apollo.analysis
BlastHandler() - Constructor for class apollo.analysis.BlastHandler
BlastParser - Class in apollo.dataadapter.analysis
BlastParser() - Constructor for class apollo.dataadapter.analysis.BlastParser
BlastXMLParser - Class in apollo.analysis
BlastXMLParser() - Constructor for class apollo.analysis.BlastXMLParser
BlastXMLParser.BlastXMLParserException - Exception in apollo.analysis
BlastXMLParser.BlastXMLParserException(String) - Constructor for exception apollo.analysis.BlastXMLParser.BlastXMLParserException
BlastXMLParserTest - Class in apollo.analysis
BlastXMLParserTest() - Constructor for class apollo.analysis.BlastXMLParserTest
BlatParser - Class in apollo.dataadapter.analysis
BlatParser() - Constructor for class apollo.dataadapter.analysis.BlatParser
BlixemRunner - Class in apollo.gui.detailviewers.blixem
BlixemRunner(CurationSet, Vector, int, int) - Constructor for class apollo.gui.detailviewers.blixem.BlixemRunner
blueGreen - Static variable in class apollo.config.FeatureProperty
BookmarkMenu - Class in apollo.gui.menus: This menu allows for the bookmarking of annots.
bop - Class in apollo.bop
bop() - Constructor for class apollo.bop.bop
BopException - Exception in apollo.dataadapter.exception
BopException() - Constructor for exception apollo.dataadapter.exception.BopException
BopException(String) - Constructor for exception apollo.dataadapter.exception.BopException
BopException(String, String) - Constructor for exception apollo.dataadapter.exception.BopException
BopException(String, Exception) - Constructor for exception apollo.dataadapter.exception.BopException
BopException(String, String, Exception) - Constructor for exception apollo.dataadapter.exception.BopException
BOTH - Static variable in class apollo.gui.genomemap.ApolloLayoutManager
BOTHENDS - Static variable in interface apollo.gui.drawable.DrawableAnnotationConstants: Indicates both ends of a feature.
boxBounds - Variable in class apollo.gui.drawable.DrawableSeqFeature: Allocate a rectangle to put bounding box in because instantiation // is so slow.
breakSingle(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter: Formats a string so that it does not run beyond a specified line length.
breakSingle(String, int) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
brown - Static variable in class apollo.config.FeatureProperty
browseButton - Variable in class apollo.gui.GenericFileAdapterGUI
browseFiles(JComboBox) - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI: Called from browse button, sets browser with currently selected path if there is one, and then calls browser to get a file.
browseFiles(JComboBox) - Method in class apollo.gui.GenericFileAdapterGUI: Called from browse button, sets browser with currently selected path if there is one, and then calls browser to get a file
BUFFER_SIZE - Static variable in class apollo.dataadapter.synteny.SyntenyComparaAdapter
buildEditList() - Method in class apollo.datamodel.FeatureSet
buildEditList() - Method in interface apollo.datamodel.FeatureSetI
BuilderAdapter - Class in apollo.dataadapter.synteny.builder
BuilderAdapter() - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapter
BuilderAdapterGUI - Class in apollo.dataadapter.synteny.builder
BuilderAdapterGUI(IOOperation, Model) - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
BuilderAdapterGUI.ModelChangeListener - Class in apollo.dataadapter.synteny.builder
BuilderAdapterGUI.ModelChangeListener() - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapterGUI.ModelChangeListener
buildFeatures(StrandedFeatureSet, Hashtable, int, PropertyScheme) - Method in class apollo.dataadapter.FeatureSetBuilder
buildFeaturesHash(Vector, Hashtable, Hashtable) - Method in class apollo.dataadapter.ensj.EnsJFeatureSetBuilder
buildFeaturesHash(Vector, Hashtable, Hashtable) - Method in class apollo.dataadapter.FeatureSetBuilder
buildGUI() - Method in class apollo.analysis.filter.BlastFilterPanel
buildGUI() - Method in class apollo.analysis.filter.GenscanFilterPanel
buildGUI() - Method in class apollo.analysis.filter.NoFilterPanel
buildGUI() - Method in class apollo.analysis.filter.Sim4FilterPanel
buildGUI() - Method in class apollo.analysis.SeqAnalysisGUI
buildGUI() - Method in class apollo.dataadapter.analysis.AnalysisPanel
buildGUI() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
buildGUI() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
buildGUI() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI
buildGUI() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
buildGUI() - Method in class apollo.dataadapter.FileTabPanel: Add in browse button
buildGUI() - Method in class apollo.dataadapter.flychadoxml.LocationChadoPanel
buildGUI() - Method in class apollo.dataadapter.flygamexml.LocationGAMEPanel
buildGUI() - Method in class apollo.dataadapter.GbrowseAdapterGUI
buildGUI() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI
buildGUI() - Method in class apollo.dataadapter.GFFAdapterGUI
buildGUI() - Method in class apollo.dataadapter.graph.GraphAdapterGUI
buildGUI() - Method in class apollo.dataadapter.GuiTabPanel
buildGUI() - Method in class apollo.dataadapter.otter.OtterAdapterGUI
buildGUI() - Method in class apollo.dataadapter.otter.OtterXMLAdapterGUI
buildGUI() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI
buildGUI() - Method in class apollo.gui.GenericFileAdapterGUI
buildGUI() - Method in class apollo.gui.ProgressFrame
buildGUI() - Method in class apollo.gui.SliderWindow
buildGUIForReading() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
buildGUIForReading() - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI: Loops through TabPanels and inserts into tabbed pane, Also hafta add our own buttons, since DataAdapterChooser does not add buttons for AbstractIntDataAdapUIs although i think there should be a way for an AbstractIntDAI to say hey i want those buttons like boolean addOKCancelButtons()
buildGUIForWriting() - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI
buildIncludePanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
buildLocationPanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
buildMenu() - Method in class apollo.gui.menus.FileMenu
buildmRNAEditList() - Method in class apollo.datamodel.SeqFeature
buildORFEditList() - Method in class apollo.datamodel.FeatureSet
buildPAM() - Static method in class apollo.seq.ResidueProperties

C

c - Variable in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
c - Variable in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
cacheAnalysisTable() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
cacher - Variable in class apollo.datamodel.seq.AbstractLazySequence
CacheSeqIdLoader - Class in apollo.datamodel.seq: This presently will only work with parent as GAMESequence.
CacheSeqIdLoader(GAMESequence) - Constructor for class apollo.datamodel.seq.CacheSeqIdLoader
CacheSequenceLoader - Class in apollo.datamodel.seq
CacheSequenceLoader(LazySequenceI) - Constructor for class apollo.datamodel.seq.CacheSequenceLoader
CacheSequenceLoader.SequenceRange - Class in apollo.datamodel.seq
CacheSequenceLoader.SequenceRange(String, int, int) - Constructor for class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange
cacheUI(IOOperation, DataAdapterUI) - Method in class apollo.dataadapter.AbstractApolloAdapter
calcTickInterval(int[]) - Static method in class apollo.gui.genomemap.PlotUtil
calcTickInterval(int[], Graphics, Transformer, Vector) - Static method in class apollo.gui.genomemap.PlotUtil
calcTranslationStartForLongestPeptide() - Method in class apollo.datamodel.FeatureSet: This sets the start at a standard start codon that gives the longest peptide (which may not be the first start codon).
calcTranslationStartForLongestPeptide() - Method in interface apollo.datamodel.TranslationI
calculateHighlightRect(StrandedZoomableApolloPanel.HighlightWrapper) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
calculateTierNumber(Point) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanelHeaderTable: Calculates the tier number for a given point
canAddFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel
canAddFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
canBeAddedToSequence(SeqWrapper, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: Checks if there are any overlaps between features in sw and feature, if so return false, else true
cancelCellEditing() - Method in class apollo.gui.DisabledEditor
canHandleSelection(FeatureSelectionEvent, Object) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Does all the handle selection checks
canHaveChildren() - Method in class apollo.datamodel.Exon
canHaveChildren() - Method in class apollo.datamodel.FeatureSet: This method determines if there are any child SeqFeatures in this set (FeatureSets are NOT included).
canHaveChildren() - Method in class apollo.datamodel.Range: If SeqFeature is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then true.
canHaveChildren() - Method in interface apollo.datamodel.RangeI: If RangeI is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then return true.
canImport(JComponent, DataFlavor[]) - Method in class apollo.gui.ArrayListTransferHandler
canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.ResultRenderer
canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
canWriteData() - Method in class apollo.dataadapter.AbstractApolloAdapter: Whether write operation is supported by data adapter
canWriteData() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Whether write operation is supported by data adapter
canWriteToDirectory(String) - Static method in class apollo.util.IOUtil: Check whether specified directory is writeable
CaseInsensitiveStringHash - Class in apollo.util
CaseInsensitiveStringHash(int, float) - Constructor for class apollo.util.CaseInsensitiveStringHash
CaseInsensitiveStringHash(int) - Constructor for class apollo.util.CaseInsensitiveStringHash
CaseInsensitiveStringHash() - Constructor for class apollo.util.CaseInsensitiveStringHash
cDNA - Variable in class apollo.datamodel.Transcript
CDNA_NAME - Static variable in class apollo.editor.TransactionSubpart
CDS_END_NOT_FOUND - Static variable in class apollo.dataadapter.otter.parser.TagHandler
CDS_START_NOT_FOUND - Static variable in class apollo.dataadapter.otter.parser.TagHandler
CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
centerOnScreen(Component) - Static method in class apollo.gui.ApolloFrame: centers component on screen - put in a util class?
certainly_bad - Static variable in class apollo.analysis.filter.TwilightFilter
certainly_good - Static variable in class apollo.analysis.filter.TwilightFilter
CGI - Class in apollo.dataadapter
CGI(String, int, String, Hashtable, PrintStream, String) - Constructor for class apollo.dataadapter.CGI
CGI(String, int, String, Hashtable, PrintStream) - Constructor for class apollo.dataadapter.CGI
CGI(String, int, String, PrintStream) - Constructor for class apollo.dataadapter.CGI
CGI(String, String, PrintStream) - Constructor for class apollo.dataadapter.CGI
CHADO_DB - Static variable in class apollo.dataadapter.chado.ChadoAdapter
chado_dbs - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI: List of Chado databases read by the ChadoAdapter from its configuration file.
ChadoAdapter - Class in apollo.dataadapter.chado: A data adapter that allows Apollo to communicate with a Chado-compliant relational database.
ChadoAdapter() - Constructor for class apollo.dataadapter.chado.ChadoAdapter
ChadoAdapterGUI - Class in apollo.dataadapter.chado: In the Apollo data adapter specification each data adapter has two parts: a class that implements the graphical user interface, and a class that interacts with the data source (as directed by the user via the GUI).
ChadoAdapterGUI(IOOperation, ChadoDatabase[]) - Constructor for class apollo.dataadapter.chado.ChadoAdapterGUI
ChadoAdHocFlatFileWriter - Class in apollo.dataadapter.chado: Writes a curation set to an ad-hoc chado-based flat file format.
ChadoAdHocFlatFileWriter() - Constructor for class apollo.dataadapter.chado.ChadoAdHocFlatFileWriter
ChadoDatabase - Class in apollo.dataadapter.chado: Connection and configuration information for a Chado database.
ChadoDatabase() - Constructor for class apollo.dataadapter.chado.ChadoDatabase: Default constructor.
ChadoDatabase(String, String, String, String, String, String) - Constructor for class apollo.dataadapter.chado.ChadoDatabase
chadoDb - Variable in class apollo.dataadapter.chado.ChadoDatabase: Name of the specific Chado database instance/schema on the database server.
chadoDb - Variable in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Schema/database name of the Chado database instance.
chadoDbPrompt - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
chadoDbTextField - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
chadoFeatureExists(Connection, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Check whether a particular feature exists in a given Chado database.
chadoFeatureExists(Connection, String, String, StringBuilder) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Check whether a particular feature exists in a given Chado database.
ChadoInstance - Interface in apollo.dataadapter.chado.jdbc: An interface whose goal is to capture all the observed differences between disparate sites' (e.g., FlyBase, TIGR) chado database usage.
ChadoJdbcNameAdapter - Class in apollo.config
ChadoJdbcNameAdapter() - Constructor for class apollo.config.ChadoJdbcNameAdapter
ChadoProgram - Class in apollo.dataadapter.chado.jdbc: A set of chado.analysis rows that have the same value in their 'program' column.
ChadoProgram(String, String, String, boolean) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram
ChadoProgram(String, boolean) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram
ChadoProgram(String) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram
ChadoTransaction - Class in apollo.dataadapter.chado: Class that represents the chado XML counterpart of an Apollo transaction.
ChadoTransaction() - Constructor for class apollo.dataadapter.chado.ChadoTransaction
ChadoTransaction.Operation - Class in apollo.dataadapter.chado: INNER CLASS Operation
ChadoTransactionTransformer - Class in apollo.dataadapter.chado: This class is used to translate Apollo Transaction objects to Chado Transaction objects.
ChadoTransactionTransformer() - Constructor for class apollo.dataadapter.chado.ChadoTransactionTransformer
ChadoTransactionXMLTemplate - Class in apollo.dataadapter.chadoxml: This class is used to process xml template for transactions.
ChadoTransactionXMLTemplate(String) - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
ChadoTransactionXMLTemplate(String, String, String) - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
ChadoTransactionXMLWriter - Class in apollo.dataadapter.chadoxml: This class is used to write Transaction objects to Chado transaction XML.
ChadoTransactionXMLWriter() - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter: Default constructor
ChadoUpdateTransaction - Class in apollo.dataadapter.chado
ChadoUpdateTransaction() - Constructor for class apollo.dataadapter.chado.ChadoUpdateTransaction
ChadoUpdateTransaction(String, String) - Constructor for class apollo.dataadapter.chado.ChadoUpdateTransaction
chadoVersion - Variable in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Chado schema version - should this be merged with chado instance?
ChadoXmlAdapter - Class in apollo.dataadapter.chadoxml: A FlyBase-specific reader for Chado XML files.
ChadoXmlAdapter() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Must have empty constructor to work with org.bdgp.io.DataAdapterRegistry instance creation from config string
ChadoXmlAdapterGUI - Class in apollo.dataadapter.chadoxml
ChadoXmlUtils - Class in apollo.dataadapter.chadoxml
ChadoXmlUtils() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlUtils
ChadoXmlWrite - Class in apollo.dataadapter.chadoxml: ChadoXmlWrite: writes Chado XML to a file.
ChadoXmlWrite() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlWrite
ChainedRepaintEvent - Class in apollo.gui.event
ChainedRepaintEvent(Object) - Constructor for class apollo.gui.event.ChainedRepaintEvent
ChainedRepaintListener - Interface in apollo.gui.event
CHANGE_DATABASE - Static variable in class apollo.dataadapter.ensj.controller.Controller
ChangeDatabaseHandler - Class in apollo.dataadapter.ensj.controller: The user has typed into the host, port etc database fields, so we clear off the ensembl-db list selected ensembl-db.
ChangeDatabaseHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ChangeDatabaseHandler
changeEnd(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
changeEnd(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
ChangeList - Class in apollo.editor: TransactionManager does the real coalescing for saving transactions.
ChangeList(Controller) - Constructor for class apollo.editor.ChangeList: for gene edit panel
changeStart(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
changeStart(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
changeTierHeight(int) - Method in class apollo.gui.genomemap.AnnotationView
changeTierHeight(int) - Method in class apollo.gui.genomemap.TierView
changeTierHeights(int) - Method in class apollo.gui.genomemap.ApolloPanel
changeTypeColor(FeatureView, Selection) - Method in class apollo.gui.genomemap.FeatureTierManager: Pop up the color chooser for the selected feature type
changeYOrientation() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASDsnContentHandler
characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASEntryPointContentHandler
characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASFeatureContentHandler
characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASSequenceContentHandler
characters(char[], int, int) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: implementing sax handler interface
characters(char[], int, int) - Method in class apollo.dataadapter.das2.SegmentParser
characters(char[], int, int) - Method in class apollo.dataadapter.das2.SourceParser
characters(char[], int, int) - Method in class apollo.dataadapter.gamexml.XMLParser
characters(char[], int, int) - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
charAt(int) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Returns the base on the reference sequence for a given position
charAt(int) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
charHeight - Variable in class apollo.gui.TierManager
checkAdjacent(Transcript, Vector) - Method in class apollo.editor.AnnotationEditor: Determines if two exons are adjacent to one another in the transcript.
checkBoolean(String, String) - Method in class apollo.config.Style
checkCuration(CurationSet, DataOutputStream) - Method in class apollo.dataadapter.genbank.GenbankValidator: Writing G
checkFeature(FeatureSetI, String, String) - Method in class apollo.dataadapter.genbank.GenbankValidator
checkFocusDrivenEdits() - Method in class apollo.gui.annotinfo.FeatureEditPanel: Focus driven edits occur in textboxes -> synonyms, names, and ids.
checkFocusDrivenEdits() - Method in class apollo.gui.annotinfo.GeneEditPanel: Focus driven edits occur in textboxes -> synonyms, names, and ids.
checkForLocation(DataInput) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: If dataInput is a location, change its SO type to be getLocationSeqType()
checkFormat(SeqFeatureI, String) - Method in interface apollo.config.ApolloNameAdapterI: Returns true if id jibes with seq feature's ID format.
checkFormat(SeqFeatureI, String) - Method in class apollo.config.ChadoJdbcNameAdapter: Returns true if id jibes with seq feature's ID format.
checkFormat(SeqFeatureI, String) - Method in class apollo.config.DefaultNameAdapter: Returns true if seq feature's ID format is ok.
checkFormat(SeqFeatureI, String) - Method in class apollo.config.ParameciumNameAdapter: Returns true if id jibes with seq feature's ID format.
checkFormat(SeqFeatureI, String) - Method in class apollo.config.TigrAnnotNameAdapter
checkFreeMemory() - Method in class apollo.gui.CheckMemoryThread
CheckMemoryThread - Class in apollo.gui
CheckMemoryThread(long) - Constructor for class apollo.gui.CheckMemoryThread
checkName(String, Class) - Method in interface apollo.config.ApolloNameAdapterI
checkName(String, Class) - Method in class apollo.config.ChadoJdbcNameAdapter
checkName(String, Class) - Method in class apollo.config.DefaultNameAdapter
checkName(String, Class) - Method in class apollo.config.ParameciumNameAdapter
checkName(String, Class) - Method in class apollo.config.TigrAnnotNameAdapter
checkRefFeatures(FeatureSetI) - Static method in class apollo.dataadapter.debug.DisplayTool
checkValidColor(String, String) - Method in class apollo.config.Style
child_0 - Variable in class apollo.analysis.filter.HuffNode
child_1 - Variable in class apollo.analysis.filter.HuffNode
CHILD_TYPE - Static variable in class apollo.dataadapter.synteny.builder.AdapterModel
childrenReady(SeqFeatureI) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: Returns true if all children of this feature have already been read in
CHIMERA_GAP - Static variable in class apollo.analysis.filter.AnalysisFilter
chooseTab(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI
chooseTab(String) - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI
CHROMOSOME - Static variable in class apollo.dataadapter.otter.parser.TagHandler
Chromosome - Class in apollo.datamodel
Chromosome(String, String, Vector) - Constructor for class apollo.datamodel.Chromosome
Chromosome(String, String, int) - Constructor for class apollo.datamodel.Chromosome
Chromosome(String, String, int, int, int) - Constructor for class apollo.datamodel.Chromosome
chromosome - Variable in class apollo.datamodel.GenomicRange
ChromosomeAdapter - Class in apollo.dataadapter
ChromosomeAdapter(String) - Constructor for class apollo.dataadapter.ChromosomeAdapter
ChromosomeAdapter() - Constructor for class apollo.dataadapter.ChromosomeAdapter
ChromosomeBand - Class in apollo.datamodel
ChromosomeBand(String, String, int, int, String) - Constructor for class apollo.datamodel.ChromosomeBand
ChromosomeDrawer - Class in apollo.dataadapter.synteny
ChromosomeDrawer(Chromosome, Vector, Hashtable, boolean) - Constructor for class apollo.dataadapter.synteny.ChromosomeDrawer
ChromosomeField - Class in apollo.gui: Chromsome field is either a combo box or text field depending on if config has a chromosome vector
ChromosomeField() - Constructor for class apollo.gui.ChromosomeField
ChromosomeField(Vector) - Constructor for class apollo.gui.ChromosomeField
ChromosomePanel - Class in apollo.dataadapter.synteny
ChromosomePanel(Chromosome, Vector) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel
ChromosomePanel(Chromosome, Vector, StatusBar) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel
ChromosomePanel(Chromosome, Vector, Hashtable, StatusBar) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel
ChromosomePanel(Chromosome, Vector, Hashtable, StatusBar, AbstractDataAdapterUI, String, String) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel
CigarUtil - Class in apollo.util
CigarUtil() - Constructor for class apollo.util.CigarUtil
CLASS - Static variable in class apollo.dataadapter.synteny.builder.Model
clean() - Method in class apollo.dataadapter.gamexml.XMLParser
cleanUp(CurationSet, String, AnalysisInput) - Method in class apollo.analysis.filter.AnalysisFilter
cleanUp(CurationSet, String, AnalysisInput) - Method in interface apollo.analysis.filter.AnalysisFilterI: All filters on computed results must support this interface.
cleanUp(Vector, FeatureSetI, FeatureSetI, int, AnalysisFilter) - Static method in class apollo.analysis.filter.Coverage
cleanUp() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: cleanup extra components when closing down
cleanupByType(FeatureSetI, String) - Method in class apollo.analysis.filter.AnalysisFilter: Experimental--not currently being used.
cleanUpTwilightZone(FeaturePairI, FeaturePairI, boolean, boolean) - Method in class apollo.analysis.filter.TwilightFilter
clear() - Method in class apollo.datamodel.LinkSet
clear() - Method in class apollo.editor.TransactionManager
clear(boolean) - Method in class apollo.gui.Controller: Clear called by handleDataLoadEvent with clearOnDataLoadEvent set to true, for species controllers not master controllers also called by CurationState when removed
clear() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
clear() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
clear() - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent
clear() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
clear() - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
clear() - Method in class apollo.gui.detailviewers.sequencealigner.Tier
clear() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
clear() - Method in class apollo.gui.evidencepanel.EvidencePanelContainer
clear(boolean) - Method in class apollo.gui.genomemap.AnnotationView
clear() - Method in class apollo.gui.genomemap.FeatureView: sets internal vars to null: fset, dfset, visibleDrawables, graphics should it set them to empty vectors instead of null? T
clear(boolean) - Method in class apollo.gui.genomemap.FeatureView
clear() - Method in class apollo.gui.genomemap.GraphView
clear() - Method in class apollo.gui.genomemap.LinearView
clear() - Method in class apollo.gui.genomemap.ManagedView
clear(boolean) - Method in class apollo.gui.genomemap.ResultView: Clear out mem leaks
clear() - Method in class apollo.gui.genomemap.ScaleView
clear() - Method in class apollo.gui.genomemap.TierView
clear() - Method in interface apollo.gui.genomemap.ViewI
clear() - Method in class apollo.gui.menus.AnnotationMenu: Clean up dangling references (mem leaks)
clear() - Method in class apollo.gui.menus.TierPopupMenu: Clean up dangling references (mem leaks)
clear() - Method in class apollo.gui.Selection: This does deselection.
clear() - Method in class apollo.util.CaseInsensitiveStringHash
CLEAR_EDIT - Static variable in interface apollo.datamodel.SequenceI: I question if CLEAR_EDIT shouold be a separate type - its just a deletion of the above types - refactor?
CLEAR_SEQ_REGIONS - Static variable in class apollo.dataadapter.ensj.controller.Controller
clearActionListeners() - Method in class apollo.dataadapter.synteny.builder.Controller
clearAll() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser
clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: removes all the annotations from the annotation list and the annotation panel
clearCache() - Method in class apollo.datamodel.seq.CacheSequenceLoader
clearComments() - Method in class apollo.datamodel.AnnotatedFeature
clearComments() - Method in interface apollo.datamodel.AnnotatedFeatureI
clearCutSites() - Method in class apollo.gui.genomemap.ScaleView
clearData() - Method in interface apollo.gui.genomemap.ApolloPanelHolderI
clearData() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
clearEdges() - Method in class apollo.gui.genomemap.ApolloPanel
clearEdges() - Method in class apollo.gui.genomemap.FeatureView
clearFeature() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser
clearFeatures() - Method in class apollo.gui.genomemap.DrawableTierManager: Clears features from tiers, and clear tiers
clearFeatures() - Method in interface apollo.gui.genomemap.FeatureTierManagerI
clearFeatures() - Method in class apollo.gui.genomemap.FeatureView: just clears out features from view
clearFindsButton - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
clearFindsButton - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
clearHighlights() - Method in class apollo.gui.genomemap.FeatureView
clearKids() - Method in class apollo.datamodel.FeatureSet
clearKids() - Method in class apollo.datamodel.SeqFeature: by default no kids - no-op
clearKids() - Method in interface apollo.datamodel.SeqFeatureI: clear out allkids - if have any
clearLog4JDiagnosticContext() - Static method in class apollo.main.Apollo: Clears/removes the Log4J Nested Diagnostic Context (NDC) for a Thread.
clearOldData() - Method in class apollo.dataadapter.AbstractApolloAdapter: This has to be called in the subclass.getCurationSet (super.clearOldData()) to do the new data notification(clears old features) - also it notifies Config of style change.
clearProperties() - Method in class apollo.datamodel.SeqFeature
clearProperties() - Method in interface apollo.datamodel.SeqFeatureI
clearProperties() - Method in class apollo.datamodel.Synonym
clearRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
clearResidues() - Method in class apollo.datamodel.AbstractSequence: sets residues to empty string
clearResidues() - Method in class apollo.datamodel.Sequence
clearResidues() - Method in interface apollo.datamodel.SequenceI: clears out residues (set to empty string)
clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: removes all of the results from the results list and the result panel
clearSelected() - Method in class apollo.gui.genomemap.Sites
clearSelection() - Method in class apollo.gui.genomemap.ApolloPanel
clearSelection() - Method in interface apollo.gui.genomemap.ApolloPanelI
clearSelections() - Method in class apollo.gui.genomemap.SiteView: Clear all selections in all Sites
clearSelections() - Method in class apollo.gui.SelectionManager: clear() is called on the currently selected Selection.
clearSeqChoiceComboBox() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI: Reset the seqChoiceComboBox to its original state; called when the current database changes.
ClearSeqRegionsHandler - Class in apollo.dataadapter.ensj.controller: The user has selected a new coordinate system, so I flush the known seq-regions and update.
ClearSeqRegionsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ClearSeqRegionsHandler
clearSites() - Method in class apollo.gui.genomemap.Sites
clearStateInformation() - Method in class apollo.dataadapter.AbstractApolloAdapter: This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
clearStateInformation() - Method in class apollo.dataadapter.BaseGFFAdapter
clearStateInformation() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
clearStateInformation() - Method in class apollo.dataadapter.das2.DAS2Adapter
clearStateInformation() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
clearStateInformation() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
clearStateInformation() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
clearStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyAdapter: Does nothing yet, because the state info isn't being used on this adapter yet.
clearSynonyms() - Method in class apollo.datamodel.AnnotatedFeature
clearSynonyms() - Method in interface apollo.datamodel.AnnotatedFeatureI
clearSynonyms() - Method in class apollo.datamodel.Identifier
clearTransactions() - Method in class apollo.editor.AnnotationChangeLog: if new data is loaded transactions need to be cleared out.
clip - Variable in class apollo.gui.genomemap.FastClippingGraphics
ClipboardUtil - Class in apollo.util
ClipboardUtil() - Constructor for class apollo.util.ClipboardUtil
clipRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
clone() - Method in class apollo.config.ColumnProperty
clone() - Method in class apollo.config.FeatureProperty: this needs to be a deep clone not a shallow one
clone() - Method in class apollo.config.TierProperty
clone() - Method in class apollo.datamodel.AnnotatedFeature
clone() - Method in class apollo.datamodel.Comment: to get a field-by-field replica of this feature
clone() - Method in class apollo.datamodel.FeatureSet: to get a field-by-field replica of this feature
clone() - Method in class apollo.datamodel.Identifier
clone() - Method in class apollo.datamodel.SeqFeature: to get a field-by-field replica of this feature
clone() - Method in interface apollo.datamodel.SeqFeatureI: to get a field-by-field replica of this feature
clone() - Method in class apollo.gui.Transformer
cloneAnnot() - Method in class apollo.datamodel.AnnotatedFeature
cloneAnnot() - Method in interface apollo.datamodel.AnnotatedFeatureI
cloneComment() - Method in class apollo.datamodel.Comment
cloneFeature() - Method in class apollo.datamodel.SeqFeature
cloneFeature() - Method in interface apollo.datamodel.SeqFeatureI: clones feature
cloneInstance() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
cloneList() - Method in class apollo.util.FeatureList: Returns a FeatureList that contains seq feature clones of all features in current list.
cloneSynonym() - Method in class apollo.datamodel.Synonym
close() - Method in class apollo.dataadapter.CGI
close() - Method in interface apollo.gui.EditWindowI
closeConnection(Connection) - Method in class apollo.dataadapter.ensj.controller.EventHandler
closeMode() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
coalesce() - Method in class apollo.editor.TransactionManager: Coalesce all Transaction instances in this TransactionManager.
CODING - Static variable in interface apollo.datamodel.CodingPropertiesI
CODING_PROPERTIES - Static variable in class apollo.gui.DetailInfo
CodingPropertiesI - Interface in apollo.datamodel
codonHash - Static variable in class apollo.seq.ResidueProperties
codonTranslate(String) - Static method in class apollo.seq.ResidueProperties
coincidence - Variable in class apollo.analysis.filter.AnalysisInput
collapse - Variable in class apollo.analysis.filter.AnalysisInput
collapseAll() - Method in class apollo.gui.featuretree.FeatureTreePanel
collapseResults(boolean) - Method in class apollo.analysis.filter.AnalysisInput
collapseResults() - Method in class apollo.analysis.filter.AnalysisInput
collapseTier(String) - Method in class apollo.gui.genomemap.FeatureTierManager
collapseTier(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager: The next few methods are used by TierPopupMenu and AnnotationMenu
collapseTier(String) - Method in interface apollo.gui.genomemap.FeatureTierManagerI
CollectionUtil - Class in apollo.util: This class provides static utility methods for handling Collections.
CollectionUtil() - Constructor for class apollo.util.CollectionUtil
collectShadows() - Method in class apollo.gui.genomemap.DragView
colName - Variable in class apollo.dataadapter.chado.jdbc.TableColumn
color - Static variable in class apollo.gui.FindPanel
color - Variable in class apollo.util.interval.RbNode
colorAllAnnotsByOwner() - Method in class apollo.config.Style
colorIndex - Static variable in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
colorList - Static variable in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
colour - Variable in class apollo.config.FeatureProperty
colourHash - Static variable in class apollo.config.FeatureProperty
cols - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
cols - Variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: The number of base pairs displayed in a single row
ColumnApolloLayout - Class in apollo.gui.genomemap: An ApolloLayoutManager which lays out its views in a single column.
ColumnApolloLayout() - Constructor for class apollo.gui.genomemap.ColumnApolloLayout
ColumnProperty - Class in apollo.config
ColumnProperty(String) - Constructor for class apollo.config.ColumnProperty
ColumnProperty(String, int) - Constructor for class apollo.config.ColumnProperty
ColumnProperty(ColumnProperty) - Constructor for class apollo.config.ColumnProperty
columns - Variable in class apollo.config.FeatureProperty
comboBox - Variable in class apollo.dataadapter.GuiTabPanel
CommandLine - Class in apollo.main: Class for dealing with command line options.
commandLineXmlFileFormatIsConfigged() - Static method in class apollo.config.Config: Returns true if commandLineXmlFileFormat is nonnull and is "game" or "chado"
Comment - Class in apollo.datamodel
Comment() - Constructor for class apollo.datamodel.Comment
Comment(String, String, String, long) - Constructor for class apollo.datamodel.Comment
COMMENT - Static variable in class apollo.editor.TransactionClass
COMMENT - Static variable in class apollo.editor.TransactionSubpart
comments - Variable in class apollo.config.FeatureProperty
comments - Variable in class apollo.config.TierProperty
comments - Variable in class apollo.config.TiersIO
commitAccessions(boolean) - Method in class apollo.dataadapter.genbank.GenbankAdapter
commitAddTransaction(String, AddTransaction, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
commitChanges(CurationSet) - Method in class apollo.dataadapter.AbstractApolloAdapter
commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.AbstractApolloAdapter: SyntenyAdapter and SerialDiskAdapter override this
commitChanges(Object) - Method in class apollo.dataadapter.AbstractApolloAdapter
commitChanges(Object, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter: GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results
commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter
commitChanges(CompositeDataHolder, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter
commitChanges(CurationSet) - Method in interface apollo.dataadapter.ApolloDataAdapterI: writes the changes from a featureChangeLog to a writeable datasource.
commitChanges(CompositeDataHolder) - Method in interface apollo.dataadapter.ApolloDataAdapterI: Write out composite data holder to multiple data adapters (only SyntenyAdapter actually implements this)
commitChanges(Object) - Method in interface apollo.dataadapter.ApolloDataAdapterI: Straight from DataAdapterGUI.doOp.
commitChanges(Object, boolean, boolean) - Method in interface apollo.dataadapter.ApolloDataAdapterI: GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results
commitChanges(CurationSet) - Method in class apollo.dataadapter.BaseGFFAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.chado.ChadoAdapter: Writes back curation set via jdbc, using the curations sets transactions
commitChanges(CurationSet) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Main method for writing ChadoXML file
commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Main method for writing ChadoXML file
commitChanges(CurationSet) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.das2.DAS2Adapter: Main method for writing DAS2XML file
commitChanges(CurationSet) - Method in class apollo.dataadapter.EnsCGIAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter: Write the (now edited) curation set back to the otter server or file, depending on what was nominated.
commitChanges(CurationSet) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.gamexml.GAMEAdapter
commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.gamexml.GAMEAdapter: Writes XML If the input type is not FILE, prompts user for a file to save to.
commitChanges(CurationSet) - Method in class apollo.dataadapter.GbrowseAdapter
commitChanges(CurationSet, boolean) - Method in class apollo.dataadapter.genbank.GenbankAdapter: Write GenBank report in tabular or human-readable format, as requested
commitChanges(CurationSet) - Method in class apollo.dataadapter.gff3.GFF3Adapter: Commit data
commitChanges(CurationSet) - Method in class apollo.dataadapter.otter.OtterAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
commitChanges(CurationSet) - Method in class apollo.dataadapter.SerialDiskAdapter
commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.SerialDiskAdapter: If multi cur set, appends curset name to filename - or should it appends the cur set # so its retrievable?
commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.synteny.SyntenyAdapter: Write out composite data holder to multiple data adapters - called by DataLoader/FileMenu not SynAdapGUI
commitChanges(CurationSet) - Method in class apollo.dataadapter.synteny.SyntenyAdapter: I think this is now pase and should be deleted - always gets a CompositeDataHolder now - this is actually not called by SyntenyAdapterGUI.doOp(WRITE) - calls child adapter guis doOp this is called by DataLoader though
commitDeleteTransaction(String, DeleteTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
commitTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Commit a transaction using the current JDBC Connection.
commitTransaction(String, int, Transaction, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
commitTransactions(TransactionManager) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Write a set of transactions to the database using adapter
commitTransactions(TransactionManager) - Method in class apollo.dataadapter.TransactionOutputAdapter: The client to this class should call this method to commit (save or write changes to the database) transactions.
commitTransformedTransactions(List) - Method in class apollo.dataadapter.chado.jdbc.JDBCTransactionWriter: This takes a list of chado transactions (not apollo transactions) and commits them
commitTransformedTransactions(List) - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter
commitTransformedTransactions(List) - Method in class apollo.dataadapter.TransactionOutputAdapter: A subclass to this class should implement this method to provide its own behaviors.
commitUpdateParentTransaction(String, UpdateParentTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
commitUpdateTransaction(String, UpdateTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
CompactFeaturePlaceFinder - Class in apollo.gui.detailviewers.sequencealigner: This class encapsulates a 'compact' place finding algorithm.
CompactFeaturePlaceFinder() - Constructor for class apollo.gui.detailviewers.sequencealigner.CompactFeaturePlaceFinder
Comparable - Interface in apollo.datamodel
Comparator - Interface in apollo.util
ComparatorBase<T> - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorBase() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorBase
ComparatorFactory - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorFactory() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorFactory
ComparatorFactory.TYPE - Enum in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorReverse<T> - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorReverse(Comparator<T>) - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorReverse
ComparatorSeqFeatureDisplayType - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorSeqFeatureDisplayType() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureDisplayType
ComparatorSeqFeatureFrame - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorSeqFeatureFrame() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureFrame
ComparatorSeqFeatureLength - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorSeqFeatureLength() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureLength
ComparatorSeqFeatureName - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorSeqFeatureName() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureName
ComparatorSeqFeatureScore - Class in apollo.gui.detailviewers.sequencealigner.comparators
ComparatorSeqFeatureScore() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureScore
compare(Object, Object) - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationFeatureComparator
compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorBase
compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorReverse
compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureDisplayType
compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureFrame
compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureLength
compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureName
compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureScore
compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.MultiComparatorArrayList
compare(Object, Object) - Method in class apollo.gui.detailviewers.sequencealigner.ResultFeatureComparator
compare(Object, Object) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator
compare(Object, Object) - Method in interface apollo.util.Comparator
compare(Object, Object) - Method in class apollo.util.FeatureAlphabeticalComparator
compare(Object, Object) - Method in class apollo.util.FeatureComparator
compareDoubles(Double, Double) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator
compareIntegers(Integer, Integer) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator
compareRanges(Range, Range) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator
compareStrings(String, String) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator
compareTo(Object) - Method in interface apollo.datamodel.Comparable
compareTo(Object) - Method in class apollo.datamodel.SeqFeature
compareTo(Object) - Method in interface apollo.datamodel.SeqFeatureI
compareTo(Object) - Method in class apollo.util.interval.Interval
complain(String) - Method in class apollo.config.Style: Print message to stderr
completeGUIInitialization() - Method in class apollo.gui.ApolloFrame: This is only called once, from ApolloRunner when the gui is first coming up, after the first dataset is loaded (CAF.loadData())
componentInit() - Method in class apollo.gui.FindPanel
componentInit() - Method in class apollo.gui.SeqMatchPanel
CompositeApolloFrame - Class in apollo.gui.synteny: The synteny panels need to display many stranded-zoomable-apollo-panels at once, (unlike the standard apollo frame).
CompositeApolloFrame.MacApplicationSupport - Class in apollo.gui.synteny
CompositeApolloFrame.MacApplicationSupport() - Constructor for class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
CompositeDataHolder - Class in apollo.datamodel: Holds multiple curation sets for synteny.
CompositeDataHolder() - Constructor for class apollo.datamodel.CompositeDataHolder
CompositeDataHolder(SpeciesComparison) - Constructor for class apollo.datamodel.CompositeDataHolder
CompositeDataHolder(CurationSet) - Constructor for class apollo.datamodel.CompositeDataHolder: Puts composite curation sets into species comparisons
CompositeDataSourceConfigurationPanel - Class in apollo.dataadapter.ensj19: This is a panel which composes a number of the standard DataSourceConfiguration panels - one for the results, one for variations, one for sequences.
CompositeDataSourceConfigurationPanel(String[]) - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel: Automatically takes the first chooser name passed in as the default.
CompositeDataSourceConfigurationPanel(String[], boolean) - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
CompositeDataSourceConfigurationPanel() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
CompositeDataSourceConfigurationPanel.ChooserActionListener - Class in apollo.dataadapter.ensj19: Exposes the chosen panel, hides the one that was previously chosen
CompositeDataSourceConfigurationPanel.ChooserActionListener() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.ChooserActionListener
CompositeDataSourceConfigurationPanel.DatabaseFindListener - Class in apollo.dataadapter.ensj19: When the user hits "find" on the _default_ data config panel, we need to find all core ensembl databases, as well as variations.
CompositeDataSourceConfigurationPanel.DatabaseFindListener() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.DatabaseFindListener
CompoundTransaction - Class in apollo.editor: A CompoundTransaction contains a list of Transactions (children).
CompoundTransaction(Object) - Constructor for class apollo.editor.CompoundTransaction: phase out -> require source!
Compress - Class in apollo.analysis.filter
Compress() - Constructor for class apollo.analysis.filter.Compress
compress(String, int, boolean) - Static method in class apollo.analysis.filter.Compress
compress_threshold - Variable in class apollo.analysis.filter.BlastFilterPanel
compressedCodonHash - Static variable in class apollo.seq.ResidueProperties
computeMD5Checksum(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
Config - Class in apollo.config: A class with static data members and static methods for setting and retrieving configuration information for the apollo gui.
Config() - Constructor for class apollo.config.Config
confirmSaved(Object[], DataLoader) - Static method in class apollo.main.LoadUtil: should this be done on a per curationState basis?
connect() - Method in class apollo.dataadapter.mysql.MySQLDatabase
connect() - Method in class apollo.dataadapter.mysql.MySQLInstance
connection - Variable in class apollo.dataadapter.CGI
CONNECTION_STRING - Static variable in class apollo.dataadapter.StateInformation
constraints - Variable in class apollo.dataadapter.GuiTabPanel
construct() - Method in class apollo.gui.SwingWorker: Compute the value to be returned by the get method.
ContainerView - Class in apollo.gui.genomemap
ContainerView(JComponent, String, boolean) - Constructor for class apollo.gui.genomemap.ContainerView
ContainerViewI - Interface in apollo.gui.genomemap
contains(RangeI) - Method in class apollo.datamodel.CurationSet: Overrides Range.contains.
contains(Link) - Method in class apollo.datamodel.LinkSet
contains(RangeI) - Method in class apollo.datamodel.Range
contains(int) - Method in class apollo.datamodel.Range
contains(RangeI) - Method in interface apollo.datamodel.RangeI: Returns true if range of sf is entierly within this RangeI
contains(int) - Method in interface apollo.datamodel.RangeI
contains(Object) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
contains(Point, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
contains(Object) - Method in class apollo.util.CaseInsensitiveStringHash
containsAll(Collection<?>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
containsCoding() - Method in class apollo.datamodel.Exon: Convenience function that uses getCodingProperties() and returns true if its codingProperty has coding
containsCoding() - Method in interface apollo.datamodel.ExonI: Returns true if exon contains any coding region.
containsFeature(SeqFeatureI) - Method in class apollo.gui.Selection: Returns true if there is a SelectionItem in Selection with sf
containsFeature(SeqFeatureI, SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil: Returns true if container contains query (or is query)
containsKey(String) - Method in class apollo.util.CaseInsensitiveStringHash
CONTIG - Static variable in class apollo.dataadapter.DataInputType
CONTIG_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
ControlledObjectI - Interface in apollo.gui: Interface defining methods required to add a Controller to an object getControllerWindow and needs AutoRemoval used by Controller to remove listeners when their controller window is closing.
ControlledPanel - Class in apollo.gui: An extension of JPanel to make automatic Controller window management possible.
ControlledPanel() - Constructor for class apollo.gui.ControlledPanel
Controller - Class in apollo.dataadapter.ensj.controller
Controller(Model, View) - Constructor for class apollo.dataadapter.ensj.controller.Controller
Controller - Class in apollo.dataadapter.synteny.builder
Controller(Model, View) - Constructor for class apollo.dataadapter.synteny.builder.Controller
Controller - Class in apollo.gui: An event controller forwarding multiple types of event to registered listeners.
Controller() - Constructor for class apollo.gui.Controller
controller - Variable in class apollo.gui.genomemap.ApolloPanel
controller - Variable in class apollo.gui.genomemap.ContainerView
controller - Variable in class apollo.gui.genomemap.TierView
controller - Variable in class apollo.gui.NonWindowControlledObject
controller - Variable in class apollo.gui.TierManager
ControllerDebugListener - Class in apollo.gui
ControllerDebugListener(Controller) - Constructor for class apollo.gui.ControllerDebugListener
convertFromBaseOrientedToInterbase() - Method in class apollo.datamodel.Range
convertFromBaseOrientedToInterbase() - Method in interface apollo.datamodel.RangeI: Converts base oriented range to interbase range
convertFromInterbaseToBaseOriented() - Method in class apollo.datamodel.Range
convertFromInterbaseToBaseOriented() - Method in interface apollo.datamodel.RangeI: Converts interbase range to base oriented range
convertLogicalNameToSpeciesName(String) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter: Use the synteny style to convert from logical to actual species names.
coord_seq - Variable in class apollo.dataadapter.analysis.AlignmentParser
COORD_SYSTEM - Static variable in class apollo.dataadapter.ensj.EnsJAdapter
copyAnnotatedGenesIntoResultTier(StrandedFeatureSet, StrandedFeatureSet, String, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: A method that copies all the annotated protein-coding genes into a result tier.
copyArea(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
copyElements(Collection<? extends T>, Collection<? super T>, boolean) - Static method in class apollo.util.CollectionUtil: Copy elements from src to dest.
copyFile(String, String) - Static method in class apollo.util.IOUtil
copyOnWrite - Variable in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
copySeqToClipboard(Sequence) - Static method in class apollo.util.ClipboardUtil: should this go in SequenceUtil?
copyTextToClipboard(String) - Static method in class apollo.util.ClipboardUtil
count - Variable in class apollo.analysis.filter.HuffNode
Coverage - Class in apollo.analysis.filter
Coverage() - Constructor for class apollo.analysis.filter.Coverage
creaateIntronMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
create() - Method in class apollo.gui.genomemap.FastClippingGraphics
create(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
CREATE_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller
CREATE_SET_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller
createAdaptersAndGUIs(String) - Method in class apollo.dataadapter.synteny.builder.Model
createAnnotation() - Method in class apollo.editor.AnnotationEditor
createAnnotation(String) - Method in class apollo.editor.AnnotationEditor: The default createAnnotation method for creating an unsupported annotation.
createAnnotation(int, int, String) - Method in class apollo.editor.AnnotationEditor: This method puts up a dialog asking for the size of the new exon, and then calls #createAnnotation(int,int,int).
createAnnotation(int, int, int, String) - Method in class apollo.editor.AnnotationEditor: This method uses #addAnnotation(Vector,false,type) to create an unsupported transcript or gene, or one level?
createAnnotationAllowed() - Method in class apollo.editor.AnnotationEditor: Determine whether or not the SelectionSets are compatible with creating an unsupported (no evidence) annotation.
createBorder(String) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
createCacher() - Method in class apollo.datamodel.seq.AbstractLazySequence: Overriden by GAMESequence
createCacher() - Method in class apollo.datamodel.seq.GAMESequence
createChangeList() - Method in class apollo.gui.annotinfo.FeatureEditPanel
createClassFromName(String) - Method in class apollo.config.FeatureProperty
createDefaultFeatureProperty() - Method in class apollo.config.PropertyScheme
createDialog() - Method in class apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel
createDragView(MouseEvent, Selection) - Method in class apollo.gui.genomemap.TierView
createDragView(MouseEvent, Selection) - Method in interface apollo.gui.genomemap.TierViewI: Interface of method required for starting a drag from this TierView
createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableEnsemblFeatureSet
createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableFeatureSet
createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableGeneFeatureSet
createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawablePhaseHighlightGeneFeatureSet
createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableResultFeatureSet
createDrawable(SeqFeatureI) - Static method in class apollo.gui.drawable.DrawableUtil: Creates and returns a DrawableFeatureSet from a FeatureSetI.
CreateExonAction - Class in apollo.gui.detailviewers.sequencealigner.actions: An Action class for creating a single base exon within an intron region.
CreateExonAction(String, GuiCurationState, AnnotationEditor) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.CreateExonAction: Constructor
createExonMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
createExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
createExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
createFeature(OBOParser) - Method in class apollo.dataadapter.gff3.GFF3Entry: Create the implementing class of AnnotatedFeatureI given the type
createFinder(FeaturePlaceFinder.Type) - Static method in class apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder
createFP() - Method in class apollo.dataadapter.analysis.BlatParser
createGlyph(String) - Static method in class apollo.gui.drawable.DrawableUtil: Glyph name may be whole path (apollo.gui.drawable.Zigzag), just the class name(Zigzag)
createGraphics(Graphics, int, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
createGraphics(Graphics, int, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
CreateIntronAction - Class in apollo.gui.detailviewers.sequencealigner.actions: An Action class for creating a single base intron within an exon region.
CreateIntronAction(String, GuiCurationState, AnnotationEditor) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.CreateIntronAction: Constructor
createLinksFromSpeciesComp(SpeciesComparison) - Method in interface apollo.dataadapter.synteny.LinkerI
createMenuManager(ApolloFrame) - Static method in class apollo.gui.menus.MenuManager
createNameAdapter() - Method in class apollo.config.FeatureProperty
createNameFromClass(Object) - Method in class apollo.config.FeatureProperty: Given a class, e.g.
createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.AnnotationView
createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.FeatureView: This is overridden by ResultView and AnnotView - make abstract?
createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.ResultView
createRightClickMenu() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
createRightClickMenu() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
createSrcFeatureIDTransaction(String, String) - Method in class apollo.dataadapter.chado.ChadoTransactionTransformer
createStateInformation() - Method in interface apollo.dataadapter.ApolloDataAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
createStateInformation() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI: Convert the Model (which has all the UI's state information) into a properties object to be passed to the dataadapter.
createStateInformation() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI: We make sure (in addition to the superclass's setStateInfo) that we have added the names of the chosen annotation input and output files.
createStateInformation() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI
createStateInformation() - Method in class apollo.dataadapter.GFFAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.graph.GraphAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
createStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI: add on the hit-information to the query-information already in there.
createStyle(String) - Static method in class apollo.config.Config: If already have style for styleFilename, return that.
createTransferable(JComponent) - Method in class apollo.gui.ArrayListTransferHandler
createUnixShellCommand(SeqAnalysisLocal) - Method in class apollo.analysis.BlastHandler: different analysis programs require different ways of running them this method is only called by SeqAnalysisLocal
createUnixShellCommand(SeqAnalysisLocal) - Method in class apollo.analysis.GenericProgramHandler: different analysis programs require different ways of running them assumes a command line is made by programPath programParams inputSequence [datasourcePath]
createUnixShellCommand(SeqAnalysisLocal) - Method in interface apollo.analysis.ProgramHandlerI: different analysis programs require different ways of running them
curated - Variable in class apollo.config.TierProperty
curation - Variable in class apollo.dataadapter.analysis.AnalysisPanel
curation - Variable in class apollo.gui.genomemap.SiteView
curation_set - Variable in class apollo.dataadapter.AbstractApolloAdapter
CurationManager - Class in apollo.gui.synteny: Holds CurationState objects.
curationSet - Variable in class apollo.analysis.SeqAnalysisBase
CurationSet - Class in apollo.datamodel: I am the central holder of renderable data - results, annotations etc.
CurationSet() - Constructor for class apollo.datamodel.CurationSet
CurationSet(StrandedFeatureSetI, StrandedFeatureSetI, String) - Constructor for class apollo.datamodel.CurationSet
curationSet - Variable in class apollo.test.ApolloTest
curationSetIsLoaded(boolean) - Method in class apollo.gui.Controller
CurationState - Class in apollo.dataadapter
CurationState(int) - Constructor for class apollo.dataadapter.CurationState
current_job_id - Variable in class apollo.bop.JDBCPipelineAdapter
CUSTOM - Static variable in class apollo.gui.genomemap.StrandedZoomableApolloPanel
CUSTOM_DB_PROMPT - Static variable in class apollo.dataadapter.chado.ChadoAdapterGUI: Prompt for the pull-down menu that allows the user to select a Chado database from among those read from the Chado adapter's configuration file.
CUSTOM_SEQ_PROMPT - Static variable in class apollo.dataadapter.chado.ChadoAdapterGUI: Prompt for the area in which the user can enter the ID of the sequence he/she wishes to load.
CutSite - Class in apollo.gui.tweeker
CutSite(int, int, RestrictionEnzyme) - Constructor for class apollo.gui.tweeker.CutSite
Cys - Static variable in class apollo.seq.ResidueProperties
CYTOLOGY - Static variable in class apollo.dataadapter.DataInputType

D

DAS2Adapter - Class in apollo.dataadapter.das2: I implement a AbstractDataAdapter, allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI, DASDsn etc.
DAS2Adapter() - Constructor for class apollo.dataadapter.das2.DAS2Adapter
DAS2AdapterGUI - Class in apollo.dataadapter.das2: This actually constructs a completely different GUI for reading vs.
DAS2AdapterGUI() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI
DAS2AdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI
DAS2AdapterGUI.DSNListener - Class in apollo.dataadapter.das2
DAS2AdapterGUI.DSNListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.DSNListener
DAS2AdapterGUI.HistoryListener - Class in apollo.dataadapter.das2
DAS2AdapterGUI.HistoryListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.HistoryListener
DAS2AdapterGUI.ProxyListener - Class in apollo.dataadapter.das2: This listener gets fired when the user wants to set a Proxy Server for the session
DAS2AdapterGUI.ProxyListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.ProxyListener
DAS2AdapterGUI.ServerListener - Class in apollo.dataadapter.das2
DAS2AdapterGUI.ServerListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.ServerListener
DAS2FeatureSaxParser - Class in apollo.dataadapter.das2: Parser that reads features from das2xml and stores them in Apollo datamodels (the top level of which is a CurationSet).
DAS2FeatureSaxParser() - Constructor for class apollo.dataadapter.das2.DAS2FeatureSaxParser
DAS2Request - Class in apollo.dataadapter.das2: Adapted from das/simple/SimpleDASServer I don't understand why that class was called "server", since it's client-side.
DAS2Request(String) - Constructor for class apollo.dataadapter.das2.DAS2Request: You must pass in the URL of a DAS-reference server, used in all further requests.
DAS2Writer - Class in apollo.dataadapter.das2: writeXML: writes DAS2XML to a file
DAS2Writer() - Constructor for class apollo.dataadapter.das2.DAS2Writer
DASDsn - Interface in apollo.dataadapter.das
DASDsnContentHandler - Class in apollo.dataadapter.das.simple: I am the ContentHandler used when SimpleDASServer parses the result of a 'dsn' call to a das data source.
DASDsnContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASDsnContentHandler
DASEntryPointContentHandler - Class in apollo.dataadapter.das.simple: I am the ContentHandler used when SimpleDASServer parses the result of a 'entry_points' call to a das data source and dsn.
DASEntryPointContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASEntryPointContentHandler
DASFeature - Interface in apollo.dataadapter.das
DASFeatureContentHandler - Class in apollo.dataadapter.das.simple: I am the ContentHandler used when SimpleDASServer parses the result of a 'features' call to a das data source (with a specified dsn and segment).
DASFeatureContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASFeatureContentHandler
DASFeatureContentHandler(DASServerI, DASDsn, HashMap, HashMap, long, long) - Constructor for class apollo.dataadapter.das.simple.DASFeatureContentHandler
DASLazySequence - Class in apollo.dataadapter.das: I am a Sequence class for implementing lazy load using a DASServer
DASLazySequence(String, Controller, RangeI, DASServerI, DASDsn, DASSegment) - Constructor for class apollo.dataadapter.das.DASLazySequence
DASSegment - Interface in apollo.dataadapter.das: I represent the contained in a Segment (as defined by the DAS-spec) needed by Apollo to request features for the segment, and display the features of the segment.
DASSequence - Interface in apollo.dataadapter.das: I represent the data contained in a dna sequence (as defined by the DAS-spec) needed by Apollo to display a sequence.
DASSequenceContentHandler - Class in apollo.dataadapter.das.simple: I am the ContentHandler used when SimpleDASServer parses the result of a 'dna' call to a das data source (passing in dsn and segment).
DASSequenceContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASSequenceContentHandler
DASSequenceContentHandler(DASServerI, DASDsn, DASSegment[]) - Constructor for class apollo.dataadapter.das.simple.DASSequenceContentHandler
DASServerI - Interface in apollo.dataadapter.das: I represent the capability of a general DASServer, as required by Apollo to make das-data requests.
data - Variable in class apollo.dataadapter.CGI
DATA_ADAPTER - Static variable in class apollo.dataadapter.StateInformation
DATA_FILE_NAME - Static variable in class apollo.dataadapter.StateInformation
DATA_RETRIEVE_BEGIN - Static variable in class apollo.dataadapter.DataLoadEvent
DATA_RETRIEVE_DONE - Static variable in class apollo.dataadapter.DataLoadEvent
dataAdapterIsAvailable(IOOperation) - Static method in class apollo.config.Config
dataArray - Variable in class apollo.io.FileParse
database - Variable in class apollo.analysis.filter.AnalysisInput
Database - Class in apollo.dataadapter.mysql
Database(String, String, String, String) - Constructor for class apollo.dataadapter.mysql.Database
Database(String, String, String, String, int) - Constructor for class apollo.dataadapter.mysql.Database
DATABASE - Static variable in class apollo.dataadapter.StateInformation
databaseChoicePrompt - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
databaseComboBox - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
databaseHasStyle(String) - Method in class apollo.config.Style: Returns true if have style for db
DatabaseModel - Class in apollo.dataadapter.ensj.model
DatabaseModel() - Constructor for class apollo.dataadapter.ensj.model.DatabaseModel
DatabasePanel - Class in apollo.dataadapter.ensj.view
DatabasePanel(View) - Constructor for class apollo.dataadapter.ensj.view.DatabasePanel
DataFetcher - Class in apollo.dataadapter.ensj: I am just a separate helper class to stop the EnsJAdapter from becoming too huge.
DataFetcher(EnsJAdapter) - Constructor for class apollo.dataadapter.ensj.DataFetcher
DataInput - Class in apollo.dataadapter: This lumps together DataInputType and getInput String in ApolloDataAdapterI.
DataInput(DataInputType, String) - Constructor for class apollo.dataadapter.DataInput
DataInput(String, String) - Constructor for class apollo.dataadapter.DataInput
DataInput(String, String, String) - Constructor for class apollo.dataadapter.DataInput
DataInput(String, String, String, String) - Constructor for class apollo.dataadapter.DataInput: Constructor for a location with Strings for chrom, start, & end & so type
DataInput(DataInputType) - Constructor for class apollo.dataadapter.DataInput
DataInput(String) - Constructor for class apollo.dataadapter.DataInput
DataInputType - Class in apollo.dataadapter: A value class for the different types of Data input
DataInputType.UnknownTypeException - Exception in apollo.dataadapter
DataListener - Interface in apollo.dataadapter: Interface to get notification when an adapter is about to create new data Should this be merged with DataLoadListener? YES! and go through controller perhaps Controller should go in a different package than gui? Should there be one method with a DataEvent that distinguishes beginning and ending load? 7.26.04 This has been merged with DataLoadListener.
DataLoader - Class in apollo.main: This class handles loading of data into Apollo.
DataLoader() - Constructor for class apollo.main.DataLoader
DataLoadEvent - Class in apollo.dataadapter: DataLoadEvent are sent out on new data being loaded.
DataLoadEvent(Object, int) - Constructor for class apollo.dataadapter.DataLoadEvent: If type is DATA_RETRIEVE_BEGIN then we dont have apolloData nor region yet
DataLoadEvent(Object, CurationSet) - Constructor for class apollo.dataadapter.DataLoadEvent
dataLoadingDone() - Method in interface apollo.dataadapter.DataListener
DataLoadListener - Interface in apollo.dataadapter
DataModelConversionUtil - Class in apollo.dataadapter.ensj
DataModelConversionUtil() - Constructor for class apollo.dataadapter.ensj.DataModelConversionUtil
dataRetrievalBeginning() - Method in class apollo.dataadapter.DataLoadEvent: New data is about to be fetched and made.
dataRetrievalDone() - Method in class apollo.dataadapter.DataLoadEvent: New data has been retrieved/created.
DataSourceConfigurationPanel - Class in apollo.dataadapter.ensj19: This panel allows the user to configure the parameters necessary for the EnsJ-interface to an ensembl database.
DataSourceConfigurationPanel() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
DataSourceConfigurationPanel(String) - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
DataSourceConfigurationPanel.DataChangeListener - Class in apollo.dataadapter.ensj19: Triggered when the user types into any data field
DataSourceConfigurationPanel.DataChangeListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.DataChangeListener
DataSourceConfigurationPanel.EnsemblDBSelectionListener - Class in apollo.dataadapter.ensj19: Triggered when the user selects a particular database
DataSourceConfigurationPanel.EnsemblDBSelectionListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.EnsemblDBSelectionListener
DataSourceConfigurationPanel.HostListener - Class in apollo.dataadapter.ensj19: Triggered when the user pushes the "find" button
DataSourceConfigurationPanel.HostListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.HostListener
DataUtil - Class in apollo.datamodel.seq
date - Variable in class apollo.editor.Transaction
date_formats - Static variable in class apollo.util.DateUtil
dateNoTime(Date) - Static method in class apollo.util.DateUtil: Return a date in the format 18-JAN-2004 (Used by GenbankReport)
DateUtil - Class in apollo.util
DateUtil() - Constructor for class apollo.util.DateUtil
db - Variable in class apollo.dataadapter.mysql.BaseAdaptor
DBAdaptor - Class in apollo.dataadapter.gbrowse
DBAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.gbrowse.DBAdaptor
dbname - Variable in class apollo.dataadapter.GbrowseAdapter
DbXref - Class in apollo.datamodel
DbXref(String, String, String) - Constructor for class apollo.datamodel.DbXref
DbXref(String, String, String, boolean) - Constructor for class apollo.datamodel.DbXref
DBXREF - Static variable in class apollo.editor.TransactionSubpart
debug - Variable in class apollo.analysis.filter.AnalysisInput
DEBUG - Static variable in class apollo.config.Config: Debug mode for Apollo developers; references to this variable are scattered throughout the Apollo code.
debug - Variable in class apollo.gui.genomemap.FeatureTierManager
debug - Variable in class apollo.gui.genomemap.LinearView
debug_str - Variable in class apollo.analysis.filter.AnalysisInput
debugFeature(SeqFeatureI, SeqFeatureI, String, boolean) - Method in class apollo.analysis.filter.AnalysisFilter
debugFeature(SeqFeatureI, String) - Method in class apollo.analysis.filter.AnalysisFilter
debugFeature(SeqFeatureI, String, boolean) - Method in class apollo.analysis.filter.AnalysisFilter
debugFilter(String) - Method in class apollo.analysis.filter.AnalysisInput
DebugLazySequence - Class in apollo.datamodel.seq
DebugLazySequence(String, Controller, String) - Constructor for class apollo.datamodel.seq.DebugLazySequence
debugName(SeqFeatureI) - Method in class apollo.analysis.filter.AnalysisFilter
debugName(SeqFeatureI) - Method in class apollo.dataadapter.analysis.Sim4Parser
debugName(SeqFeatureI) - Static method in class apollo.dataadapter.gamexml.GAMESave
DECORATED - Static variable in class apollo.gui.drawable.DrawableSeqFeature
decrementGeneTranscriptRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
decrementTierHeight() - Method in class apollo.gui.genomemap.TierView
decrementTierHeight() - Method in interface apollo.gui.genomemap.TierViewI
decrementTierHeight() - Method in class apollo.gui.TierManager
decrementTierHeight() - Method in interface apollo.gui.TierManagerI
decrementTranscriptExonRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
DEFAULT - Static variable in class apollo.dataadapter.synteny.builder.Model
default_3prime - Static variable in class apollo.analysis.filter.AnalysisFilter
DEFAULT_COLOR - Static variable in class apollo.config.FeatureProperty
default_columns - Static variable in class apollo.config.FeatureProperty
DEFAULT_CONFIG_FILE - Static variable in class apollo.dataadapter.ensj19.EnsJAdapterGUI
DEFAULT_STYLE - Static variable in class apollo.config.FeatureProperty
DEFAULT_TIER - Static variable in class apollo.dataadapter.analysis.AnalysisPanel
DEFAULT_TYPE - Static variable in class apollo.dataadapter.analysis.AnalysisPanel
DefaultBaseRenderer - Class in apollo.gui.detailviewers.exonviewer
DefaultBaseRenderer(int, int) - Constructor for class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
DefaultBaseRenderer - Class in apollo.gui.detailviewers.sequencealigner
DefaultBaseRenderer(int, int) - Constructor for class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
DefaultDisplayPrefs - Class in apollo.config
DefaultDisplayPrefs() - Constructor for class apollo.config.DefaultDisplayPrefs
DefaultNameAdapter - Class in apollo.config: If no name adapter is specified, and no or human gene def, then DefaultNameAdapter is used.
DefaultNameAdapter() - Constructor for class apollo.config.DefaultNameAdapter
defaultRowHeader - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
DELETE - Static variable in class apollo.dataadapter.chado.ChadoTransaction
DELETE - Static variable in class apollo.editor.FeatureChangeEvent
DELETE - Static variable in class apollo.editor.TransactionOperation
DELETE_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller
DELETE_SET_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller
deleteCDS(long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteComment(long, Comment) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteComment(Comment) - Method in class apollo.datamodel.AnnotatedFeature
deleteComment(int) - Method in class apollo.datamodel.AnnotatedFeature
deleteComment(Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI
deleteComment(int) - Method in interface apollo.datamodel.AnnotatedFeatureI
deleteDbXref(long, DbXref) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteDbXref(DbXref) - Method in class apollo.datamodel.Identifier
deleteDrawable(Drawable) - Method in interface apollo.gui.drawable.Drawable: If drawable contains child, deletes it
deleteDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableFeatureSet
deleteDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableSeqFeature: Default no-op implementation, DrawableSeqFeature doesnt have children, do nothing.
deleteDrawable(Drawable) - Method in interface apollo.gui.drawable.DrawableSetI
deleteEvidence(String) - Method in class apollo.datamodel.AnnotatedFeature
deleteEvidence(String) - Method in interface apollo.datamodel.AnnotatedFeatureI
deleteEvidence(String) - Method in class apollo.datamodel.EvidenceSet
deleteEvidence(Evidence) - Method in class apollo.datamodel.EvidenceSet
deleteExon(long, long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Delete an exon from the database (defaults to not checking if it is a shared exon
deleteExon(long, long, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Delete an exon from the database
deleteExon(ExonI) - Method in class apollo.datamodel.Transcript
deleteExon() - Method in class apollo.editor.AnnotationEditor: The default edit for deleting an exon from a transcript.
DeleteExonAction - Class in apollo.gui.detailviewers.sequencealigner.actions: An Action class for deleting an exon
DeleteExonAction(String, GuiCurationState, AnnotationEditor) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.DeleteExonAction: Constructor
deleteExonAllowed() - Method in class apollo.editor.AnnotationEditor: Determine if the default purgeExon is compatible with the current SelectionSets.
deleteExonMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
deleteExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
deleteExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
deleteFeature(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet
deleteFeature(SeqFeatureI) - Method in interface apollo.datamodel.FeatureSetI: The number of directly containd features.
deleteFeature(SeqFeatureI) - Method in class apollo.datamodel.StrandedFeatureSet
deleteFeatureAt(int) - Method in class apollo.datamodel.FeatureSet
deleteFeatureAt(int) - Method in interface apollo.datamodel.FeatureSetI
deleteFeatureAt(int) - Method in class apollo.datamodel.StrandedFeatureSet
deleteFeatureDbXrefRow(long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
deleteFeaturepropRow(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
deleteFeatureRelationshipRow(Long, Long, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
deleteFeatureSynonymRow(Long, Long, Integer) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
deleteGene(long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deletePolypeptide(long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteReferencingRows(String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
deleteRow(String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Recursive delete of a row and all the rows that reference it via a foreign key constraint.
deleteSelectedFeatures() - Method in class apollo.editor.AnnotationEditor: The default deleteSelectedFeatures which deletes any features in the viewSet.
deleteSelectedFeatures(Vector, String) - Method in class apollo.editor.AnnotationEditor: Deletes the Vector of features.
deleteSelectionAllowed() - Method in class apollo.editor.AnnotationEditor: True if can delete selection
deleteSynonym(long, String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Delete a synonym from the database
deleteSynonym(String) - Method in class apollo.datamodel.AnnotatedFeature
deleteSynonym(Synonym) - Method in class apollo.datamodel.AnnotatedFeature
deleteSynonym(String) - Method in interface apollo.datamodel.AnnotatedFeatureI
deleteSynonym(Synonym) - Method in interface apollo.datamodel.AnnotatedFeatureI
deleteSynonym(Synonym) - Method in class apollo.datamodel.Identifier
deleteSynonym(String) - Method in class apollo.datamodel.Identifier
deleteSynonymRowIfNoLongerNeeded(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
DeleteTransaction - Class in apollo.editor: The transaction class for deleting operation in Apollo.
DeleteTransaction() - Constructor for class apollo.editor.DeleteTransaction: Default Constructor.
DeleteTransaction(SeqFeatureI, SeqFeatureI) - Constructor for class apollo.editor.DeleteTransaction
DeleteTransaction(SeqFeatureI, Object) - Constructor for class apollo.editor.DeleteTransaction
DeleteTransaction(SeqFeatureI, SeqFeatureI, Object) - Constructor for class apollo.editor.DeleteTransaction: source should come first to be consistent with add trans
DeleteTransaction(SeqFeatureI, TransactionSubpart) - Constructor for class apollo.editor.DeleteTransaction
DeleteTransaction(SeqFeatureI, TransactionSubpart, Object) - Constructor for class apollo.editor.DeleteTransaction
DeleteTransaction(Object, SeqFeatureI, TransactionSubpart, Object, int) - Constructor for class apollo.editor.DeleteTransaction
deleteTranscript(long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteTranscript(long, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
deleteUnreferencedRow(String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Delete a row known not to be referenced by any other (e.g., because deleteReferencingRows has already been called on the row)
DELETION - Static variable in interface apollo.datamodel.SequenceI
deletionMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
deletionMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
deletionMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
descendsFrom(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature: This is the opposite of contains.
descendsFrom(SeqFeatureI) - Method in interface apollo.datamodel.SeqFeatureI: This is the opposite of isAncestor.
DESCRIPTION - Static variable in class apollo.editor.TransactionSubpart
description - Variable in class apollo.gui.GenericFileFilter
detachEnsemblDatabaseDropdownListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
detachTranscript(Transcript) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
detachTranscript(Transcript) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
DetailInfo - Class in apollo.gui: This class is mainly for EvidencePanel and its SetDetailPanel, but there is handy methods that could be widely used.
DetailInfo() - Constructor for class apollo.gui.DetailInfo
dfset - Variable in class apollo.gui.genomemap.FeatureView
digForConfigFile(String) - Static method in class apollo.config.Config: Look around for style file, pulling out of the jar if necessary (needed for webstart)
DIR - Static variable in class apollo.dataadapter.DataInputType
Directions - Interface in apollo.gui.detailviewers.exonviewer: Currently only used by SeqAlignPanel so putting in detailwindows package, if other classes use then should be moved, could probably be declared in SeqAlignPanel itself
Directions - Interface in apollo.gui.detailviewers.sequencealigner: Currently only used by SeqAlignPanel so putting in detail windows package, if other classes use then should be moved, could probably be declared in SeqAlignPanel itself
disableAdapterPanel() - Method in class apollo.dataadapter.synteny.builder.View
DisabledEditor - Class in apollo.gui: A TableCellEditor which disables edits in the cells.
DisabledEditor() - Constructor for class apollo.gui.DisabledEditor
DiscreteGraphView - Class in apollo.gui.genomemap: This is a view for a discrete graph
DiscreteGraphView(JComponent, String, Color, Transformer) - Constructor for class apollo.gui.genomemap.DiscreteGraphView: Construct a new DiscreteGraphView object
disown(Vector) - Method in class apollo.editor.AnnotationEditor
display_type - Variable in class apollo.analysis.filter.AnalysisInput
displayBothLinks() - Method in class apollo.gui.synteny.SyntenyLinkPanel
displayJustDnaLinks() - Method in class apollo.gui.synteny.SyntenyLinkPanel
displayJustProteinLinks() - Method in class apollo.gui.synteny.SyntenyLinkPanel
displayMessage(String) - Method in class apollo.dataadapter.ensj.controller.Controller
displayMessage(String) - Method in class apollo.dataadapter.ensj.view.View
DisplayPrefsI - Interface in apollo.config
displayRightClickMenu(int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
displayRightClickMenu(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
DisplaySequenceAction - Class in apollo.gui.detailviewers.sequencealigner.actions: An action class for brining up the display sequence window
DisplaySequenceAction(String, GuiCurationState) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.DisplaySequenceAction: Constructor
displaySequenceMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
displaySplashScreen() - Static method in class apollo.main.Apollo
displayTierBox - Variable in class apollo.dataadapter.analysis.AnalysisPanel
DisplayTool - Class in apollo.dataadapter.debug
DisplayTool() - Constructor for class apollo.dataadapter.debug.DisplayTool
displayTypeBox - Variable in class apollo.dataadapter.analysis.AnalysisPanel
dispose() - Method in class apollo.gui.annotinfo.FeatureEditorDialog: disposes commentator, then calls super.dispose (Window)
dispose() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
dispose() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
dispose() - Method in class apollo.gui.genomemap.FastClippingGraphics
disposeAllEditors() - Static method in class apollo.gui.annotinfo.FeatureEditorDialog: Dispose all FeatureEditorDialogs currently in existence.
disposeAllEditors() - Static method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor: Dispose all editors currently in existence.
disposeAllEditors() - Static method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor: Dispose all editors currently in existence.
disposeCommentator() - Method in class apollo.gui.annotinfo.GeneEditPanel
distinctHSPs - Variable in class apollo.analysis.filter.AnalysisInput
DITAG_FEATURE_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
DITAGFEATURE - Static variable in class apollo.dataadapter.ensj.model.TypesModel
DNA - Static variable in interface apollo.datamodel.SequenceI
DNA - Static variable in class apollo.gui.detailviewers.blixem.BlixemRunner
DNA_DNA_ALIGN_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
DNA_PROTEIN_ALIGN_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
DNADNA - Static variable in class apollo.dataadapter.ensj.model.TypesModel
DNAMultiSequenceAlignerPanel - Class in apollo.gui.detailviewers.sequencealigner.DNAPanel: The main class for the DNA view.
DNAMultiSequenceAlignerPanel(GuiCurationState, Strand) - Constructor for class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel: Constructor
DNAPROTEIN - Static variable in class apollo.dataadapter.ensj.model.TypesModel
DNAResultRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers
DNAResultRenderer() - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
DNAResultRenderer(boolean) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
DO_ONE_LEVEL_ANNOTS - Static variable in class apollo.config.Config
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ChangeDatabaseHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ClearSeqRegionsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.EventHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.FindCoordSystemsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.FindEnsemblDatabaseNamesHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.FindSeqRegionsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.HideShowAnnotationsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.HideShowDatabasesHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.HideShowLocationsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.HideShowOptionsHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.HideShowTypesHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.LoadSeqRegionByHistoryHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ReadHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.SelectNewEnsemblDatabaseHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.SelectSeqRegionHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowAbInitioCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDitagFeatureCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDnaDnaAlignCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDnaProteinAlignCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowGeneCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.ShowSimpleFeatureCountsByTypeHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.UpdateHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.UseSeqRegionLocationHandler
doAction(Model) - Method in class apollo.dataadapter.ensj.controller.UseStableIDLocationHandler
doctype(String, String, String) - Method in class apollo.dataadapter.gamexml.XMLParser
doLayout() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI: If this JPanel is not displayed in the parent component, setVisible(boolean) will not have any effect.
doLayout() - Method in class apollo.gui.genomemap.ApolloPanel
doLayoutTiers() - Method in class apollo.gui.TierManager
doLayoutTiers() - Method in interface apollo.gui.TierManagerI
doMiddleClick(MouseEvent) - Method in class apollo.gui.genomemap.ApolloPanel
doOperation(Object) - Method in class apollo.analysis.SeqAnalysisGUI
doOperation(Object) - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.das2.DAS2AdapterGUI: This is where the real work starts--we read the data or write it.
doOperation(Object) - Method in class apollo.dataadapter.EnsCGIAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.gamexml.GAMEAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.GbrowseAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.GFFAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.graph.GraphAdapterGUI: Main method to be executed for appending data
doOperation(Object) - Method in class apollo.dataadapter.otter.OtterAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.otter.OtterXMLAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.sample.SampleAdapterGUI: The central method - called by the DataAdapterChooser - when the user hits the "OK" button.
doOperation(Object) - Method in class apollo.dataadapter.SerialAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
doOperation(Object) - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI: We need to post-process this composite curation set.
doOperation(Object) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI
doParse(String) - Method in class apollo.config.TiersIO
doRead() - Method in class apollo.dataadapter.ensj.controller.Controller
doRead() - Method in class apollo.dataadapter.ensj.controller.EventHandler
doSave(File, Vector) - Method in class apollo.config.TiersIO
doSearch() - Method in class apollo.gui.detailviewers.sequencealigner.FindDialog
doTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.ApolloPanel
DoubleHeadedArrow - Class in apollo.gui.drawable: Draws a double-headed arrow (an arrowhead pointing inwards on each end of a rectangle).
DoubleHeadedArrow() - Constructor for class apollo.gui.drawable.DoubleHeadedArrow
DoubleHeadedArrow(SeqFeatureI) - Constructor for class apollo.gui.drawable.DoubleHeadedArrow
doubleSort(double[], int, int, Object[]) - Static method in class apollo.util.QuickSort
doUpdate() - Method in class apollo.dataadapter.ensj.controller.Controller
doUpdate() - Method in class apollo.dataadapter.ensj.controller.EventHandler
doUserTranscriptColouring() - Static method in class apollo.config.Config
doUserTranscriptColouring() - Method in class apollo.config.Style
doViewDrag(MouseEvent) - Method in class apollo.gui.genomemap.ApolloPanel
DOWN - Static variable in class apollo.gui.Transformer
downstream_button - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
downstream_button - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
dragSources - Variable in class apollo.gui.genomemap.TierView
dragTierView - Variable in class apollo.gui.genomemap.ApolloPanel
DragView - Class in apollo.gui.genomemap: A FeatureView which has extra methods to handle dragging.
DragView(JComponent, String, Selection) - Constructor for class apollo.gui.genomemap.DragView
DragViewI - Interface in apollo.gui.genomemap: Defines the methods required for dragging.
draw(Graphics, int, int, int, int) - Method in class apollo.dataadapter.synteny.ChromosomeDrawer
draw(Graphics, Transformer, TierManagerI, PixelMaskI) - Method in interface apollo.gui.drawable.Drawable: Draws the Drawable onto the Graphics
draw(Graphics, Transformer, TierManagerI) - Method in interface apollo.gui.drawable.Drawable
draw(Graphics, Transformer, TierManagerI, PixelMaskI) - Method in class apollo.gui.drawable.DrawableFeatureSet: Need to change cached feature property - resynch with feature and synch up descendants
draw(Graphics, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableFeatureSet: draw method using the Transformer to do coord conversions.
draw(Graphics, Transformer, TierManagerI, PixelMaskI) - Method in class apollo.gui.drawable.DrawableSeqFeature: This method draws the feature on the Graphics using a Transformer for coordinate transformations.
draw(Graphics, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature: This method draws the feature on the Graphics using a Transformer for coordinate transformations.
draw3DRect(int, int, int, int, boolean) - Method in class apollo.gui.genomemap.FastClippingGraphics
draw_level - Variable in class apollo.gui.drawable.DrawableSeqFeature
Drawable - Interface in apollo.gui.drawable: An interface defining methods necessary for a drawable object
drawable_parent - Variable in class apollo.gui.drawable.DrawableSeqFeature
DrawableAnnotationConstants - Interface in apollo.gui.drawable: Constants used in drawing annotations (which stops to display etc).
DrawableDisplayTool - Class in apollo.gui.drawable
DrawableDisplayTool() - Constructor for class apollo.gui.drawable.DrawableDisplayTool
DrawableEnsemblFeatureSet - Class in apollo.gui.drawable: A drawable for drawing ensembl style (box around set) feature sets.
DrawableEnsemblFeatureSet() - Constructor for class apollo.gui.drawable.DrawableEnsemblFeatureSet
DrawableEnsemblFeatureSet(FeatureSetI) - Constructor for class apollo.gui.drawable.DrawableEnsemblFeatureSet
DrawableFeatureSet - Class in apollo.gui.drawable: A drawable for drawing a feature set.
DrawableFeatureSet() - Constructor for class apollo.gui.drawable.DrawableFeatureSet: Since this is not an abstract class, allow it to be used as a visible drawn feature
DrawableFeatureSet(boolean) - Constructor for class apollo.gui.drawable.DrawableFeatureSet
DrawableFeatureSet(FeatureSetI, boolean) - Constructor for class apollo.gui.drawable.DrawableFeatureSet
DrawableGeneFeatureSet - Class in apollo.gui.drawable: A drawable for drawing result (computational analysis) feature sets.
DrawableGeneFeatureSet() - Constructor for class apollo.gui.drawable.DrawableGeneFeatureSet
DrawableGeneFeatureSet(FeatureSetI) - Constructor for class apollo.gui.drawable.DrawableGeneFeatureSet
DrawableGeneSeqFeature - Class in apollo.gui.drawable: This is currently used by ensembl - see ensembl.tiers.
DrawableGeneSeqFeature() - Constructor for class apollo.gui.drawable.DrawableGeneSeqFeature
DrawableGeneSeqFeature(SeqFeatureI) - Constructor for class apollo.gui.drawable.DrawableGeneSeqFeature
DrawableHalfArrow - Class in apollo.gui.drawable
DrawableHalfArrow(boolean) - Constructor for class apollo.gui.drawable.DrawableHalfArrow
DrawableHalfArrow(SeqFeatureI, boolean) - Constructor for class apollo.gui.drawable.DrawableHalfArrow
drawableOverlaps(FeatureTier, Drawable) - Method in class apollo.gui.genomemap.FeatureTierManager: This still doesn't really work.
DrawablePhaseHighlightGeneFeatureSet - Class in apollo.gui.drawable: A drawable for drawing result (computational analysis) feature sets.
DrawablePhaseHighlightGeneFeatureSet() - Constructor for class apollo.gui.drawable.DrawablePhaseHighlightGeneFeatureSet
DrawablePhaseHighlightGeneSeqFeature - Class in apollo.gui.drawable
DrawablePhaseHighlightGeneSeqFeature() - Constructor for class apollo.gui.drawable.DrawablePhaseHighlightGeneSeqFeature
DrawablePhaseHighlightGeneSeqFeature(SeqFeatureI) - Constructor for class apollo.gui.drawable.DrawablePhaseHighlightGeneSeqFeature
DrawablePhaseHighlightNoHatGeneFeatureSet - Class in apollo.gui.drawable
DrawablePhaseHighlightNoHatGeneFeatureSet() - Constructor for class apollo.gui.drawable.DrawablePhaseHighlightNoHatGeneFeatureSet
DrawablePrimerSet - Class in apollo.gui.drawable
DrawablePrimerSet() - Constructor for class apollo.gui.drawable.DrawablePrimerSet
DrawablePrimerSet(FeatureSetI, boolean) - Constructor for class apollo.gui.drawable.DrawablePrimerSet
DrawableResultFeatureSet - Class in apollo.gui.drawable: A drawable for drawing result (computational analysis) feature sets.
DrawableResultFeatureSet() - Constructor for class apollo.gui.drawable.DrawableResultFeatureSet
DrawableResultFeatureSet(FeatureSetI) - Constructor for class apollo.gui.drawable.DrawableResultFeatureSet
DrawableResultSeqFeature - Class in apollo.gui.drawable: A drawable for drawing result (computational analysis) spans.
DrawableResultSeqFeature() - Constructor for class apollo.gui.drawable.DrawableResultSeqFeature
DrawableResultSeqFeature(SeqFeatureI) - Constructor for class apollo.gui.drawable.DrawableResultSeqFeature
drawables - Variable in class apollo.gui.genomemap.DragView
drawables - Variable in class apollo.gui.genomemap.DrawableTierManager
drawables - Variable in class apollo.gui.genomemap.FeatureView
DrawableSeqFeature - Class in apollo.gui.drawable: A drawable for drawing basic sequence features.
DrawableSeqFeature(boolean) - Constructor for class apollo.gui.drawable.DrawableSeqFeature
DrawableSeqFeature(SeqFeatureI, boolean) - Constructor for class apollo.gui.drawable.DrawableSeqFeature
DrawableSetI - Interface in apollo.gui.drawable: An interface defining methods necessary for a drawable object Merge this with Drawable? Drawables optionally have children? It would make descending the heirarchy easier.
drawablesForDrag(Selection) - Method in class apollo.gui.genomemap.TierView: Returns a FeatureSet of Drawables/view, not a model FeatureSet.
DrawableTierManager - Class in apollo.gui.genomemap
DrawableTierManager() - Constructor for class apollo.gui.genomemap.DrawableTierManager
DrawableTierManagerI - Interface in apollo.gui.genomemap
DrawableUtil - Class in apollo.gui.drawable
DrawableUtil() - Constructor for class apollo.gui.drawable.DrawableUtil
drawArc(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawArrow(Graphics, Rectangle, Transformer, TierManagerI, PixelMaskI, boolean) - Method in class apollo.gui.drawable.DrawablePrimerSet
drawArrowHead(Graphics, int, int, int, int) - Method in class apollo.gui.drawable.DoubleHeadedArrow
drawBytes(byte[], int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawChars(char[], int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawDashedLines(Graphics, Rectangle, Transformer, TierManagerI, Color, int) - Method in class apollo.gui.drawable.DrawableFeatureSet
drawDashedLines(Graphics, Rectangle, Transformer, TierManagerI, Color, int) - Method in class apollo.gui.drawable.DrawablePrimerSet
drawDashedLines(Graphics, Rectangle, Transformer, TierManagerI, Color, int) - Method in class apollo.gui.drawable.DrawableResultFeatureSet: Draws either a dashed or solid intron line.
drawDragRectangle(Graphics) - Method in class apollo.gui.genomemap.FeatureView
drawImage(Image, int, int, Color, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawImage(Image, int, int, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawImage(Image, int, int, int, int, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawLast(Graphics) - Method in class apollo.gui.genomemap.Rubberband
drawLast(Graphics) - Method in class apollo.gui.genomemap.RubberbandRectangle
drawLine(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawMissing(Graphics, Rectangle, boolean, int, Color, Color) - Method in class apollo.gui.drawable.DrawableSeqFeature
drawNext(Graphics) - Method in class apollo.gui.genomemap.Rubberband
drawNext(Graphics) - Method in class apollo.gui.genomemap.RubberbandRectangle
drawOval(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawPolygon(int[], int[], int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawPolygon(Polygon) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawPolyline(int[], int[], int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawRoundRect(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawSelected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableFeatureSet
drawSelected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableGeneSeqFeature
drawSelected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
drawSelected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Triangle
drawSequence(Graphics, Transformer) - Method in class apollo.gui.genomemap.TranslationView
drawSite(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Triangle
drawSpliceBases(Graphics, Transformer, int, int, String, int, int, int) - Method in class apollo.gui.genomemap.ScaleView
drawSpliceLines(Graphics, Transformer, int, int, String, int) - Method in class apollo.gui.genomemap.ScaleView
drawStartAndStopCodons(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
drawString(AttributedCharacterIterator, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawString(String, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DoubleHeadedArrow
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableEnsemblFeatureSet
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableFeatureSet
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableGeneFeatureSet: Draws arced intron line
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableGeneSeqFeature
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableHalfArrow
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawablePhaseHighlightGeneSeqFeature
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawablePhaseHighlightNoHatGeneFeatureSet
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.PromoterGlyph
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.ThinRectangle
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Triangle
drawUnselected(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Zigzag
driver - Variable in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
driver - Variable in class apollo.dataadapter.das2.DAS2AdapterGUI
driver - Variable in class apollo.dataadapter.EnsCGIAdapterGUI
DRIVER - Static variable in class apollo.dataadapter.ensj.EnsJConnectionUtil
driver - Variable in class apollo.dataadapter.GbrowseAdapterGUI
driver - Variable in class apollo.dataadapter.otter.OtterAdapterGUI
driver - Variable in class apollo.dataadapter.synteny.SyntenyAdapterGUI
driver - Variable in class apollo.gui.GenericFileAdapterGUI
DRIVER_CLASS - Static variable in class apollo.dataadapter.chado.ChadoAdapter
DRIVER_CLASSES - Static variable in class apollo.dataadapter.chado.ChadoAdapterGUI: NOTE - subclasses of JdbcChadoAdapter must be explicitly added to this list in order to be usable in the Chado adapter.
driverClassComboBox - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
driverClassPrompt - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI
driverConf - Variable in class apollo.dataadapter.synteny.SyntenyComparaAdapter
DriverDialog - Class in apollo.dataadapter.ensj19
DriverDialog(JFrame, Properties) - Constructor for class apollo.dataadapter.ensj19.DriverDialog
DROPDOWN_KEY_PRESSED - Static variable in class apollo.dataadapter.synteny.builder.Controller
DROPDOWN_SELECT_SET - Static variable in class apollo.dataadapter.synteny.builder.Controller
dropSpaceSize - Variable in class apollo.gui.genomemap.ManagedView
DropTargetViewI - Interface in apollo.gui.genomemap: Interface defining methods for handling a drop in a View
dsn - Variable in class apollo.dataadapter.das.simple.DASFeatureContentHandler
dsn - Variable in class apollo.dataadapter.das.simple.DASSequenceContentHandler
DSN_DESCRIPTION - Static variable in class apollo.dataadapter.StateInformation
dsn_listener - Variable in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
dsn_listener - Variable in class apollo.dataadapter.das2.DAS2AdapterGUI
DSN_MAP_MASTER - Static variable in class apollo.dataadapter.StateInformation
DSN_SOURCE - Static variable in class apollo.dataadapter.StateInformation
DSN_SOURCE_ID - Static variable in class apollo.dataadapter.StateInformation
DSN_SOURCE_VERSION - Static variable in class apollo.dataadapter.StateInformation
DummySequenceAdapter - Class in apollo.dataadapter
DummySequenceAdapter() - Constructor for class apollo.dataadapter.DummySequenceAdapter
duplicateTranscript(Transcript) - Method in class apollo.editor.AnnotationEditor: Duplicates a transcript.

E

EAST - Static variable in interface apollo.gui.detailviewers.exonviewer.Directions
EAST - Static variable in interface apollo.gui.detailviewers.sequencealigner.Directions
edit_offset_adjust - Variable in class apollo.datamodel.SeqFeature: When translating the offset for the stop codon in genome coordinates needs to be adjusted to account for edits to the mRNA that alter the relative position of the Stop codon on the mRNA vs.
EditMenu - Class in apollo.gui.menus
EditMenu(ApolloFrame) - Constructor for class apollo.gui.menus.EditMenu
editModel() - Method in class apollo.editor.AddTransaction
editModel() - Method in class apollo.editor.DeleteTransaction
editModel() - Method in class apollo.editor.UpdateTransaction
editor - Variable in class apollo.gui.genomemap.AnnotationView: The AnnotationEditor for performing edits in this view.
editorPanel - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
editorPanel - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor: RAY: This is where the annotations get added
editTypeSettings(FeatureView, Selection) - Method in class apollo.gui.genomemap.FeatureTierManager: Pop up the settings tab dialog for the selected feature type
EditWindowI - Interface in apollo.gui: This was used solely by FeatureEditorDialog but no longer - once its established that the FED is not going back to commit/cancel/clone/replace this interface should be deleted
EditWindowListener - Class in apollo.gui.event: Move to annotinfo package.
EditWindowListener() - Constructor for class apollo.gui.event.EditWindowListener
EfetchSequenceAdapter - Class in apollo.dataadapter: Is this class still being used? - delete?
EfetchSequenceAdapter() - Constructor for class apollo.dataadapter.EfetchSequenceAdapter
elementAt(int) - Method in class apollo.gui.genomemap.Sites
elements() - Method in class apollo.util.CaseInsensitiveStringHash
emptyNameAdapter() - Method in class apollo.dataadapter.CurationState
emptyTransactions() - Method in class apollo.editor.TransactionManager: Remove all transactions in the memory.
enableAdapterPanel() - Method in class apollo.dataadapter.synteny.builder.View
end - Variable in class apollo.dataadapter.das.simple.SimpleDASFeature
END - Static variable in class apollo.dataadapter.ensj.EnsJAdapter
END - Static variable in class apollo.dataadapter.otter.parser.TagHandler
END - Static variable in class apollo.gui.DetailInfo
END - Static variable in interface apollo.gui.drawable.DrawableAnnotationConstants: Indicates the end of a feature (got with getEnd()).
end(Point) - Method in class apollo.gui.genomemap.Rubberband
END_BOUNDARY - Static variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
END_PHASE - Static variable in class apollo.gui.DetailInfo
endDocument() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: implementing sax content handler interface
endDocument() - Method in class apollo.dataadapter.gamexml.XMLParser
endElement(String, String, String) - Method in class apollo.dataadapter.das.simple.DASDsnContentHandler
endElement(String, String, String) - Method in class apollo.dataadapter.das.simple.DASEntryPointContentHandler
endElement(String, String, String) - Method in class apollo.dataadapter.das.simple.DASFeatureContentHandler
endElement(String, String, String) - Method in class apollo.dataadapter.das.simple.DASSequenceContentHandler
endElement(String, String, String) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser: implementing sax content handler interface
endElement(String, String, String) - Method in class apollo.dataadapter.das2.SegmentParser
endElement(String, String, String) - Method in class apollo.dataadapter.das2.SourceParser
endElement(String, String, String) - Method in class apollo.dataadapter.gamexml.XMLParser
endElement(String, String, String) - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
endPrefixMapping(String) - Method in class apollo.dataadapter.gamexml.XMLParser
endPt - Variable in class apollo.gui.genomemap.Rubberband
endTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.ApolloPanel
endTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.FeatureView
endTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.TierView
endTierDrag(MouseEvent) - Method in interface apollo.gui.genomemap.TierViewI: end a tier drag
endToggle - Variable in class apollo.gui.featuretree.FeatureTreePanel
endToggling() - Method in class apollo.gui.featuretree.FeatureTreePanel
endViewDrag(MouseEvent) - Method in class apollo.gui.genomemap.ApolloPanel
EnsCGIAdapter - Class in apollo.dataadapter
EnsCGIAdapter(String) - Constructor for class apollo.dataadapter.EnsCGIAdapter
EnsCGIAdapter() - Constructor for class apollo.dataadapter.EnsCGIAdapter
EnsCGIAdapterGUI - Class in apollo.dataadapter
EnsCGIAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.EnsCGIAdapterGUI
EnsCGIAdapterGUI.ChrStartEndListener - Class in apollo.dataadapter
EnsCGIAdapterGUI.ChrStartEndListener() - Constructor for class apollo.dataadapter.EnsCGIAdapterGUI.ChrStartEndListener
EnsCGISequence - Class in apollo.datamodel.seq: EnsCGISequence:
EnsCGISequence(String, Controller, RangeI, String) - Constructor for class apollo.datamodel.seq.EnsCGISequence
ENSEMBL_DRIVER - Static variable in class apollo.dataadapter.StateInformation
EnsJAdapter - Class in apollo.dataadapter.ensj: EnsJ - Direct Access for Ensembl Databases (Schema 20 and above)
EnsJAdapter() - Constructor for class apollo.dataadapter.ensj.EnsJAdapter
EnsJAdapter - Class in apollo.dataadapter.ensj19: Adaptor providing access to the ensembl database via the ensj-core library.
EnsJAdapter() - Constructor for class apollo.dataadapter.ensj19.EnsJAdapter
EnsJAdapterGUI - Class in apollo.dataadapter.ensj
EnsJAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.ensj.EnsJAdapterGUI
EnsJAdapterGUI - Class in apollo.dataadapter.ensj19: Configuration GUI for the EnsJAdapter class.
EnsJAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.ensj19.EnsJAdapterGUI
EnsJAdapterGUI.ChromosomeDropdownPopupListener - Class in apollo.dataadapter.ensj19: When the user pops up the chromosome dropdown, it is populated - this listener makes the call to the driver, in turn to retrieve the chromsome list.
EnsJAdapterGUI.ChromosomeDropdownPopupListener() - Constructor for class apollo.dataadapter.ensj19.EnsJAdapterGUI.ChromosomeDropdownPopupListener
EnsJAdapterGUI.DataSourceChangeListener - Class in apollo.dataadapter.ensj19: This class clears out chromosome dd, leaving the initialisation taks to the dd's popup menu listener
EnsJAdapterGUI.DataSourceChangeListener() - Constructor for class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataSourceChangeListener
EnsJAdapterGUI.DataTypeButton - Class in apollo.dataadapter.ensj19
EnsJAdapterGUI.DataTypeButton(String, String, String) - Constructor for class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataTypeButton
EnsJAdapterUtil - Class in apollo.dataadapter.ensj
EnsJAdapterUtil() - Constructor for class apollo.dataadapter.ensj.EnsJAdapterUtil
EnsJConnectionUtil - Class in apollo.dataadapter.ensj
EnsJConnectionUtil() - Constructor for class apollo.dataadapter.ensj.EnsJConnectionUtil
EnsjDisplayPrefs - Class in apollo.config
EnsjDisplayPrefs() - Constructor for class apollo.config.EnsjDisplayPrefs
EnsJFeatureSetBuilder - Class in apollo.dataadapter.ensj
EnsJFeatureSetBuilder() - Constructor for class apollo.dataadapter.ensj.EnsJFeatureSetBuilder
EnsJSequence - Class in apollo.dataadapter.ensj19
EnsJSequence(String, Controller, Location, String) - Constructor for class apollo.dataadapter.ensj19.EnsJSequence
ensureExists(File, String, boolean) - Static method in class apollo.config.Config
ensureExists(File, String) - Static method in class apollo.config.Config: Default is not to recreate.
ensureMinimumWidth(int) - Method in class apollo.gui.Transformer.PixelRange
equals(Object) - Method in class apollo.util.interval.Interval
equals(Object) - Method in class apollo.util.Pair: Overload Object.equals to compare if the two elements are the same
equals(CurationSet, CurationSet) - Static method in class apollo.util.SeqFeatureUtil
equals(SeqFeatureI, SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil
equals(FeaturePairI, FeaturePairI) - Static method in class apollo.util.SeqFeatureUtil
equals(FeatureSetI, FeatureSetI) - Static method in class apollo.util.SeqFeatureUtil
equals(SequenceI, SequenceI) - Static method in class apollo.util.SeqFeatureUtil
equalsFeatures(SeqFeatureI, SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil
errorCheck() - Method in class apollo.dataadapter.analysis.BlatParser
errorDialog(String) - Static method in class apollo.util.IOUtil: Put up a dialog box if we're not running in batch mode or in headless mode.
errorPopup(String) - Method in class apollo.gui.annotinfo.FeatureEditPanel
establishRange(SeqFeatureI, int, int, boolean) - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
establishRange(SeqFeatureI, int, int, boolean) - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
EventHandler - Class in apollo.dataadapter.ensj.controller
EventHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.EventHandler
EventRouter - Class in apollo.dataadapter.ensj.controller: Generic class to forward any old events onto central handler.
EventRouter(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.EventRouter
EVIDENCE - Static variable in class apollo.dataadapter.otter.parser.TagHandler
Evidence - Class in apollo.datamodel
Evidence(String, String, int) - Constructor for class apollo.datamodel.Evidence
Evidence(String, int) - Constructor for class apollo.datamodel.Evidence
Evidence(String) - Constructor for class apollo.datamodel.Evidence
EVIDENCE - Static variable in class apollo.editor.TransactionClass
EVIDENCE - Static variable in class apollo.gui.DetailInfo
EVIDENCE_HOTSPOT - Static variable in class apollo.gui.genomemap.DragView
EvidenceConstants - Interface in apollo.datamodel
EvidenceFinder - Class in apollo.datamodel
EvidenceFinder(FeatureSetI) - Constructor for class apollo.datamodel.EvidenceFinder
EvidenceNameTagHandler - Class in apollo.dataadapter.otter.parser
EvidenceNameTagHandler() - Constructor for class apollo.dataadapter.otter.parser.EvidenceNameTagHandler
EvidencePanel - Class in apollo.gui.evidencepanel: A panel containing a table of selected result feature sets.
EvidencePanel(GuiCurationState) - Constructor for class apollo.gui.evidencepanel.EvidencePanel
EvidencePanelContainer - Class in apollo.gui.evidencepanel: JPanel that holds evidence panels for all of the szaps/species, handle orientation change.
EvidencePanelOrientationManager - Class in apollo.gui.evidencepanel: EvidencePanelOrientationManager class deals with orientation of evidence panel(s).
EvidenceSet - Class in apollo.datamodel
EvidenceSet() - Constructor for class apollo.datamodel.EvidenceSet
EvidenceTagHandler - Class in apollo.dataadapter.otter.parser: I will create a new Evidence element when my tag is found.
EvidenceTagHandler() - Constructor for class apollo.dataadapter.otter.parser.EvidenceTagHandler
EvidenceTypeTagHandler - Class in apollo.dataadapter.otter.parser
EvidenceTypeTagHandler() - Constructor for class apollo.dataadapter.otter.parser.EvidenceTypeTagHandler
ExampleFileFilter - Class in apollo.util: A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
ExampleFileFilter() - Constructor for class apollo.util.ExampleFileFilter: Creates a file filter.
ExampleFileFilter(String) - Constructor for class apollo.util.ExampleFileFilter: Creates a file filter that accepts files with the given extension.
ExampleFileFilter(String, String) - Constructor for class apollo.util.ExampleFileFilter: Creates a file filter that accepts the given file type.
ExampleFileFilter(String[]) - Constructor for class apollo.util.ExampleFileFilter: Creates a file filter from the given string array.
ExampleFileFilter(String[], String) - Constructor for class apollo.util.ExampleFileFilter: Creates a file filter from the given string array and description.
executeChanges() - Method in class apollo.editor.ChangeList: calls coalesceChanges which seems to be broken.
executeLoggedSelectQuery(String, Connection, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Execute a single SQL query and return the corresponding ResultSet.
executeLoggedSelectQuery(String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Alternate form of executeLoggedSelectQuery that uses getConnection() instead of an expicitly-passed Connection object.
executeLoggedUpdate(String, Connection, String, String[], Object[], Map) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Execute an SQL update statement (update, insert, or delete) and return the number of rows affected.
EXON - Static variable in class apollo.dataadapter.otter.parser.TagHandler
Exon - Class in apollo.datamodel
Exon(SeqFeatureI) - Constructor for class apollo.datamodel.Exon
Exon() - Constructor for class apollo.datamodel.Exon
EXON - Static variable in class apollo.editor.TransactionClass
EXON - Static variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
EXON - Static variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
exonColorIndex - Variable in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
exonColorIndex - Variable in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
ExonEndTagHandler - Class in apollo.dataadapter.otter.parser
ExonEndTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonEndTagHandler
ExonFrameTagHandler - Class in apollo.dataadapter.otter.parser
ExonFrameTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonFrameTagHandler
ExonI - Interface in apollo.datamodel
ExonStableIdTagHandler - Class in apollo.dataadapter.otter.parser
ExonStableIdTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonStableIdTagHandler
ExonStartTagHandler - Class in apollo.dataadapter.otter.parser
ExonStartTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonStartTagHandler
ExonStrandTagHandler - Class in apollo.dataadapter.otter.parser
ExonStrandTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonStrandTagHandler
ExonTagHandler - Class in apollo.dataadapter.otter.parser: I will create a new Exon when my tag is found.
ExonTagHandler() - Constructor for class apollo.dataadapter.otter.parser.ExonTagHandler
expandAllTiers(boolean) - Method in class apollo.config.PropertyScheme
expanded - Variable in class apollo.config.TierProperty
expandSquiggle(String) - Static method in class apollo.util.IOUtil
expandTier(String) - Method in class apollo.gui.genomemap.FeatureTierManager
expandTier(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager
expandTier(String) - Method in interface apollo.gui.genomemap.FeatureTierManagerI
exportDone(JComponent, Transferable, int) - Method in class apollo.gui.ArrayListTransferHandler
exportFragment(boolean) - Method in class apollo.gui.tweeker.CutSite
exportFragment() - Method in class apollo.gui.tweeker.CutSite
EXT_NAME - Static variable in class apollo.dataadapter.gamexml.TransactionXMLAdapter
extendWith(SeqFeatureI, SeqFeatureI) - Method in class apollo.dataadapter.analysis.Sim4Parser
extensions - Variable in class apollo.gui.GenericFileFilter

F

factor - Variable in class apollo.gui.ScoreCalculator
FALSEVAL - Static variable in class apollo.dataadapter.chado.jdbc.SybaseChadoAdapter
FastaFile - Class in apollo.seq.io: Parses a fasta file into a Vector of Sequence objects, which can be retrieved with getSeqs
FastaFile(Reader, boolean) - Constructor for class apollo.seq.io.FastaFile: Construct a FastaFile object from a Reader.
FastaFile(DataInputStream, boolean) - Constructor for class apollo.seq.io.FastaFile
FastaFile(String) - Constructor for class apollo.seq.io.FastaFile
FastaFile(String, String, CurationSet) - Constructor for class apollo.seq.io.FastaFile
FastaFile(String, String) - Constructor for class apollo.seq.io.FastaFile
FastaHeader - Class in apollo.util
FastaHeader(String) - Constructor for class apollo.util.FastaHeader
FastClippingGraphics - Class in apollo.gui.genomemap
FastClippingGraphics(Graphics) - Constructor for class apollo.gui.genomemap.FastClippingGraphics
fatalError(String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
FatalException - Exception in apollo.dataadapter.ensj
FatalException(String) - Constructor for exception apollo.dataadapter.ensj.FatalException
FatalException(String, Throwable) - Constructor for exception apollo.dataadapter.ensj.FatalException
featFromCurSet1(SeqFeatureI) - Method in class apollo.datamodel.SpeciesComparison
featToId - Variable in class apollo.config.TigrAnnotNameAdapter
featToName - Variable in class apollo.config.TigrAnnotNameAdapter
feature - Variable in class apollo.gui.drawable.DrawableSeqFeature
FEATURE - Static variable in class apollo.gui.Selection
FEATURE - Static variable in class apollo.gui.SelectionType
feature_draw(Graphics, Transformer, TierManagerI, Rectangle) - Method in class apollo.gui.drawable.DrawableSeqFeature
feature_set - Variable in class apollo.gui.featuretree.FeatureTreePanel
FeatureAdaptor - Class in apollo.dataadapter.gbrowse
FeatureAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.gbrowse.FeatureAdaptor
FeatureAlphabeticalComparator - Class in apollo.util
FeatureAlphabeticalComparator() - Constructor for class apollo.util.FeatureAlphabeticalComparator
featureAt(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets the feature that contains a given position
featureAt(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
featureAt(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: Given a pixel position return the feature at that position
featureAt(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
FeatureChangeEvent - Class in apollo.editor: A controller managed event class which signals when a change is made to a set of features and what type of change occurred.
FeatureChangeEvent(Object, SeqFeatureI, int, SeqFeatureI, SeqFeatureI) - Constructor for class apollo.editor.FeatureChangeEvent: This constructor needs to be vanquished i think.
FeatureChangeEvent(Object, SeqFeatureI) - Constructor for class apollo.editor.FeatureChangeEvent: No subpart
FeatureChangeEvent(Object, SeqFeatureI, TransactionSubpart) - Constructor for class apollo.editor.FeatureChangeEvent: With subpart
FeatureChangeEvent(Object) - Constructor for class apollo.editor.FeatureChangeEvent: For edit session done event.
FeatureChangeListener - Interface in apollo.editor
FeatureComparator - Class in apollo.util
FeatureComparator() - Constructor for class apollo.util.FeatureComparator
featureContains(SeqFeatureI, int) - Method in class apollo.gui.genomemap.ScrollAdjustedView
FeatureEditorDialog - Class in apollo.gui.annotinfo: FeatureEditorDialog Editor for comments, gene and transcript names, etc Editing is disabled in browser mode.
featureEditorDialog - Variable in class apollo.gui.annotinfo.FeatureEditPanel
FeatureEditPanel - Class in apollo.gui.annotinfo: A JPanel to display Transcript & Gene info.
featureExsitsAt(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Determines if there exsists a feature at a given position
featureExsitsAt(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
featureForAnalysisType(String) - Method in class apollo.config.TierProperty
featureHasBeenEdited(SeqFeatureI) - Method in class apollo.editor.TransactionManager: convenience function.
featureIn(Range, boolean, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets the first(?) feature within a given range inclusive(?)
featureIn(Range, boolean, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
FeatureIterator - Class in apollo.util: Iterator for FeatureList, puts out SeqFeatureIs, add more Iterator methods as needed.
FeatureIterator(FeatureList) - Constructor for class apollo.util.FeatureIterator
featureIterator() - Method in class apollo.util.FeatureList
FeatureList - Class in apollo.util: Just a little helper class.
FeatureList() - Constructor for class apollo.util.FeatureList
FeatureList(int) - Constructor for class apollo.util.FeatureList
FeatureList(Vector) - Constructor for class apollo.util.FeatureList
FeatureList(boolean) - Constructor for class apollo.util.FeatureList: if unique check is true, check that feat doesnt already exist on adding
FeatureList(SeqFeatureI, boolean) - Constructor for class apollo.util.FeatureList: Create FeatureList from seqFeat.
FeatureNavigationI - Interface in apollo.gui: Interface for JFrames that will respond when a interior component wants them to do something with a feature that has been selected.
FeaturePair - Class in apollo.datamodel
FeaturePair(SeqFeatureI, SeqFeatureI) - Constructor for class apollo.datamodel.FeaturePair: f1 is query feature, f2 is hit feature
FeaturePairI - Interface in apollo.datamodel
FeaturePlaceFinder - Class in apollo.gui.detailviewers.sequencealigner
FeaturePlaceFinder() - Constructor for class apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder
FeaturePlaceFinder.Type - Enum in apollo.gui.detailviewers.sequencealigner
FeatureProperty - Class in apollo.config: FeatureProperty comes from "Types" in the tiers file.
FeatureProperty(TierProperty, String, Vector, Color, String, boolean, float, float) - Constructor for class apollo.config.FeatureProperty
FeatureProperty(TierProperty, String, Vector) - Constructor for class apollo.config.FeatureProperty
FeatureProperty(FeatureProperty) - Constructor for class apollo.config.FeatureProperty
FeatureProperty(FeatureProperty, boolean) - Constructor for class apollo.config.FeatureProperty
FeatureProperty(TierProperty, String, Vector, Color, String) - Constructor for class apollo.config.FeatureProperty
FeatureProperty(TierProperty, String, Vector, Color) - Constructor for class apollo.config.FeatureProperty
FeatureProperty() - Constructor for class apollo.config.FeatureProperty
FeaturePropertyPanel - Class in apollo.gui: A panel which renders a configuration tab dialog for a FeatureProperty
FeaturePropertyPanel(FeatureProperty, ApolloPanel) - Constructor for class apollo.gui.FeaturePropertyPanel
features - Variable in class apollo.datamodel.FeatureSet
FEATURES - Static variable in class apollo.gui.event.FeatureSelectionEvent
FEATURES - Static variable in class apollo.gui.genomemap.ScaleView
featureSelected(SeqFeatureI) - Method in class apollo.gui.annotinfo.FeatureEditorDialog: Listen to selections from the tree view and respond to FeatureSelection events.
featureSelected(SeqFeatureI) - Method in interface apollo.gui.FeatureNavigationI
featureSelected(SeqFeatureI) - Method in class apollo.gui.featuretree.FeatureTreeFrame
FeatureSelectionEvent - Class in apollo.gui.event
FeatureSelectionEvent(Object, Vector, int) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionEvent(Object, FeatureList) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionEvent(Object, SeqFeatureI) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionEvent(Object, Vector) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionEvent(Object, Selection) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionEvent(Object, Selection, boolean) - Constructor for class apollo.gui.event.FeatureSelectionEvent
FeatureSelectionListener - Interface in apollo.gui.event
FeatureSet - Class in apollo.datamodel: I think SeqFeature should implement all the functions of FeatureSet, so its polymorphic, so when you have a SeqFeatureI you dont have to care whether its a SeqFeature or a FeatureSet, so you dont have to keep downcasting to descend the datamodel (or do any other feature set functionality) As now you go through the Vector of SeqFeatures, cast to SeqFeature, then ask instanceof FeatureSetI and cast to FeatureSetI, which is potentially confusing.
FeatureSet() - Constructor for class apollo.datamodel.FeatureSet
FeatureSet(SeqFeatureI) - Constructor for class apollo.datamodel.FeatureSet
FeatureSet(String, int) - Constructor for class apollo.datamodel.FeatureSet
FeatureSet(int, int, String, int) - Constructor for class apollo.datamodel.FeatureSet
FeatureSet(FeatureList, String, String, int) - Constructor for class apollo.datamodel.FeatureSet
FeatureSet(FeatureSetI, String) - Constructor for class apollo.datamodel.FeatureSet
FeatureSetBuilder - Class in apollo.dataadapter
FeatureSetBuilder() - Constructor for class apollo.dataadapter.FeatureSetBuilder
FeatureSetI - Interface in apollo.datamodel
featuresIn(Range, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets all of the features within a given range
featuresIn(Range, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
FeatureTier - Class in apollo.gui.genomemap: A Tier to hold features.
FeatureTier() - Constructor for class apollo.gui.genomemap.FeatureTier
FeatureTierManager - Class in apollo.gui.genomemap: Extended from TierManager but still abstract (no layoutTiers methods) Implements FeatureTierManagerI which implements ControlledObjectI extends DrawableTierManager which extends TierManager which is where the ControlledObjectI methods are implemented.
FeatureTierManager(Controller) - Constructor for class apollo.gui.genomemap.FeatureTierManager
FeatureTierManagerI - Interface in apollo.gui.genomemap
FeatureTreeFrame - Class in apollo.gui.featuretree: A scrollpane containing a SWING tree of the annotations (not related to the FeatureTree or FeatureTreeNode).
FeatureTreeFrame(FeatureSetI, GuiCurationState) - Constructor for class apollo.gui.featuretree.FeatureTreeFrame
FeatureTreePanel - Class in apollo.gui.featuretree: A scrollpane containing a SWING tree of the annotations (not related to the FeatureTree or FeatureTreeNode).
FeatureTreePanel(FeatureNavigationI, GuiCurationState) - Constructor for class apollo.gui.featuretree.FeatureTreePanel
FeatureValidatorI - Interface in apollo.dataadapter.genbank: FeatureValidator interface Used to perform an integrity check whatever datasource
FeatureView - Class in apollo.gui.genomemap: FeatureView is a View for displaying DrawableSeqFeatures and DrawableFeatureSets (and maybe other Drawables), in linear tiers.
FeatureView(JComponent, String, SelectionManager) - Constructor for class apollo.gui.genomemap.FeatureView
fetchAllAlignFeatures(String, String, int, int, HashMap, String) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
fetchAllAnalysis() - Method in class apollo.dataadapter.gbrowse.AnalysisAdaptor
fetchAllDatabases() - Method in class apollo.dataadapter.mysql.MySQLInstance
fetchByDbId(int) - Method in class apollo.dataadapter.gbrowse.AnalysisAdaptor
fetchByReferenceStartEnd(String, int, int) - Method in class apollo.dataadapter.gbrowse.FeatureAdaptor
fetchDatabaseByName(String) - Method in class apollo.dataadapter.mysql.MySQLInstance
FgeneshGFFParser - Class in apollo.dataadapter.analysis
FgeneshGFFParser() - Constructor for class apollo.dataadapter.analysis.FgeneshGFFParser
FgeneshParser - Class in apollo.dataadapter.analysis
FgeneshParser() - Constructor for class apollo.dataadapter.analysis.FgeneshParser
field - Variable in class apollo.gui.SliderWindow
FIELD_LABEL - Static variable in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: For labeling flat fields (which are stored as properties) so they can be written out properly.
FILE - Static variable in class apollo.dataadapter.DataInputType
file_prop - Static variable in class apollo.dataadapter.analysis.AnalysisPanel
fileBox - Variable in class apollo.dataadapter.analysis.AnalysisPanel
fileBrowser(File, Component) - Static method in class apollo.dataadapter.genbank.GenbankAdapterGUI: Brings up JFileChooser, returns null on cancel or null file.
fileBrowser(File, Component) - Static method in class apollo.gui.GenericFileAdapterGUI
fileBrowser(File, Component, FileFilter, IOOperation) - Static method in class apollo.gui.GenericFileAdapterGUI: Brings up JFileChooser, returns null on cancel or null file
FileMenu - Class in apollo.gui.menus
FileMenu(ApolloFrame) - Constructor for class apollo.gui.menus.FileMenu
filename - Variable in class apollo.config.TiersIO
FileParse - Class in apollo.io
FileParse() - Constructor for class apollo.io.FileParse
FileParse(String, String) - Constructor for class apollo.io.FileParse
filePaths - Variable in class apollo.gui.GenericFileAdapterGUI
fileSize - Variable in class apollo.io.FileParse
FileTabPanel - Class in apollo.dataadapter: A guiTabPanel (panel in JTabbed pane of ApolloAdapterUI) that has a browse button that brings up a file browser
FileTabPanel(Component, Color) - Constructor for class apollo.dataadapter.FileTabPanel
FileUtil - Class in apollo.util
FileUtil() - Constructor for class apollo.util.FileUtil
FileUtilTest - Class in apollo.util
FileUtilTest() - Constructor for class apollo.util.FileUtilTest
fill3DRect(int, int, int, int, boolean) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillArc(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillInDatabase(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter: Replace %DATABASE% field with selected database.
fillInDatabase(String) - Method in class apollo.dataadapter.gamexml.GAMEAdapter: Replace %DATABASE% field with selected database.
fillInPadding(String) - Method in class apollo.dataadapter.gamexml.GAMEAdapter: Replace %PadLeft/Right% with pad ints
fillOval(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillPolygon(int[], int[], int) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillPolygon(Polygon) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillRoundRect(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
fillTiers() - Method in class apollo.gui.genomemap.DrawableTierManager
fillTiers() - Method in class apollo.gui.genomemap.FeatureTierManager: First calls installDrawables to add all the DSFs to tiers with sorting.
fillTiers() - Method in class apollo.gui.genomemap.SiteTierManager
fillTiers() - Method in class apollo.gui.TierManager
filter - Variable in class apollo.analysis.filter.AnalysisInput
filter - Variable in class apollo.dataadapter.analysis.AnalysisPanel
Filter<T> - Interface in apollo.gui.detailviewers.sequencealigner.filters
filter(Collection<SeqFeatureI>, Filter) - Static method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Passes a collection of features through a filter
filter - Variable in class apollo.gui.GenericFileAdapterGUI
filter_input - Variable in class apollo.analysis.filter.AnalysisFilter
filterByFrame(Collection<SeqFeatureI>, ReadingFrame) - Static method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
filterConfigurationPanel - Variable in class apollo.analysis.filter.BlastFilterPanel
FilterDisplayType - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterDisplayType(String) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterDisplayType
FilterFactory - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterFactory() - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterFactory
filterForFeaturePairs() - Method in class apollo.util.FeatureList
FilterInverse<T> - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterInverse(Filter<T>) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterInverse
FilterName - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterName(String) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterName
FilterPanel - Class in apollo.analysis.filter
FilterPanel() - Constructor for class apollo.analysis.filter.FilterPanel
filterPanel - Variable in class apollo.dataadapter.analysis.AnalysisPanel
FilterPanelI - Interface in apollo.analysis.filter
FilterReadingFrame - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterReadingFrame(ReadingFrame) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterReadingFrame
FilterSequenceType - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterSequenceType(SequenceType) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterSequenceType
filterShadows(boolean) - Method in class apollo.analysis.filter.AnalysisInput
FilterStrand - Class in apollo.gui.detailviewers.sequencealigner.filters
FilterStrand(Strand) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.FilterStrand
finalize() - Method in class apollo.gui.genomemap.ApolloPanel
finalize() - Method in class apollo.gui.genomemap.FastClippingGraphics
finalize() - Method in class apollo.gui.genomemap.FeatureView
FIND_COORD_SYSTEMS - Static variable in class apollo.dataadapter.ensj.controller.Controller
FIND_ENSEMBL_DATABASE_NAMES - Static variable in class apollo.dataadapter.ensj.controller.Controller
FIND_SEQ_REGIONS - Static variable in class apollo.dataadapter.ensj.controller.Controller
FIND_START_ENDS - Static variable in class apollo.dataadapter.ensj.controller.Controller
findAnnots(Vector) - Method in class apollo.gui.menus.AnnotationMenu
findButton - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
findButton - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
findCoordinateSystems(Connection) - Method in class apollo.dataadapter.ensj.controller.EventHandler
findCoordSystemForNamedSeqRegion(Model) - Method in class apollo.dataadapter.ensj.controller.EventHandler
FindCoordSystemsHandler - Class in apollo.dataadapter.ensj.controller: Find the coord systems (with their versions concatenated on) for the user to choose from.
FindCoordSystemsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.FindCoordSystemsHandler
FindDialog - Class in apollo.gui.detailviewers.sequencealigner
FindDialog(BaseScrollable, MultiTierPanel, SequenceI, boolean) - Constructor for class apollo.gui.detailviewers.sequencealigner.FindDialog
findDrawable(SeqFeatureI) - Method in interface apollo.gui.drawable.Drawable
findDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableFeatureSet
findDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableSeqFeature
findDrawableForFeatureInResultViews(SeqFeatureI) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
findDrawables(Rectangle, boolean) - Method in class apollo.gui.genomemap.FeatureView: returns a Vector of Drawable instances that overlap the area of the rectangle passed in The selected_only is ignored: first check children (if its a feature set), if no children hit check self this follows the old logic and you dont have to make 2 calls one with setFlag=false and if that didnt hit then with setFlag=false This is the only way i have seen this used so it seems ok to change.
findDrawables(Rectangle, boolean) - Method in class apollo.gui.genomemap.SiteView: Finds all the sites in rect and creates SiteCodon for them.
findDrawables(Point) - Method in class apollo.gui.genomemap.TierView: CANT do selection here as this is called for mouse over as well!
findDrawables(Rectangle) - Method in class apollo.gui.genomemap.TierView: Finds all the sites in rect and creates SiteCodon for them.
findDrawables(Rectangle, boolean) - Method in class apollo.gui.genomemap.TierView
FindEnsemblDatabaseNamesHandler - Class in apollo.dataadapter.ensj.controller: Find the coord systems (with their versions concatenated on) for the user to choose from
FindEnsemblDatabaseNamesHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.FindEnsemblDatabaseNamesHandler
findEvidence(String) - Method in class apollo.datamodel.EvidenceFinder
findFeaturePair(Point) - Method in class apollo.gui.synteny.SyntenyLinkPanel
findFeatureProp(String) - Method in class apollo.gui.annotinfo.GeneEditPanel
findFeatures(Point) - Method in class apollo.gui.genomemap.TierView: returns a FeatureList of SeqFeatureI instances that fall beneath the point passed in
findFeatures(Vector) - Method in class apollo.gui.genomemap.TierView: returns a FeatureList of SeqFeatureI instances that overlap any of the areas in the Vector of rectangles that is passed in
findFeatures(Rectangle) - Method in class apollo.gui.genomemap.TierView: returns a FeatureList of SeqFeatureI instances (model not drawables) overlap any of the areas in the Vector of rectangles that is passed in
findFeaturesByAllNames(String) - Method in class apollo.datamodel.FeatureSet: Searches recursively on both name and hit name
findFeaturesByAllNames(String, boolean) - Method in class apollo.datamodel.FeatureSet
findFeaturesByAllNames(String, boolean, boolean) - Method in class apollo.datamodel.FeatureSet: useRegExp is whether to search using pattern as a regular expression In fact, we ALWAYS do a RegExp search with the ORO pattern matchers.
findFeaturesByAllNames(String) - Method in interface apollo.datamodel.FeatureSetI: Search for names and hit names
findFeaturesByAllNames(String, boolean) - Method in interface apollo.datamodel.FeatureSetI
findFeaturesByAllNames(String, boolean, boolean) - Method in interface apollo.datamodel.FeatureSetI: searchString is pattern to search, useRegExp - whether pattern is reg exp, kidNamesOverParent if descendants match then ignore self match
findFeaturesByAllNames(String) - Method in class apollo.gui.drawable.DrawableFeatureSet
findFeaturesByAllNames(String, boolean) - Method in class apollo.gui.drawable.DrawableFeatureSet
findFeaturesByHitName(String) - Method in class apollo.datamodel.FeatureSet: Returns FeatureList of Features with hit name.
findFeaturesByHitName(String) - Method in interface apollo.datamodel.FeatureSetI
findFeaturesByName(String) - Method in class apollo.datamodel.FeatureSet: Returns a FeatureList of all SeqFeatureIs that have this name empty if no features match.
findFeaturesByName(String, boolean) - Method in class apollo.datamodel.FeatureSet
findFeaturesByName(String) - Method in interface apollo.datamodel.FeatureSetI
findFeaturesByName(String, boolean) - Method in interface apollo.datamodel.FeatureSetI
findFeaturesForSelection(Point, boolean) - Method in class apollo.gui.genomemap.ContainerView
findFeaturesForSelection(Rectangle) - Method in class apollo.gui.genomemap.ContainerView
findFeaturesForSelection(Rectangle, boolean) - Method in class apollo.gui.genomemap.FeatureView: From PickViewI -
findFeaturesForSelection(Point, boolean) - Method in interface apollo.gui.genomemap.PickViewI: Find features for selection.
findFeaturesForSelection(Rectangle) - Method in interface apollo.gui.genomemap.PickViewI: Same as above for rectangle, no selectParents needed
findFeaturesForSelection(Rectangle) - Method in class apollo.gui.genomemap.ScaleView: Triggered by rubberbanding.
findFeaturesForSelection(Point, boolean) - Method in class apollo.gui.genomemap.ScaleView
findFeaturesForSelection(Rectangle, boolean) - Method in class apollo.gui.genomemap.SiteView: From PickViewI for selection, selectParents is ignored here
findFeaturesForSelection(Point, boolean) - Method in class apollo.gui.genomemap.TierView: Find geared to selection.
findFeaturesForSelection(Rectangle) - Method in class apollo.gui.genomemap.TierView
findFeaturesForSelection(Rectangle, boolean) - Method in class apollo.gui.genomemap.TierView
findFile(String) - Method in class apollo.dataadapter.BaseGFFAdapter
findFile(String) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI: Trys to locate file using apollo's Config class first and by searching the classpath second.
findFile(String) - Static method in class apollo.util.IOUtil: Look in various sensible places for the file with a given name (which may be a full path, a relative path, or just a filename).
findFile(String, boolean) - Static method in class apollo.util.IOUtil
findLinksWithName(String) - Method in class apollo.datamodel.LinkSet: Return LinkSet? yes
findMatches() - Method in class apollo.gui.SequenceSelector: Finds positions in the sequence which match the query sequence.
findNamedNodeInTree(String) - Method in class apollo.dataadapter.synteny.builder.View
findObject(Object) - Method in class apollo.gui.featuretree.FeatureTreePanel: If object found, collapses tree, selects path to object and scrolls to it
findOverlappingAnnots(Vector) - Method in class apollo.editor.AnnotationEditor: Looks through all first-tier annotations (genes, etc.) in the annotationCollection looking for overlapping (according to the current gene definition) annots.
FindPanel - Class in apollo.gui: A ControlledPanel which displays the find dialog (for name, base position and sequence).
FindPanel(GuiCurationState) - Constructor for class apollo.gui.FindPanel
findSelected(FeatureSelectionEvent) - Method in class apollo.gui.genomemap.TranslationView
findSeqMatches() - Method in class apollo.gui.SeqMatchPanel
findSeqRegions(Model) - Method in class apollo.dataadapter.ensj.controller.EventHandler
FindSeqRegionsHandler - Class in apollo.dataadapter.ensj.controller: Find the coord systems (with their versions concatenated on) for the user to choose from
FindSeqRegionsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.FindSeqRegionsHandler
findSequenceMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
findSequenceMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
findSequenceMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
findSplices(MultiTierPanel, int, int, boolean, int, int) - Static method in class apollo.gui.detailviewers.sequencealigner.Utils: returns the positions of the donor and acceptor splice sites in coordinates relative to the genomic sequence.
findTierForFeature(List<TierI>, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.CompactFeaturePlaceFinder
findTierForFeature(List<TierI>, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder
findTierForFeature(List<TierI>, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SemiCompactFeaturePlaceFinder
findTiersForTypes(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager: Returns a Vector of Strings which are the labels of the TierProperties of the current selection.
findTreeNode(String) - Method in class apollo.dataadapter.synteny.builder.View
findTreeNode(Object) - Method in class apollo.gui.featuretree.FeatureTreePanel
findUnescaped(String, char) - Static method in class apollo.config.TiersIO
findUnescaped(String, char, int, int) - Static method in class apollo.config.TiersIO
FINISHED - Static variable in class apollo.editor.TransactionSubpart
finished() - Method in class apollo.gui.SwingWorker: Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
finishGUIForReading() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI: Not currently used
fireAnnotEvent(AnnotationChangeEvent) - Method in class apollo.gui.annotinfo.FeatureEditorDialog
fireAnnotEvent(AnnotationChangeEvent) - Method in class apollo.gui.annotinfo.FeatureEditPanel
fireBaseFocusEvent(int, SeqFeatureI) - Method in class apollo.gui.featuretree.FeatureTreeFrame: the one method that a featureNavigator must support Takes whatever action is needed when a feature is selected in the tree
fireBaseFocusEvent(String) - Method in class apollo.gui.FindPanel: Doesnt need to check if its numeric because of NumericKeyFilter.
fireBaseFocusEvent(int) - Method in class apollo.gui.FindPanel
fireBaseFocusEvent(String) - Method in class apollo.gui.SeqMatchPanel
fireBaseFocusEvent(int) - Method in class apollo.gui.SeqMatchPanel
fireFeatureSelectionEvent(SeqFeatureI) - Method in class apollo.gui.featuretree.FeatureTreeFrame: The SeqFeature passed to this might be a single exon, a transcript (FeatureSet of exons), or an annotation/gene (FeatureSet of FeatureSet of exons).
fireLazyLoadEvent(int) - Method in class apollo.datamodel.seq.AbstractLazySequence.LazyLoadControlledObject
firePropSchemeChangeEvent() - Method in class apollo.config.PropertyScheme
fireRubberbandEvent(RubberbandEvent) - Method in class apollo.gui.genomemap.Rubberband
fireTierManagerEvent(TierManagerEvent) - Method in class apollo.gui.TierManager
fireTierManagerEvent(int) - Method in class apollo.gui.TierManager
fireTierManagerEvent(int) - Method in interface apollo.gui.TierManagerI
fireViewEvent(ViewEvent) - Method in class apollo.gui.genomemap.LinearView
fireViewEvent(int) - Method in class apollo.gui.genomemap.TierView
first() - Method in class apollo.util.FeatureList
fitToScreen(int, int) - Static method in class apollo.util.GuiUtil: constrain width,height to screen size, returns as Dimension
fitToScreen(Dimension) - Static method in class apollo.util.GuiUtil: constrain Dimension to screen size
FIVE_AND_THREE_PRIME - Static variable in interface apollo.datamodel.EvidenceConstants
FIVE_PRIME - Static variable in interface apollo.datamodel.EvidenceConstants
fkcMap - Static variable in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
flags - Variable in class apollo.datamodel.FeatureSet: This flag is just for the use of bop to indicate that the feature has already had a an exon removed.
flags - Variable in class apollo.gui.drawable.DrawableSeqFeature
flash() - Method in class apollo.gui.PropertyPanel
flattenOnAddingToCompTrans() - Method in class apollo.editor.CompoundTransaction: Returns true.
flattenOnAddingToCompTrans() - Method in class apollo.editor.UpdateParentTransaction: Returns false.
flipBoolean(AnnotatedFeatureI, TransactionSubpart) - Static method in class apollo.editor.TransactionUtil
flipFlop() - Method in class apollo.datamodel.FeatureSet: Overrides SeqFeature.flipFlop.
flipFlop() - Method in class apollo.datamodel.SeqFeature: Flips strand - FeatureSet overrides with a recursive version
flipFlop() - Method in interface apollo.datamodel.SeqFeatureI: This is used simply to move the feature directly to the opposite strand, without complementation of the Reference Sequence
flipOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
flipOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
flipOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Flipping the orientation will not work, more work is needed to implement...
flipResult() - Method in class apollo.editor.AnnotationEditor: Move a result to other strand
FlybaseChadoInstance - Class in apollo.dataadapter.chado.jdbc: we need an AbstractChadoInstance super class for generic stuff, like gene prediction programs.
FlybaseChadoInstance() - Constructor for class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
FlybaseWrite - Class in apollo.dataadapter.chado.jdbc
FlyChadoXmlAdapter - Class in apollo.dataadapter.flychadoxml: A FlyBase-specific reader for Chado XML files.
FlyChadoXmlAdapter() - Constructor for class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter: Must have empty constructor to work with org.bdgp.io.DataAdapterRegistry instance creation from config string
FlyChadoXmlAdapterGUI - Class in apollo.dataadapter.flychadoxml: Holds LoaderPanels in its tabbed pane.
FlyChadoXmlAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI
FlyDisplayPrefs - Class in apollo.config
FlyDisplayPrefs() - Constructor for class apollo.config.FlyDisplayPrefs
FlyGAMEAdapter - Class in apollo.dataadapter.flygamexml: Reader for Drosophila GAME XML files.
FlyGAMEAdapter() - Constructor for class apollo.dataadapter.flygamexml.FlyGAMEAdapter
FlyGAMEAdapter(DataInputType, String) - Constructor for class apollo.dataadapter.flygamexml.FlyGAMEAdapter
FlyGAMEAdapter(DataInputType, String, boolean) - Constructor for class apollo.dataadapter.flygamexml.FlyGAMEAdapter
FlyGAMEAdapterGUI - Class in apollo.dataadapter.flygamexml: Most of the smarts here are actually in GAMEPanel and its subclasses This just holds the game panels in its tabbed pane
FlyGAMEAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI
FlyIdValidator - Class in apollo.dataadapter.genbank
FlyIdValidator() - Constructor for class apollo.dataadapter.genbank.FlyIdValidator
FlyNameAdapter - Class in apollo.config
FlyNameAdapter() - Constructor for class apollo.config.FlyNameAdapter
fm - Variable in class apollo.gui.genomemap.FeatureTierManager
FMB - Static variable in class apollo.dataadapter.chado.jdbc.SchemaVersion: Flybase migration build
focus - Variable in class apollo.gui.genomemap.ApolloPanel
fontColorForBackground(Color) - Method in class apollo.gui.drawable.DrawableSeqFeature
FORCE - Static variable in class apollo.dataadapter.chado.ChadoTransaction
forceSelection() - Method in class apollo.gui.event.FeatureSelectionEvent: whether this event requires attention.
foregroundColour - Variable in class apollo.gui.genomemap.LinearView
form(double) - Method in class apollo.util.Format: Formats a double into a string (like sprintf in C)
form(long) - Method in class apollo.util.Format: Formats a long integer into a string (like sprintf in C)
form(char) - Method in class apollo.util.Format: Formats a character into a string (like sprintf in C)
form(String) - Method in class apollo.util.Format: Formats a string into a larger string (like sprintf in C)
format(String, String, int) - Static method in class apollo.seq.io.FastaFile
Format - Class in apollo.util
Format(String) - Constructor for class apollo.util.Format: Formats the number following printf conventions.
formatDate(Date) - Static method in class apollo.util.DateUtil: The opposite of makeADate: converts a Date object to a String in the current format.
formatRightClickMenu() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
formatRightClickMenu(int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu: Updates menu to reflect the options available at the given position and tier.
formatRightClickMenu() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
formatRightClickMenu(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.ResultRightClickMenu: Updates menu to reflect the options available at the given position and tier.
formatSequence(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter: Return GenBank-formatted sequence, e.g.
forSameFeature(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature
forward - Variable in class apollo.datamodel.StrandedFeatureSet
forwardAnnotView - Variable in class apollo.gui.genomemap.StrandedZoomableApolloPanel
FRAGMENT_OFFSET - Static variable in class apollo.dataadapter.otter.parser.TagHandler
FRAGMENT_ORI - Static variable in class apollo.dataadapter.otter.parser.TagHandler
FRAME - Static variable in class apollo.dataadapter.otter.parser.TagHandler
frame - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
frame - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
frame - Variable in class apollo.gui.detailviewers.sequencealigner.FindDialog
frame - Variable in class apollo.gui.SliderWindow
frameHeight - Static variable in class apollo.gui.tweeker.Tweeker
FrameShiftAction - Class in apollo.gui.detailviewers.sequencealigner.actions: An Action class for performing a frame shift on a feature NOTE: I think that there might be some kind of limit to the number of frame shifts allowed on a feature.
FrameShiftAction(String, GuiCurationState, AnnotationEditor, FrameShiftAction.FrameShiftType) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.FrameShiftAction: Constructor
FrameShiftAction.FrameShiftType - Enum in apollo.gui.detailviewers.sequencealigner.actions
frameWidth - Static variable in class apollo.gui.tweeker.Tweeker
fromPixel(Point) - Method in class apollo.gui.Transformer
fromUser(Point) - Method in class apollo.gui.Transformer
fromXML() - Static method in class apollo.dataadapter.synteny.builder.Model: Creates an instance of a Model from an XML file (which must be in adapterbuilder.conf) explicitly loads a file APOLLO_ROOT/conf/adapterbuilder.conf create a new Model instance: populateAllowedAdapterClasses: vector read off XML populateAllowedAdapterTypes: vector read off XML populate(the actual) AdapterModels: AdapterModel = name, type, class, Properties - get an array of these into the return Model create (the actual) Adapters and GUIs This is called when the BuilderAdapter is first created.
FullEnsJDBCSyntenyPanel - Class in apollo.dataadapter.synteny
FullEnsJDBCSyntenyPanel(String, String, KaryotypeAdapterI, SyntenyAdapterI, AbstractDataAdapterUI) - Constructor for class apollo.dataadapter.synteny.FullEnsJDBCSyntenyPanel
FullSyntenyPanel - Class in apollo.gui: This doesnt seem to be used anymore - delete?
FullSyntenyPanel() - Constructor for class apollo.gui.FullSyntenyPanel
FullSyntenyPanel(String, String) - Constructor for class apollo.gui.FullSyntenyPanel

G

g - Variable in class apollo.gui.genomemap.FastClippingGraphics
GAMEAdapter - Class in apollo.dataadapter.gamexml: Reader for GAME XML files.
GAMEAdapter() - Constructor for class apollo.dataadapter.gamexml.GAMEAdapter
GAMEAdapter(DataInputType, String) - Constructor for class apollo.dataadapter.gamexml.GAMEAdapter
GAMEAdapter(DataInputType, String, boolean) - Constructor for class apollo.dataadapter.gamexml.GAMEAdapter
GAMEAdapterGUI - Class in apollo.dataadapter.gamexml
GAMEAdapterGUI() - Constructor for class apollo.dataadapter.gamexml.GAMEAdapterGUI
GAMEAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.gamexml.GAMEAdapterGUI
GAMEPanel - Class in apollo.dataadapter.flygamexml: This is only used by FlyGAMEAdapterGUI.
GAMEPanel(String, String, Color) - Constructor for class apollo.dataadapter.flygamexml.GAMEPanel
GAMEPanel(String, String, DataInputType, Color) - Constructor for class apollo.dataadapter.flygamexml.GAMEPanel
GAMEPanel(String, String, DataInputType, String, Color) - Constructor for class apollo.dataadapter.flygamexml.GAMEPanel
GAMESave - Class in apollo.dataadapter.gamexml
GAMESave() - Constructor for class apollo.dataadapter.gamexml.GAMESave
GAMESequence - Class in apollo.datamodel.seq: Currently GAMESequence is not lazy.
GAMESequence(String, Controller, String) - Constructor for class apollo.datamodel.seq.GAMESequence
gameVersion - Static variable in class apollo.dataadapter.gamexml.GAMESave: The latest version should be the default (1.1 for 11/05) but this should be a configuration - if DO-ONE-LEVEL-ANNOTS is false this should probably be set to 1.0? move to game adapter?
GbrowseAdapter - Class in apollo.dataadapter
GbrowseAdapter() - Constructor for class apollo.dataadapter.GbrowseAdapter
GbrowseAdapterGUI - Class in apollo.dataadapter
GbrowseAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.GbrowseAdapterGUI
GbrowseAdapterGUI.ChrStartEndListener - Class in apollo.dataadapter
GbrowseAdapterGUI.ChrStartEndListener() - Constructor for class apollo.dataadapter.GbrowseAdapterGUI.ChrStartEndListener
GC - Static variable in class apollo.gui.tweeker.Tweeker
GCScoreCalculator - Class in apollo.gui: changed long positions to int positions to be consistent with rest of apollo using ints for positions, hope this is ok
GCScoreCalculator(CurationSet, int) - Constructor for class apollo.gui.GCScoreCalculator
GenbankAdapter - Class in apollo.dataadapter.genbank
GenbankAdapter() - Constructor for class apollo.dataadapter.genbank.GenbankAdapter
GenbankAdapter(DataInputType, String) - Constructor for class apollo.dataadapter.genbank.GenbankAdapter
GenbankAdapter(DataInputType, String, boolean) - Constructor for class apollo.dataadapter.genbank.GenbankAdapter
GenbankAdapterGUI - Class in apollo.dataadapter.genbank
GenbankAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.genbank.GenbankAdapterGUI
GenbankFormatter - Class in apollo.dataadapter.genbank: GenbankFormatter.java Created: Mon Sep 1 18:32:20 2003
GenbankFormatter() - Constructor for class apollo.dataadapter.genbank.GenbankFormatter
GenbankRead - Class in apollo.dataadapter.genbank
GenbankRead() - Constructor for class apollo.dataadapter.genbank.GenbankRead
GenbankReport - Class in apollo.dataadapter.genbank: GenbankReport.java Created: Mon Sep 1 16:04:06 2003
GenbankReport(CurationSet) - Constructor for class apollo.dataadapter.genbank.GenbankReport
GenbankSequence - Class in apollo.datamodel.seq: Currently GenbankSequence is not lazy.
GenbankSequence(String, String) - Constructor for class apollo.datamodel.seq.GenbankSequence
GenbankValidator - Class in apollo.dataadapter.genbank
GenbankValidator() - Constructor for class apollo.dataadapter.genbank.GenbankValidator
GENE - Static variable in class apollo.dataadapter.DataInputType
GENE - Static variable in class apollo.dataadapter.ensj.model.TypesModel
GENE_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel
GeneEditPanel - Class in apollo.gui.annotinfo: GeneEditPanel Panel to layout comments, gene and transcript names, etc Editing is disabled in browser mode.
GeneFinderParser - Class in apollo.dataadapter.analysis
GeneFinderParser() - Constructor for class apollo.dataadapter.analysis.GeneFinderParser
geneIdPattern - Variable in class apollo.config.TigrSybilNameAdapter: Regular expression pattern used to parse a gene's ID from the chado uniquename.
generateAnnotationChangeEvent() - Method in class apollo.editor.AddTransaction
generateAnnotationChangeEvent() - Method in class apollo.editor.CompoundTransaction
generateAnnotationChangeEvent() - Method in class apollo.editor.DeleteTransaction
generateAnnotationChangeEvent(Object) - Method in class apollo.editor.Transaction: different source than trans.
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in interface apollo.config.ApolloNameAdapterI: Generate a name for a gene split
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.ChadoJdbcNameAdapter: Generate a name for a gene split
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.DefaultNameAdapter
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.FlyNameAdapter
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.GmodNameAdapter: generates both temp names and split names.
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.ParameciumNameAdapter: Generate a name for a gene split
generateAnnotSplitName(SeqFeatureI, StrandedFeatureSetI, String) - Method in class apollo.config.TigrAnnotNameAdapter
generateAnnotURL(AnnotatedFeatureI, String) - Method in class apollo.config.FlyDisplayPrefs: For annotations, try to find the appropriate identifier to add to the base URL.
generateChadoCdsIdFromTranscriptId(String) - Method in interface apollo.config.ApolloNameAdapterI
generateChadoCdsIdFromTranscriptId(String) - Method in class apollo.config.ChadoJdbcNameAdapter
generateChadoCdsIdFromTranscriptId(String) - Method in class apollo.config.DefaultNameAdapter
generateChadoCdsIdFromTranscriptId(String) - Method in class apollo.config.ParameciumNameAdapter
generateChadoCdsIdFromTranscriptId(String) - Method in class apollo.config.TigrAnnotNameAdapter
generateChadoCdsNameFromTranscriptName(String) - Method in interface apollo.config.ApolloNameAdapterI: Generate a CDS name given a transcript name.
generateChadoCdsNameFromTranscriptName(String) - Method in class apollo.config.ChadoJdbcNameAdapter
generateChadoCdsNameFromTranscriptName(String) - Method in class apollo.config.DefaultNameAdapter
generateChadoCdsNameFromTranscriptName(String) - Method in class apollo.config.ParameciumNameAdapter
generateChadoCdsNameFromTranscriptName(String) - Method in class apollo.config.TigrAnnotNameAdapter
generateEditTransaction(Map<Integer, AnnotationEditor.FeatChangeData>, CompoundTransaction) - Method in class apollo.editor.AnnotationEditor
generateEditTransaction(Map<Integer, AnnotationEditor.FeatChangeData>) - Method in class apollo.editor.AnnotationEditor: Creates add/delete transactions for the top level feature edits.
generateElement(ChadoTransaction) - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
generateExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in interface apollo.config.ApolloNameAdapterI
generateExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.ChadoJdbcNameAdapter
generateExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.DefaultNameAdapter
generateExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.ParameciumNameAdapter
generateExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.TigrAnnotNameAdapter
generateFeatChangeData(Map<Integer, AnnotationEditor.FeatChangeData>, SeqFeatureI) - Method in class apollo.editor.AnnotationEditor
generateFeatChangeData(Map<Integer, AnnotationEditor.FeatChangeData>, SeqFeatureI, boolean) - Method in class apollo.editor.AnnotationEditor: Clone a top level feature and inserts the data into a FeatChangeData object, which keeps track of the unmodified feature and newly added features
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in interface apollo.config.ApolloNameAdapterI
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ChadoJdbcNameAdapter
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.DefaultNameAdapter
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.FlyNameAdapter: generates a ID for a given feature.
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.GmodNameAdapter: generates a ID for a given feature.
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ParameciumNameAdapter
generateId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter
generateId(StrandedFeatureSetI, String, SeqFeatureI, boolean) - Method in class apollo.config.TigrAnnotNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in interface apollo.config.ApolloNameAdapterI
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in interface apollo.config.ApolloNameAdapterI: Generates name for a given feature.
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ChadoJdbcNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in class apollo.config.ChadoJdbcNameAdapter: Generates name for a given feature.
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in class apollo.config.DefaultNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.DefaultNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.FlyNameAdapter: This is used by ChadoXmlWrite to generate a (new) name for exons in FlyBase Harvard's preferred style.
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.GmodNameAdapter: generates a name for a given feature - this only works for genes, transcripts and exons
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ParameciumNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in class apollo.config.ParameciumNameAdapter: Generates name for a given feature.
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in class apollo.config.SimpleNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.SimpleNameAdapter: this is a workaround until we actually have 1-level annots.
generateName(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI, Vector) - Method in class apollo.config.TigrAnnotNameAdapter
generateName(StrandedFeatureSetI, String, SeqFeatureI, boolean) - Method in class apollo.config.TigrAnnotNameAdapter
generateNewChadoFeatureUniquename(String, String) - Method in class apollo.config.TigrAnnotNameAdapter: Generate a new chado feature uniquename using newNameCommand and the specified chado database and feature type.
generateNewChadoFeatureUniquename(String, SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter: Generate a new chado feature uniquename for the specified curation set and Apollo feature.
generateNewExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in interface apollo.config.ApolloNameAdapterI
generateNewExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.ChadoJdbcNameAdapter
generateNewExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.DefaultNameAdapter
generateNewExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.ParameciumNameAdapter
generateNewExonId(StrandedFeatureSetI, String, SeqFeatureI, String) - Method in class apollo.config.TigrAnnotNameAdapter
generateNewId(StrandedFeatureSetI, String, SeqFeatureI) - Method in interface apollo.config.ApolloNameAdapterI
generateNewId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ChadoJdbcNameAdapter
generateNewId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.DefaultNameAdapter
generateNewId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.ParameciumNameAdapter
generateNewId(StrandedFeatureSetI, String, SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter
generatePeptideIdFromTranscriptId(String) - Method in interface apollo.config.ApolloNameAdapterI
generatePeptideIdFromTranscriptId(String) - Method in class apollo.config.ChadoJdbcNameAdapter
generatePeptideIdFromTranscriptId(String) - Method in class apollo.config.DefaultNameAdapter
generatePeptideIdFromTranscriptId(String) - Method in class apollo.config.GmodNameAdapter: Generates peptide id from existing transcript id.
generatePeptideIdFromTranscriptId(String) - Method in class apollo.config.ParameciumNameAdapter
generatePeptideIdFromTranscriptId(String) - Method in class apollo.config.TigrAnnotNameAdapter
generatePeptideNameFromTranscriptName(String) - Method in interface apollo.config.ApolloNameAdapterI: Generate a peptide name given a transcript name.
generatePeptideNameFromTranscriptName(String) - Method in class apollo.config.ChadoJdbcNameAdapter: Generate a peptide name given a transcript name.
generatePeptideNameFromTranscriptName(String) - Method in class apollo.config.DefaultNameAdapter
generatePeptideNameFromTranscriptName(String) - Method in class apollo.config.GmodNameAdapter: Generates peptide name from existing transcript name.
generatePeptideNameFromTranscriptName(String) - Method in class apollo.config.ParameciumNameAdapter: Generate a peptide name given a transcript name.
generatePeptideNameFromTranscriptName(String) - Method in class apollo.config.TigrAnnotNameAdapter
generateSequence() - Method in class apollo.util.FastaHeader
generateTransaction(AnnotationChangeEvent) - Method in class apollo.editor.TransactionManager: Generate a Transaction based on a specified AnnotationChangeEvent.
generateTranscriptId(SeqFeatureI) - Method in class apollo.config.GmodNameAdapter
generateTranscriptSuffix(int, Vector, boolean) - Method in class apollo.config.FlyNameAdapter: Construct a new index for transcript #t_index, following the pattern -RA, -RB, ..., -RAA, -RAB, ...
generateTranscriptSuffix(int, Vector, boolean) - Method in class apollo.config.GmodNameAdapter: Return -transcript#:temp, where # is transcript number.
generateUndoChangeEvent() - Method in class apollo.editor.AddTransaction
generateUndoChangeEvent() - Method in class apollo.editor.DeleteTransaction
generateUndoChangeEvent(Object) - Method in class apollo.editor.Transaction
generateURL(SeqFeatureI) - Method in class apollo.config.DefaultDisplayPrefs
generateURL(SeqFeatureI) - Method in interface apollo.config.DisplayPrefsI
generateURL(SeqFeatureI) - Method in class apollo.config.FlyDisplayPrefs
generateURL(SeqFeatureI) - Method in class apollo.config.TigrAnnotDisplayPrefs: URLs are generated by taking the URL template ("weburl") defined in the feature file and replacing the following special strings with values extracted from the seq feature.
generateURL(AnnotatedFeatureI) - Method in class apollo.config.TigrSybilNameAdapter
GenericFileAdapterGUI - Class in apollo.gui
GenericFileAdapterGUI() - Constructor for class apollo.gui.GenericFileAdapterGUI
GenericFileAdapterGUI(IOOperation) - Constructor for class apollo.gui.GenericFileAdapterGUI
GenericFileAdapterGUI(IOOperation, FileFilter) - Constructor for class apollo.gui.GenericFileAdapterGUI
GenericFileFilter - Class in apollo.gui: This is a generic file filter for filtering results for javax.swing.FileChooser
GenericFileFilter() - Constructor for class apollo.gui.GenericFileFilter: Builds a GenericFileFilter object
GenericFileFilter(String) - Constructor for class apollo.gui.GenericFileFilter: Builds a GenericFileFilter object
GenericFileFilterTest - Class in apollo.gui
GenericFileFilterTest() - Constructor for class apollo.gui.GenericFileFilterTest
GenericProgramHandler - Class in apollo.analysis
GenericProgramHandler() - Constructor for class apollo.analysis.GenericProgramHandler
genericReadThroughStopResidue - Variable in class apollo.datamodel.FeatureSet
GenericTagHandler - Class in apollo.dataadapter.otter.parser: SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets
GenericTagHandler(String) - Constructor for class apollo.dataadapter.otter.parser.GenericTagHandler
GenieParser - Class in apollo.dataadapter.analysis
GenieParser() - Constructor for class apollo.dataadapter.analysis.GenieParser
genomic_errors - Variable in class apollo.datamodel.AbstractSequence: allow for some adjustments if the genomic sequence has sequencing errors
GENOMIC_LENGTH - Static variable in class apollo.gui.DetailInfo
GENOMIC_RANGE - Static variable in class apollo.gui.DetailInfo
GENOMIC_SEQUENCE - Static variable in class apollo.gui.DetailInfo
genomicRange - Variable in class apollo.datamodel.AbstractSequence
GenomicRange - Class in apollo.datamodel
GenomicRange() - Constructor for class apollo.datamodel.GenomicRange
GenomicRange(String, int, int) - Constructor for class apollo.datamodel.GenomicRange
GenscanFilterPanel - Class in apollo.analysis.filter
GenscanFilterPanel(Color) - Constructor for class apollo.analysis.filter.GenscanFilterPanel
GenscanParser - Class in apollo.dataadapter.analysis
GenscanParser() - Constructor for class apollo.dataadapter.analysis.GenscanParser
get(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
get() - Method in class apollo.gui.SwingWorker: Return the value created by the construct method.
get(String) - Method in class apollo.util.CaseInsensitiveStringHash
get(int) - Method in class apollo.util.interval.RbTree
get3primeStop(AnnotatedFeatureI) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
get3PrimeSuffix() - Method in class apollo.analysis.filter.AnalysisInput
get5primeStart(AnnotatedFeatureI) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
get_cDNA() - Method in class apollo.datamodel.FeatureSet
get_cDNA() - Method in class apollo.datamodel.SeqFeature: This needs to be fixed to account for edits to the genomic sequence, but I don't think it is urgent because this case is still so extremely rare.
get_cDNA() - Method in interface apollo.datamodel.SeqFeatureI
get_cDNA() - Method in class apollo.datamodel.Transcript: Calls FeatureSet.get_cDNA which appends exon sequence (with getSplicedTranscript) where the actual sequence is retrieved from the ref sequence.
get_cDNASequence() - Method in class apollo.datamodel.AnnotatedFeature: by default return null - overridden by Transcript subclass
get_cDNASequence() - Method in interface apollo.datamodel.AnnotatedFeatureI: If annotation is a transcript return the transcripts cdna sequence
get_cDNASequence() - Method in class apollo.datamodel.Transcript
get_ORF(String) - Method in class apollo.datamodel.FeatureSet: will return an empty string if the translation start site has not been set.
get_ORF(String, int, int) - Method in class apollo.datamodel.FeatureSet
get_ORF(String) - Method in class apollo.datamodel.SeqFeature: this will always return something even if the parent has not had a start of translation set.
getAARelationshipType(String, String) - Static method in class apollo.seq.ResidueProperties
getAbbrevCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getAbbreviatedSOTypeForFeature(SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter: Determine the (sometimes abbreviated) SO type used in TIGR annotation database uniquenames/ids
getAbInitioPredictionCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getAbInitioTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getAcceptor() - Method in class apollo.datamodel.Exon
getAccession() - Method in class apollo.dataadapter.genbank.GenbankReport
getAccession() - Method in class apollo.dataadapter.genbank.PeptideNote
getAccession() - Method in class apollo.datamodel.AssemblyFeature
getAccessionNo() - Method in class apollo.datamodel.AbstractSequence
getAccessionNo() - Method in interface apollo.datamodel.SequenceI
getAction() - Method in class apollo.gui.evidencepanel.EvidencePanelOrientationManager
getActiveCurationState() - Static method in class apollo.gui.synteny.CurationManager
getActiveCurState() - Method in class apollo.gui.synteny.CurationManager
getActiveDatabase() - Method in class apollo.dataadapter.chado.ChadoAdapter: Returns active database.
getActiveStyle() - Static method in class apollo.gui.synteny.CurationManager
getAdapterClassName() - Method in class apollo.dataadapter.chado.ChadoDatabase
getAdapterClassName() - Method in class apollo.dataadapter.synteny.builder.AdapterModel
getAdapterGUI() - Method in class apollo.dataadapter.ensj.view.View
getAdapterGUIMap() - Method in class apollo.dataadapter.synteny.builder.Model
getAdapterGUIs() - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI
getAdapterHistoryFile() - Static method in class apollo.config.Config
getAdapterLabelList() - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI
getAdapterMap() - Method in class apollo.dataadapter.synteny.builder.Model
getAdapterModels(String) - Method in class apollo.dataadapter.synteny.builder.Model
getAdapterRegistry() - Static method in class apollo.config.Config
getAdapters() - Method in class apollo.dataadapter.AbstractApolloAdapter
getAdapters() - Method in interface apollo.dataadapter.ApolloDataAdapterI
getAdapters() - Method in class apollo.dataadapter.synteny.SyntenyAdapter: maps adapter "logical name"/label to the adapter itself
getAdapterSets() - Method in class apollo.dataadapter.synteny.builder.Model
getAdapterStyle() - Method in class apollo.dataadapter.FileTabPanel: This won't be called
getAdapterStyle() - Method in class apollo.dataadapter.flychadoxml.LoaderPanel
getAdapterStyle() - Method in class apollo.dataadapter.flygamexml.GAMEPanel
getAdapterStyle() - Method in class apollo.dataadapter.GuiTabPanel
getAddedFeature() - Method in class apollo.editor.AddTransaction
getAddedFeature() - Method in class apollo.editor.FeatureChangeEvent: Convenience.
getAddedFeatureClone() - Method in class apollo.editor.AddTransaction
getAddressComponent() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAddressComponent() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAddressComponent() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the address bar (shows the base numbers you are looking at)
getAggregateSizeChange() - Method in class apollo.gui.TierManager
getAggregateSizeChange() - Method in interface apollo.gui.TierManagerI
getAlignable(int) - Method in class apollo.util.FeatureList
getAlignFrame() - Method in class apollo.gui.ApolloJalviewEventBridge
getAlignment() - Method in class apollo.datamodel.SeqFeature: Alignment will be padded if peptide
getAlignment() - Method in interface apollo.datamodel.SeqFeatureI: Alignment will be padded if peptide
getAllChadoSequencesByType(String, Vector, Vector) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve the id (Chado uniquename) and description of every Chado sequence of a particular type.
getAllFeaturePairLeaves() - Method in class apollo.util.FeatureList
getAllFeatures() - Method in class apollo.gui.genomemap.FeatureTierManager: This returns a Vector of all features.
getAllLeaves() - Method in class apollo.util.FeatureList: Returns a list of all the descendants of the current list that are leaves.
getAllowedAdapterClasses() - Method in class apollo.dataadapter.synteny.builder.Model
getAllowedAdapterTypes() - Method in class apollo.dataadapter.synteny.builder.Model
getAllowedProperties() - Method in class apollo.analysis.SeqAnalysisBase
getAllowedProperties() - Method in interface apollo.analysis.SeqAnalysisI: all the known property names (in the order they should be shown in a GUI)
getAllowedValues(String) - Method in class apollo.analysis.SeqAnalysisBase
getAllowedValues(String) - Method in interface apollo.analysis.SeqAnalysisI: allowed/recommended Vector of values for a property
getAllowLoginInput() - Method in class apollo.dataadapter.chado.ChadoDatabase
getAllowPasswordInput() - Method in class apollo.dataadapter.chado.ChadoDatabase
getAllProperties() - Static method in class apollo.gui.DetailInfo
getAllPropertyStrings() - Static method in class apollo.gui.DetailInfo
getAllRawResults() - Method in class apollo.analysis.SeqAnalysisBase
getAllRawResults() - Method in interface apollo.analysis.SeqAnalysisI
getAllStyleFilesString() - Method in class apollo.config.Style: Returns a string of all the style files used to create this file
getAllTiers() - Method in class apollo.config.PropertyScheme
getAminoAcidPanel() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnalNames() - Method in class apollo.config.PropertyScheme
getAnalogousOppositeStrandFeature() - Method in class apollo.datamodel.SeqFeature: Returns null if hasAnalogousOppositeStrandFeatureSet is false.
getAnalogousOppositeStrandFeature() - Method in interface apollo.datamodel.SeqFeatureI: Returns null if hasAnalogousOppositeStrandFeatureSet is false.
getAnalysisFeatureIdentityField() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: The analysisfeature table has a column named 'identity' in the standard Chado release.
getAnalysisFeatureIdentityField() - Method in class apollo.dataadapter.chado.jdbc.SybaseChadoAdapter: analysisfeature.identity was renamed to pidentity in the TIGR/Sybase port of Chado, since identity is a reserved word in Sybase.
getAnalysisFeatureList(String) - Method in class apollo.datamodel.CurationSet: Returns a FeatureList for both strands of an analysis, the first item in list is forward strand, 2nd is rev strand.
getAnalysisPanel() - Method in class apollo.analysis.filter.FilterPanel
getAnalysisRegion() - Method in class apollo.dataadapter.BaseGFFAdapter
getAnalysisRegion(CurationSet) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter: Make a call to the chosen DSN, passing in the chosen segment/range into a das "features" command.
getAnalysisRegion(CurationSet) - Method in class apollo.dataadapter.das2.DAS2Adapter: Make a call to the chosen DSN, passing in the chosen segment/range into a das "features" command.
getAnalysisRegion(CurationSet) - Method in class apollo.dataadapter.EnsCGIAdapter
getAnalysisRegion() - Method in class apollo.dataadapter.GFFAdapter
getAnalysisRegion() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getAnalysisType() - Method in class apollo.analysis.filter.AnalysisInput
getAnalysisType() - Method in class apollo.bop.JobOutput
getAnalysisType(int) - Method in class apollo.config.FeatureProperty
getAnalysisType() - Method in class apollo.dataadapter.analysis.AbstractParser
getAnalysisType(long, String, String, String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return the Apollo analysis type for a chado analysis.
getAnalysisType(long, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getAnalysisTypes() - Method in class apollo.config.FeatureProperty: An analysis type is what comes from "datatype" in the tiers file.
getAnalysisTypesSize() - Method in class apollo.config.FeatureProperty
getAnchor() - Method in class apollo.gui.genomemap.Rubberband
getAnnot(SeqFeatureI) - Method in class apollo.gui.annotinfo.FeatureEditorDialog
getAnnotatedFeature() - Method in class apollo.datamodel.AnnotatedFeature
getAnnotatedFeature() - Method in class apollo.datamodel.SeqFeature
getAnnotatedFeature() - Method in interface apollo.datamodel.SeqFeatureI: if hasAnnotatedFeature is true, this returns the AnnotatedFeature
getAnnotatedRegion() - Method in class apollo.dataadapter.BaseGFFAdapter
getAnnotatedRegion() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getAnnotatedRegion() - Method in class apollo.dataadapter.das2.DAS2Adapter
getAnnotatedRegion() - Method in class apollo.dataadapter.EnsCGIAdapter
getAnnotatedRegion(CurationSet) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getAnnotationBackground() - Static method in class apollo.config.Config
getAnnotationBackground() - Method in class apollo.config.Style
getAnnotationColor(AnnotatedFeatureI) - Static method in class apollo.config.Config: New method take an AnnotatedFeatureI (an annot or transcript)
getAnnotationColor(String, FeatureProperty) - Static method in class apollo.config.Config
getAnnotationColor(String) - Method in class apollo.config.Style: Retrieve color for user name; if no color use defaultAnnotationColor.
getAnnotationComments() - Static method in class apollo.config.Config
getAnnotationComments() - Method in class apollo.config.Style
getAnnotationComparator() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotationComparator() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotationComparator() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the comparator used to order annotations
getAnnotationEditor(boolean) - Method in class apollo.dataadapter.CurationState
getAnnotationEditor() - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener: Gets the annotation editor.
getAnnotationEditor() - Method in class apollo.gui.detailviewers.sequencealigner.ResultMouseListener: Gets the annotation editor.
getAnnotationEditor() - Method in class apollo.gui.genomemap.AnnotationView
getAnnotationEditor(boolean) - Method in class apollo.gui.synteny.GuiCurationState
getAnnotationFeatureProps() - Method in class apollo.config.PropertyScheme: Moved from Style
getAnnotationFeatureProps() - Static method in class apollo.gui.annotinfo.GeneEditPanel: provides a list of valid annotation types (as feature properties)
getAnnotationFilter() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotationFilter() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotationFilter() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the filter used to decide which annotations to display
getAnnotationHeader() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotationHeader() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotationHeader() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the header for the annotation panel
getAnnotationLabelColor() - Static method in class apollo.config.Config
getAnnotationLabelColor() - Method in class apollo.config.Style
getAnnotationPane() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotationPane() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotationPane() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the JScrollPane which holds the Annotation Panel
getAnnotationPanel() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotationPanel() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotationPanel() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the Annotation Panel
getAnnotations(CurationSet, List, boolean) - Method in class apollo.dataadapter.ensj.DataFetcher
getAnnotations() - Method in class apollo.dataadapter.ensj.EnsJAdapter
getAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the list of annotations.
getAnnotations(SeqFeatureI) - Static method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets all the annotations in a particular feature set
getAnnotations() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getAnnotationsModel() - Method in class apollo.dataadapter.ensj.model.Model
getAnnotationUser() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getAnnotationUser() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getAnnotationUserEmail() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getAnnotationUserEmail() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getAnnotationView() - Method in class apollo.gui.genomemap.ResultView
getAnnotChild(int) - Method in class apollo.datamodel.AnnotatedFeature: Return ith AnnotatedFeatureI child
getAnnotChild(int) - Method in interface apollo.datamodel.AnnotatedFeatureI: Convenience method.
getAnnotRegion() - Method in class apollo.dataadapter.BaseGFFAdapter
getAnnotRoot(AnnotatedFeatureI) - Static method in class apollo.util.SeqFeatureUtil
getAnnots() - Method in class apollo.datamodel.CurationSet: A CurationSet has a dangling reference that needs to be cleaned up when a new curation set is loaded to replace this one, otherwise it will persist as a memory leak.
getAnnotStrandedFeatSet() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getAnnotTop() - Method in class apollo.editor.AnnotationChangeEvent: rename get change top? annot top? should this return an AnnotatedFeatureI? rename getAnnotRoot?
getAnnotTop() - Method in class apollo.editor.AnnotationCompoundEvent: returns the annot top of the first child.
getAnnotTop() - Method in class apollo.editor.AnnotationDeleteEvent
getAnnotType() - Method in class apollo.config.FeatureProperty: Type of annotation this result creates, by default
getAnnotView(int) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getApolloFrame() - Static method in class apollo.gui.ApolloFrame: I think eventually CompostieApolloFrame and ApolloFrame should be merged
getApolloFrame() - Static method in class apollo.gui.synteny.CompositeApolloFrame
getApolloLock() - Method in class apollo.gui.genomemap.ApolloPanel
getApolloOboFilename() - Static method in class apollo.config.Config
getApolloPanel() - Method in interface apollo.gui.genomemap.ApolloPanelHolderI: I think this will need to change to: ApolloPanel[] getApolloPanels()
getApolloPanel() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getAssemblyType() - Method in class apollo.datamodel.CurationSet
getAttributes() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get all attributes
getAttributeValues(String) - Method in class apollo.dataadapter.gff3.GFF3Entry: Get a list of attribute values for a given attribute name
getAuthor() - Method in class apollo.editor.Transaction
getAuthor() - Method in class apollo.editor.TransactionManager
getAutosaveFile() - Static method in class apollo.config.Config
getAutosaveInterval() - Static method in class apollo.config.Config
getAutoStraighten() - Method in class apollo.gui.synteny.SyntenyLinkPanel
getBackBuffer() - Method in class apollo.gui.genomemap.ApolloPanel
getBackBuffer() - Method in interface apollo.gui.genomemap.ApolloPanelI
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.ResultRenderer
getBackgroundBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
getBackgroundColor() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getBackgroundColor1() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: For now these just get configs ede bg color - this means alignment viewer gets same colors as ede, i alignment wants to be different needs to override these methods
getBackgroundColor1() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: For now these just get configs ede bg color - this means alignment viewer gets same colors as ede, i alignment wants to be different needs to override these methods
getBackgroundColor2() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getBackgroundColor2() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getBackgroundColour() - Method in class apollo.gui.genomemap.LinearView
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBackgroundLineColor() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
getBands() - Method in class apollo.datamodel.Chromosome
getBandUrl() - Static method in class apollo.config.Config
getBandUrl() - Method in class apollo.config.Style
getBaptizer() - Method in class apollo.analysis.filter.AnalysisInput
getBase() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBaseAt(int) - Method in class apollo.datamodel.AbstractSequence
getBaseAt(int) - Method in class apollo.datamodel.Sequence
getBaseAt(int) - Method in interface apollo.datamodel.SequenceI
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidBaseRenderer
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRenderer
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRendererSpaced
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer: Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and set isExon flag
getBaseComponent(int, TierI, Orientation) - Method in interface apollo.gui.detailviewers.sequencealigner.renderers.BaseRendererI
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
getBaseComponent(int, TierI, Orientation) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBaseHeight() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getBaseHeight() - Method in interface apollo.gui.detailviewers.sequencealigner.renderers.BaseRendererI
getBaseHeight() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBaseHeight() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: pixel size
getBaseHeight() - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI: pixel size
getBasepair() - Method in class apollo.gui.detailviewers.sequencealigner.ResultMouseListener
getBasePair(int) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Translates a position on the tier into base pair coordinates.
getBasePair(int) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.exonviewer.AminoAcidRenderer
getBaseRendererComponent(char, int, int, SequenceI) - Method in interface apollo.gui.detailviewers.exonviewer.BaseRenderer
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer: Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and set isExon flag
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.sequencealigner.ResultRenderer
getBaseRendererComponent(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer: Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and set isExon flag
getBaseWidth() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getBaseWidth() - Method in interface apollo.gui.detailviewers.sequencealigner.renderers.BaseRendererI
getBaseWidth() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBaseWidth() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: pixel size
getBaseWidth() - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI: pixel size
getBioType(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getBioTypeForDisplay(SeqFeatureI) - Method in class apollo.config.DefaultDisplayPrefs
getBioTypeForDisplay(SeqFeatureI) - Method in interface apollo.config.DisplayPrefsI
getBioTypeForDisplay(SeqFeatureI) - Method in class apollo.config.FlyDisplayPrefs: This just returns sf.getBioType() (capitalized) unless its a transcript.
getBits(String, int) - Static method in class apollo.analysis.filter.Compress
getBlixemLocation() - Static method in class apollo.config.Config
getBlixemLocation() - Method in class apollo.config.Style
getBoolean(AnnotatedFeatureI, TransactionSubpart) - Static method in class apollo.editor.TransactionUtil
getBooleanValue(boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getBooleanValue(boolean) - Method in class apollo.dataadapter.chado.jdbc.PostgresChadoAdapter
getBooleanValue(boolean) - Method in class apollo.dataadapter.chado.jdbc.SybaseChadoAdapter
getBoundaryType(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getBoundaryType(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the boundary type of the SeqFeature at a particular position on a tier.
getBoundaryType(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Returns the type of boundary of a base at a given position and level.
getBoundaryType(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getBounds() - Method in class apollo.gui.event.RubberbandEvent
getBounds() - Method in class apollo.gui.genomemap.LinearView
getBounds() - Method in class apollo.gui.genomemap.Rubberband
getBounds() - Method in interface apollo.gui.genomemap.ViewI: Get the coordinates of the rectangle containing the View.
getBoxBounds() - Method in interface apollo.gui.drawable.Drawable
getBoxBounds() - Method in class apollo.gui.drawable.DrawableSeqFeature
getBoxBounds(Vector, Transformer, TierManagerI) - Static method in class apollo.gui.drawable.DrawableUtil: This is for creating drag boxes.
getBrokenEdgeColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getBrokenEdgeColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getBrokenEdgeColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getBrowserProgram() - Static method in class apollo.config.Config
getCachedUI(IOOperation) - Method in class apollo.dataadapter.AbstractApolloAdapter
getCacher() - Method in class apollo.datamodel.seq.AbstractLazySequence
getCapabilities() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getCapabilityURI(String) - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getCdsCoordinatesFromTranscript(Transcript, int, int) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Figure out chado CDS coordinates and sequence based on the Apollo transcript.
getCDSFeatures(Connection, long, SequenceI, StrandedFeatureSet, FeatureLocImplementation, ChadoProgram[]) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Front end to the main getCDSFeatures
getCDSFeatures(Connection, long, SequenceI, StrandedFeatureSet, FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Front end to the main getCDSFeatures
getCDSFeatures(Connection, long, SequenceI, StrandedFeatureSet, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve all CDS features feature-loc'ed to a Chado sequence.
getCdsPolypeptideIds(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getCdsSql(FeatureLocImplementation) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return an SQL query that will retrieve all CDS features within a specified range.
getCdsSql(FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance: flybase query for translation start stop (cds) is different from tigrs - just shoving in a query that works with how things are set up for now - probably need a revisit - protein fields being labeled as cds - take out the sequence? (get it from the genomic on demand?)
getCdsSql(FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getCdsSql(FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getCdsTransRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getCellEditorValue() - Method in class apollo.gui.DisabledEditor
getCentre() - Method in class apollo.gui.genomemap.LinearView
getCentre() - Method in interface apollo.gui.genomemap.ViewI: Get the maximum limit.
getCentreBase() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getCentreOfSelection() - Method in class apollo.gui.menus.TierPopupMenu
getCentroLength() - Method in class apollo.datamodel.Chromosome
getCertainlyBad() - Method in class apollo.analysis.filter.TwilightFilter
getCGIHost() - Static method in class apollo.config.Config
getCGIPort() - Static method in class apollo.config.Config
getCGIScript() - Static method in class apollo.config.Config
getChadoAdapter() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getChadoCdsName(ApolloNameAdapterI, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: The the Chado name for a CDS.
getChadoCdsName(ApolloNameAdapterI, String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getChadoDatabaseByName(String) - Method in class apollo.dataadapter.chado.ChadoAdapterGUI: Retrieve one of the objects in this.chado_dbs by name.
getChadoDb() - Method in class apollo.dataadapter.chado.ChadoDatabase
getChadoFeatureId(SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getChadoIdForFeature(SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Retrieve the chado primary key value for a given feature, or -1 if the feature does not exist in the database.
getChadoInstance() - Method in class apollo.dataadapter.chado.ChadoDatabase
getChadoInstance() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getChadoIsAnalysis(SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Determine what value to place in the chado feature.is_analysis column for an Apollo feature.
getChadoJdbcAdapterConfigFile() - Static method in class apollo.config.Config
getChadoLocgroup(SeqFeatureI, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Compute the chado featureloc.locgroup for an Apollo feature.
getChadoLocgroup(long, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getChadoPeptideName(ApolloNameAdapterI, String, SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter: Get the Chado name for a peptide.
getChadoPeptideName(ApolloNameAdapterI, String, SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getChadoPrimaryDbxrefId(SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Determine what to put in the feature.dbxref_id column for an Apollo feature.
getChadoProgramWhereClause(ChadoProgram[], String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Construct a where clause that will constrain a query on analysisfeature and/or analysis to exactly those rows in the analysis table that are specified by a list of ChadoProgram objects.
getChadoRelationshipCvTermId(String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getChadoResidues(SeqFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter: Determine what value to place in the chado feature.residues column for an Apollo feature.
getChadoTemplateName() - Static method in class apollo.config.Config
getChadoTransMacros() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: This is the beginning of trying to get chado-adapter.xml and transactionXMLTemplate non-redundant, so you dont have to configure the same things twice.
getChadoVersion() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getChangedAnnot() - Method in class apollo.editor.AnnotationChangeEvent
getChangedFeature() - Method in class apollo.editor.FeatureChangeEvent: This is the feature that has been added,deleted,updated,...
getChangeTop() - Method in class apollo.editor.AnnotationChangeEvent
getChangeTop() - Method in class apollo.editor.FeatureChangeEvent
getCharacter() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getCharacterBuffer() - Method in class apollo.dataadapter.otter.parser.TagHandler
getCharacters() - Method in class apollo.dataadapter.otter.parser.TagHandler
getCharAt(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getCharAt(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getCharHeight() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getCharHeight() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getCharHigh() - Method in class apollo.gui.Tier
getCharLow() - Method in class apollo.gui.Tier
getCharWidth() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getCharWidth() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getCharY(FontMetrics, Rectangle) - Method in class apollo.gui.drawable.DrawableSeqFeature: Return y value for writing characters in the box passed in,
getCheckOwnership() - Static method in class apollo.config.Config
getChecksum() - Method in class apollo.datamodel.AbstractSequence
getChecksum() - Method in interface apollo.datamodel.SequenceI
getChild_0() - Method in class apollo.analysis.filter.HuffNode
getChild_1() - Method in class apollo.analysis.filter.HuffNode
getChildAdapter(String) - Method in class apollo.dataadapter.AbstractApolloAdapter: Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false).
getChildAdapter(int) - Method in class apollo.dataadapter.AbstractApolloAdapter: Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false).
getChildAdapter(String) - Method in interface apollo.dataadapter.ApolloDataAdapterI: if isComposite() then returns child adapter for string adapterName.
getChildAdapter(int) - Method in interface apollo.dataadapter.ApolloDataAdapterI: Returns ith child adapter if isComposite(), null otherwise
getChildAdapter(int) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getChildAdapterGUIs(String) - Method in class apollo.dataadapter.synteny.builder.Model
getChildAdapterModels(String) - Method in class apollo.dataadapter.synteny.builder.Model
getChildChangeEvent(int) - Method in class apollo.editor.AnnotationChangeEvent: Default is null.
getChildChangeEvent(int) - Method in class apollo.editor.AnnotationCompoundEvent
getChildCurationSets() - Method in class apollo.datamodel.CurationSet
getChildProperties() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
getChildSetOrderedNames() - Method in class apollo.datamodel.CurationSet
getChooser(String) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
getChrAction() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getChrButton() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getChrDropdown() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getChrEnd() - Method in class apollo.datamodel.ChromosomeBand
getChrName() - Method in class apollo.datamodel.ChromosomeBand
getChromosome() - Method in class apollo.dataadapter.Region
getChromosome() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getChromosome() - Method in class apollo.datamodel.AssemblyFeature
getChromosome() - Method in interface apollo.datamodel.AssemblyFeatureI
getChromosome() - Method in class apollo.datamodel.GenomicRange
getChromosome() - Method in class apollo.gui.ChromosomeField
getChromosome1() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getChromosome1() - Method in class apollo.datamodel.SyntenyRegion
getChromosome2() - Method in class apollo.datamodel.SyntenyRegion
getChromosomeByName(String) - Method in class apollo.datamodel.Karyotype
getChromosomeFormat() - Method in class apollo.config.FeatureProperty: Get chromosome Prefix
getChromosomes() - Static method in class apollo.config.Config: Returns a vector of chromosome names as strings, null if none given
getChromosomes() - Method in class apollo.config.Style: Returns a vector of chromosome names as strings, null if none given
getChromosomes() - Method in class apollo.datamodel.Karyotype
getChrStart() - Method in class apollo.datamodel.ChromosomeBand
getChrStartEndList() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getCigar() - Method in class apollo.datamodel.FeaturePair
getCigar() - Method in class apollo.datamodel.SeqFeature: an explicit variable for cigar strings that are compact representations of alignments
getCigar() - Method in interface apollo.datamodel.SeqFeatureI: an explicit variable for cigar strings that are compact representations of alignments
getClassString() - Method in class apollo.editor.Transaction
getClip() - Method in class apollo.gui.genomemap.FastClippingGraphics
getClipBounds() - Method in class apollo.gui.genomemap.FastClippingGraphics
getClipBounds(Rectangle) - Method in class apollo.gui.genomemap.FastClippingGraphics
getClipRect() - Method in class apollo.gui.genomemap.FastClippingGraphics: Deprecated. As of JDK 1.2
getClobLengthFunction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getClobLengthFunction() - Method in class apollo.dataadapter.chado.jdbc.PostgresChadoAdapter
getClobLengthFunction() - Method in class apollo.dataadapter.chado.jdbc.SybaseChadoAdapter
getCloneFragmentButton() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getCloneFragmentPanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getCloneSource() - Method in class apollo.datamodel.SeqFeature
getCloneSource() - Method in interface apollo.datamodel.SeqFeatureI: If this feature was cloned from another feature, return the original feature.
getCodingDNA() - Method in class apollo.datamodel.SeqFeature: Calls get_ORF with the cdna.
getCodingDNA() - Method in interface apollo.datamodel.SeqFeatureI: Returns a String of sequence from start to end of translation, in the case where a feature does not have a start and stop the cDNA is returned
getCodingProperties() - Method in interface apollo.datamodel.ExonI
getCodingProperties() - Method in class apollo.datamodel.SeqFeature: Return an integer that describes coding props.
getCodingProperties() - Method in interface apollo.datamodel.SeqFeatureI
getCodingProperties(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getCodon(String) - Static method in class apollo.seq.ResidueProperties
getCodons(String) - Static method in class apollo.seq.ResidueProperties
getCodonStart() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getCodonX(Transformer, int) - Method in class apollo.gui.drawable.DrawableSeqFeature
getCoincidence() - Method in class apollo.analysis.filter.AnalysisInput
getColForPixelPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getColForPixelPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getColForPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getColForPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getColonDashString() - Method in class apollo.dataadapter.Region
getColor(Interval) - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent
getColor() - Method in class apollo.gui.genomemap.FastClippingGraphics
getColor() - Method in class apollo.gui.tweeker.RestrictionEnzyme
getColor() - Method in class apollo.gui.WiggleScoreCalculator
getColorArray() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel: The inner array is an array of 2 colors, for alternating exon colors.
getColorArray() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel: The inner array is an array of 2 colors, for alternating exon colors.
getColorArray() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: The inner array is an array of 2 colors, for alternating exon colors.
getColour() - Method in class apollo.config.FeatureProperty
getColour() - Method in class apollo.config.TierProperty
getColour() - Method in class apollo.gui.genomemap.FeatureTier
getColourAsString() - Method in class apollo.config.FeatureProperty
getColourAsString(Color) - Method in class apollo.config.FeatureProperty
getColouringAction() - Method in class apollo.gui.genomemap.ScaleView
getColumnCount() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getColumnCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getColumnCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
getColumnCount() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getColumnCount() - Method in class apollo.gui.SeqSelectorTable.SequenceMatchModel
getColumnName(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
getColumnName(int) - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getColumnName(int) - Method in class apollo.gui.SeqSelectorTable.SequenceMatchModel
getColumns() - Method in class apollo.config.FeatureProperty
getColumns(boolean) - Method in class apollo.config.FeatureProperty
getColumnType(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
getComboBoxValue(JComboBox) - Method in class apollo.dataadapter.chado.ChadoAdapterGUI: Method that extracts the currently-selected value of a JComboBox.
getCommandLine() - Static method in class apollo.main.CommandLine
getCommandLineXmlFileFormat() - Static method in class apollo.config.Config: Indicates adapter to use for command line xml file, "game" or "chado".
getComment() - Method in class apollo.dataadapter.genbank.GenbankReport
getCommentIndex(Comment) - Method in class apollo.datamodel.AnnotatedFeature: Returns index of comment, -1 if not found
getCommentIndex(Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI
getCommentPropertyTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getComments() - Method in class apollo.config.FeatureProperty
getComments() - Method in class apollo.config.TierProperty
getComments() - Method in class apollo.datamodel.AnnotatedFeature
getComments() - Method in interface apollo.datamodel.AnnotatedFeatureI
getComponent() - Method in class apollo.gui.ChromosomeField
getComponent() - Method in interface apollo.gui.genomemap.ApolloPanelHolderI
getComponent() - Method in class apollo.gui.genomemap.LinearView: LinearViews components that are part of an ApolloPanel which is a JComponent
getComponent() - Method in class apollo.gui.genomemap.Rubberband
getComponent() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getComponent() - Method in interface apollo.gui.genomemap.ViewI: Get the component the view belongs to.
getCompositeCurationSet() - Method in class apollo.datamodel.CompositeDataHolder: Should be phased out
getCompositeDataHolder() - Method in interface apollo.datamodel.ApolloDataI
getCompositeDataHolder() - Method in class apollo.datamodel.CompositeDataHolder
getCompositeDataHolder() - Method in class apollo.datamodel.CurationSet
getCompositeDataHolder() - Method in class apollo.gui.ApolloFrame
getCompositeDataHolder() - Method in class apollo.gui.synteny.CurationManager
getCompositeDataHolder(Properties, ProgressListener) - Method in class apollo.main.DataLoader: Load data using props.
getCompositeDataHolder(String[], ProgressListener) - Method in class apollo.main.DataLoader: String[0] in the args tells which data adapter to use: -g GFF, -x GAME, -b backup (serial), -gb GenBank/EMBL followed by the filename e.g., apollo -x data/example.xml quitOnCancel is false
getCompositeDataHolder(CommandLine) - Method in class apollo.main.DataLoader
getCompoundTypeString() - Method in class apollo.editor.CompoundTransaction
getConfirmDeleteSelection() - Static method in class apollo.config.Config: Return true if configged to true AND NOT in command-line/batch mode
getConfirmOverwrite() - Static method in class apollo.config.Config: Return true if both configged to true AND NOT in command-line/batch mode this boolean causes a popup that shouldnt happen in cmd line mode and presently there is no cmd-line confirm of overwrite - if this is added then the cmd line should be tested downstream - fine with present code i think
getConnection() - Method in class apollo.bop.JDBCPipelineAdapter
getConnection() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Returns the current database connection, if one exists and is valid.
getConnection(String, String, String, String, String, String) - Static method in class apollo.dataadapter.ensj.EnsJConnectionUtil
getConnectionForModel(Model) - Method in class apollo.dataadapter.ensj.controller.EventHandler
getConnectionUsedForLastTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve the JDBC Connection used to initiate the most recent transaction.
getConnectionWithException() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: A variant of getConnection that throws an SQLException in the case of an SQL error.
getConsolidatedFeatures() - Method in class apollo.util.FeatureList: Consolidates features.
getConstraints() - Method in class apollo.dataadapter.GuiTabPanel
getContainedViewAt(Point) - Method in class apollo.gui.genomemap.ContainerView
getContainedViewAt(Point) - Method in interface apollo.gui.genomemap.ContainerViewI
getContigCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getController() - Static method in class apollo.config.Config: This should be taken out of here and made a singleton method in controller Config has nothing to do with the controller
getController() - Method in class apollo.dataadapter.ensj.controller.EventHandler
getController() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
getController() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
getController() - Method in class apollo.datamodel.seq.AbstractLazySequence.LazyLoadControlledObject
getController() - Method in class apollo.editor.AnnotationEditor: ControlledObjectI method for getting the controller for the editor.
getController() - Method in class apollo.editor.ChangeList
getController() - Method in class apollo.gui.annotinfo.FeatureEditorDialog
getController() - Method in class apollo.gui.ApolloFrame: ControlledObjectI interface - this is the master controller (set by CompositeApolloFrame)
getController() - Method in interface apollo.gui.ControlledObjectI: Gets the Controller for the object
getController() - Method in class apollo.gui.ControlledPanel
getController() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
getController() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getController() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
getController() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getController() - Method in class apollo.gui.evidencepanel.TablePanel
getController() - Method in class apollo.gui.featuretree.FeatureTreeFrame
getController() - Method in class apollo.gui.FindPanel
getController() - Method in class apollo.gui.genomemap.ApolloPanel: Gets the apollo event controller for the panel.
getController() - Method in interface apollo.gui.genomemap.ApolloPanelI
getController() - Method in class apollo.gui.genomemap.ContainerView
getController() - Method in class apollo.gui.genomemap.NavigationBar: from ControlledObjectI interface.
getController() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getController() - Method in class apollo.gui.genomemap.TierView
getController() - Method in class apollo.gui.NonWindowControlledObject
getController() - Method in class apollo.gui.PreferencesDialog: Gets the Controller for the object
getController() - Method in class apollo.gui.SelectionManager: Part of ControlledObjectI interface
getController() - Method in class apollo.gui.SeqMatchPanel
getController() - Method in class apollo.gui.synteny.GuiCurationState
getController() - Method in class apollo.gui.TierManager
getController() - Method in class apollo.gui.TypePanel
getControllerWindow() - Method in class apollo.editor.AnnotationEditor: ControlledObjectI method.
getControllerWindow() - Method in class apollo.editor.ChangeList
getControllerWindow() - Method in class apollo.gui.annotinfo.FeatureEditorDialog
getControllerWindow() - Method in class apollo.gui.ApolloFrame
getControllerWindow() - Method in interface apollo.gui.ControlledObjectI: Shouldnt this return Window - would we ever want a non-window?
getControllerWindow() - Method in class apollo.gui.ControlledPanel: Why wouldnt this return Window? why Object?
getControllerWindow() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
getControllerWindow() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getControllerWindow() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
getControllerWindow() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getControllerWindow() - Method in class apollo.gui.featuretree.FeatureTreeFrame: Controller for selection
getControllerWindow() - Method in class apollo.gui.genomemap.ApolloPanel
getControllerWindow() - Method in class apollo.gui.genomemap.ContainerView
getControllerWindow() - Method in class apollo.gui.genomemap.TierView
getControllerWindow() - Method in class apollo.gui.NonWindowControlledObject
getControllerWindow() - Method in class apollo.gui.PreferencesDialog: Gets the window to be controlled: This PreferencesDialog
getControllerWindow() - Method in class apollo.gui.SelectionManager: Part of ControlledObjectI interface.
getControllerWindow() - Method in class apollo.gui.TierManager: Even though TierManagers are not gui they are gui-associated with its view.
getCoordBackground() - Static method in class apollo.config.Config
getCoordBackground() - Method in class apollo.config.Style
getCoordForeground() - Static method in class apollo.config.Config
getCoordForeground() - Method in class apollo.config.Style
getCoordRevcompColor() - Static method in class apollo.config.Config
getCoordRevcompColor() - Method in class apollo.config.Style
getCoordSystem() - Method in class apollo.datamodel.Chromosome
getCoordSystems() - Method in class apollo.dataadapter.ensj.model.LocationModel
getCoordSystemString() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getCopyGeneModelsIntoResultTier() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getCopyOfTiers(Vector) - Method in class apollo.config.PropertyScheme
getCountForQuery(String, Connection) - Method in class apollo.dataadapter.ensj.controller.EventHandler
getCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowAbInitioCountsByTypeHandler
getCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDitagFeatureCountsByTypeHandler
getCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDnaDnaAlignCountsByTypeHandler
getCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowDnaProteinAlignCountsByTypeHandler
getCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowSimpleFeatureCountsByTypeHandler
getCurated() - Method in class apollo.config.PeptideStatus
getCurationController(int) - Method in class apollo.gui.synteny.CurationManager: Convenience for getCurationState(i).getController()
getCurationManager() - Static method in class apollo.gui.ApolloFrame
getCurationManager() - Static method in class apollo.gui.synteny.CurationManager: Singleton - there should only be one curationState holder
getCurationName() - Method in class apollo.dataadapter.CurationState
getCurationName(int) - Method in class apollo.gui.synteny.CurationManager
getCurationName() - Method in class apollo.gui.synteny.GuiCurationState
getCurationSet() - Method in class apollo.analysis.SeqAnalysisBase
getCurationSet() - Method in interface apollo.analysis.SeqAnalysisI
getCurationSet() - Method in class apollo.dataadapter.AbstractApolloAdapter
getCurationSet() - Method in class apollo.dataadapter.analysis.AnalysisAdapter: from ApolloDataAdapterI interface.
getCurationSet() - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI
getCurationSet() - Method in interface apollo.dataadapter.ApolloDataAdapterI: returns a saved CurationSet.
getCurationSet() - Method in class apollo.dataadapter.BaseGFFAdapter
getCurationSet() - Method in class apollo.dataadapter.chado.ChadoAdapter
getCurationSet(ChadoAdapter, String, String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a single chado feature/sequence.
getCurationSet(ChadoAdapter, String, String) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
getCurationSet(ChadoAdapter, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getCurationSet(ChadoAdapter, String, String) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getCurationSet(ChadoAdapter, String, String) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getCurationSet() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: This is the main method for reading the data.
getCurationSet() - Method in class apollo.dataadapter.CurationState
getCurationSet() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getCurationSet() - Method in class apollo.dataadapter.das2.DAS2Adapter
getCurationSet() - Method in class apollo.dataadapter.DataLoadEvent: Should this just be curation set for a particular species? Currently the only place this is used is in MenuManager, asks if isMultiSpecies to determine whether to put up synteny menu.
getCurationSet() - Method in class apollo.dataadapter.EnsCGIAdapter
getCurationSet() - Method in class apollo.dataadapter.ensj.EnsJAdapter: This is the main data-retrieval method.
getCurationSet() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getCurationSet() - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter: This is the main method for reading the data.
getCurationSet() - Method in class apollo.dataadapter.gamexml.GAMEAdapter: from ApolloDataAdapterI interface.
getCurationSet() - Method in class apollo.dataadapter.GbrowseAdapter
getCurationSet() - Method in class apollo.dataadapter.genbank.GenbankAdapter: from ApolloDataAdapterI interface.
getCurationSet() - Method in class apollo.dataadapter.genbank.GenbankReport: Gets the value of cs
getCurationSet() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Parse and return the CurationSet
getCurationSet() - Method in class apollo.dataadapter.otter.OtterAdapter
getCurationSet() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getCurationSet() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getCurationSet() - Method in class apollo.dataadapter.sample.SampleAdapter: This is the main method: we create some fake features, add them to the CurationSet's results, and create a fake sequence for them.
getCurationSet() - Method in class apollo.dataadapter.SerialDiskAdapter: What about getCompositeDataHolder?
getCurationSet() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getCurationSet() - Method in class apollo.dataadapter.synteny.SyntenyAdapter: Visit each child adapter and ask each one for its CurationSet.
getCurationSet() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getCurationSet() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getCurationSet() - Method in interface apollo.datamodel.ApolloDataI: if isCurationSet returns true than a real curation set would be returned here.
getCurationSet(String) - Method in class apollo.datamodel.CompositeDataHolder
getCurationSet(int) - Method in class apollo.datamodel.CompositeDataHolder: Return ith species curation set as listed in species array list - this excludes curation sets for links (if thats how links are represented) rename this - needs to lose species association.
getCurationSet() - Method in class apollo.datamodel.CompositeDataHolder: ApolloDataI method.
getCurationSet(Object) - Method in class apollo.datamodel.CurationSet
getCurationSet() - Method in class apollo.datamodel.CurationSet
getCurationSet(String) - Method in class apollo.datamodel.SpeciesComparison: Returns null if dont have species
getCurationSet() - Method in interface apollo.gui.ApolloLoaderI
getCurationSet() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getCurationSet() - Method in class apollo.gui.synteny.GuiCurationState
getCurationSet() - Method in class apollo.test.ApolloLaundry
getCurationSet() - Method in class apollo.test.WashingLine
getCurationSet1() - Method in class apollo.datamodel.SpeciesComparison
getCurationSet2() - Method in class apollo.datamodel.SpeciesComparison
getCurationSetForLink(ApolloDataAdapterI, SeqFeatureI) - Method in interface apollo.dataadapter.synteny.LinkerI
getCurationSetFromInputStream(InputStream) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter
getCurationSetInRange(ChadoAdapter, String, Region) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a given region on a single chado feature/sequence.
getCurationSetInRange(ChadoAdapter, String, Region) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
getCurationSetInRange(ChadoAdapter, String, Region) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getCurationSetInRange(ChadoAdapter, String, Region) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getCurationSetInRange(ChadoAdapter, String, Region) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getCurationSetWithoutClearingData() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getCurationState() - Method in class apollo.dataadapter.AbstractApolloAdapter
getCurationState() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Get CurationState associated with data adapter.
getCurationState(int) - Method in class apollo.gui.ApolloFrame
getCurationState() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
getCurationState(int) - Method in class apollo.gui.synteny.CurationManager
getCurrent() - Method in class apollo.datamodel.DbXref
getCurrentFile() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getCurrentGamePanel() - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI: public for testing synteny - tied in w gui unfortunately this isnt just for tetsting synteny - used to get input - crucial!
getCurrentInput() - Method in class apollo.dataadapter.analysis.AnalysisPanel: Fills in the data structure with all of the values that the user has selected
getCurrentInput() - Method in class apollo.dataadapter.flychadoxml.LocationChadoPanel
getCurrentInput() - Method in class apollo.dataadapter.flygamexml.LocationGAMEPanel
getCurrentInput() - Method in class apollo.dataadapter.GuiTabPanel: The default editing component is jcombo box so it just grabs it from that - if getEditingComponent is overridden then this has to be overriden as well
getCurrentObject() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getCurrentOperation() - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI
getCurrentPanel() - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI: public for testing synteny - tied in w gui unfortunately
getCurrentSeq() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getCurrentTier() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getCurSetFromCompCurSet(String) - Method in class apollo.datamodel.CompositeDataHolder
getCurStateForCurName(String) - Method in class apollo.gui.synteny.CurationManager: Returns null if no cur state with curationName (shouldnt happen)
getCutSite() - Method in class apollo.gui.tweeker.RestrictionEnzyme
getCvNameCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getDashSets() - Static method in class apollo.config.Config
getDashSets() - Method in class apollo.config.Style
getDASServer() - Static method in class apollo.config.Config
getDASServer() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getDASServer() - Method in class apollo.dataadapter.das2.DAS2Adapter
getData() - Method in class apollo.gui.SelectionItem
getDataAdapter() - Method in class apollo.dataadapter.CurationState
getDataAdapter() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
getDataAdapter() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getDataAdapter() - Method in class apollo.dataadapter.otter.OtterAdapterGUI
getDataAdapter() - Method in class apollo.dataadapter.sample.SampleAdapterGUI: The "setDataAdapter" is implemented in the superclass, which is where the instance variable is defined.
getDataAdapter() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
getDataAdapter() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI
getDataAdapter() - Method in class apollo.gui.synteny.CurationManager: data adapter could be composite(SyntenyAdapter) or single(the rest) depending on if we are multi or single curationState.
getDataAdapter() - Method in class apollo.gui.synteny.GuiCurationState
getDataAdapter() - Method in class apollo.main.DataLoader
getDatabase() - Method in class apollo.analysis.filter.AnalysisInput
getDatabase() - Method in class apollo.bop.JobOutput
getDatabase() - Method in class apollo.dataadapter.AbstractApolloAdapter
getDatabase() - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter
getDatabase() - Method in class apollo.dataadapter.gamexml.GAMEAdapter
getDatabase() - Method in class apollo.dataadapter.genbank.GenbankValidator
getDatabase() - Method in class apollo.dataadapter.GuiTabPanel: Returns null if no databases(FileGAMEPanel)
getDatabase() - Method in class apollo.dataadapter.mysql.BaseAdaptor
getDatabase() - Method in class apollo.datamodel.SeqFeature
getDatabase() - Method in interface apollo.datamodel.SeqFeatureI
getDatabase() - Method in class apollo.util.FastaHeader
getDatabaseList() - Method in class apollo.config.Style: If no DatabaseList set in style, defaults to a list of just the DatabaseDefault (which defaults to gadfly if not set)
getDatabaseList(String) - Method in class apollo.config.Style: Get list of databases with changes possible based on queryType.
getDatabaseList() - Method in class apollo.dataadapter.flygamexml.GAMEPanel: Overrides default getDatabaseList in guiTabPanel.
getDatabaseList() - Method in class apollo.dataadapter.GuiTabPanel
getDatabaseModel() - Method in class apollo.dataadapter.ensj.model.Model
getDatabaseNames() - Method in class apollo.dataadapter.mysql.MySQLInstance
getDatabasePanel() - Method in class apollo.dataadapter.GuiTabPanel: makes JPanel with Database label and database list JComboBox
getDatabaseURLField() - Method in class apollo.config.Style: Field in url to replace with database selection
getDataConfigChooser() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI
getDataDir() - Static method in class apollo.config.Config
getDataInput() - Method in class apollo.dataadapter.AbstractApolloAdapter
getDataInput() - Method in class apollo.dataadapter.flychadoxml.LocationChadoPanel
getDataInput() - Method in class apollo.dataadapter.flygamexml.LocationGAMEPanel
getDataInput() - Method in class apollo.dataadapter.gamexml.GAMEAdapter: if file starts with http: then its really an url so correct the type bug fix for being able to load urls from file adapter and with -x
getDataInput() - Method in class apollo.dataadapter.GuiTabPanel: This bundles/replaces getCurrentInput and getInputType
getDataLoaderBackgroundColor() - Static method in class apollo.config.Config
getDataLoaderLabelColor() - Static method in class apollo.config.Config
getDataLoaderTitleColor() - Static method in class apollo.config.Config
getDataSets() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getDataSetsForServer(String, String) - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getDataSetsForServer(String, String) - Method in class apollo.dataadapter.ensj19.OtterAnnotationSourceChooser: I expect the following response from the otter server: (1) A line which says "Datasets".
getDataType() - Method in class apollo.gui.event.LazyLoadEvent
getDataTypeButtons() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getDataTypeForSoType(String) - Static method in class apollo.dataadapter.DataInputType: This is an attempt to correlate SO terms with DataInputType.
getDate() - Method in class apollo.editor.Transaction
getDBHost() - Static method in class apollo.config.Config
getDbId(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getDBName() - Static method in class apollo.config.Config
getDbName() - Method in class apollo.datamodel.DbXref
getDbType() - Method in class apollo.datamodel.Evidence
getDbXref(SequenceI) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
getDbXref() - Method in class apollo.datamodel.Evidence
getDbXref(int) - Method in class apollo.datamodel.SeqFeature
getDbXref(int) - Method in interface apollo.datamodel.SeqFeatureI
getDbXrefId(long, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getDbXrefs() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getDbXrefs() - Method in class apollo.datamodel.AbstractSequence
getDbXrefs() - Method in class apollo.datamodel.Identifier
getDbXrefs() - Method in class apollo.datamodel.SeqFeature: These methods dealing with xrefs have been moved from AnnotatedFeature.
getDbXrefs() - Method in interface apollo.datamodel.SeqFeatureI
getDbXrefs() - Method in interface apollo.datamodel.SequenceI
getDbXrefs() - Method in class apollo.util.FastaHeader
getDebug() - Static method in class apollo.config.Config
getDebug() - Method in class apollo.gui.genomemap.FeatureTierManager
getDefaultAnnotationColor() - Static method in class apollo.config.Config
getDefaultAnnotType() - Static method in class apollo.config.FeatureProperty: Making default annotType "gene".
getDefaultDatabase() - Method in class apollo.config.Style: Used for navigation bar db (for game), also if no database list is provided, getDatabaseList defaults to a list of default db.
getDefaultFeatureLabelFont() - Static method in class apollo.config.Config: Default font for gene label if it does not have a peptide status(which has a font) gene label appears as label to feature and in gene menu list
getDefaultFont() - Static method in class apollo.config.Config: Should there be an apollo wide font as well as style level font?
getDefaultHeader() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getDefaultIDPrefix() - Method in class apollo.config.ChadoJdbcNameAdapter: The prefix to use if idFormat is not specified in tiers file for a type
getDefaultIDPrefix() - Method in class apollo.config.FlyNameAdapter: The prefix to use if idFormat is not specified in tiers file for a type
getDefaultIDPrefix() - Method in class apollo.config.GmodNameAdapter: The prefix to use if idFormat is not specified in tiers file for a type
getDefaultIDPrefix() - Method in class apollo.config.RiceNameAdapter: The prefix to use if idFormat is not specified in tiers file for a type
getDefaultPadding() - Method in class apollo.config.Style
getDefaultSingleSpeciesName() - Static method in class apollo.config.Config: doesnt matter what the string is as long as its consistent across data adapters and composite data holder - couldnt think where else to put this but Config
getDefaultStyle() - Method in class apollo.dataadapter.AbstractApolloAdapter: Return style to use if no db (file) or db is not listed.
getDefaultSyntenyDataAdapterString() - Method in class apollo.config.Style: String of class name for default synteny data adapter to use if none are specified in style file - default is null
getDefinition() - Method in class apollo.dataadapter.genbank.GenbankReport
getDeletedFeature() - Method in class apollo.editor.AnnotationChangeEvent
getDeletedFeature() - Method in class apollo.editor.DeleteTransaction: Get the deleted SeqFeatureI object.
getDeletedFeature() - Method in class apollo.editor.Transaction
getDeletedFeatureClone() - Method in class apollo.editor.DeleteTransaction
getDesc() - Method in class apollo.analysis.SeqAnalysisBase
getDesc() - Method in interface apollo.analysis.SeqAnalysisI
getDescription() - Method in interface apollo.dataadapter.das.DASDsn
getDescription() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getDescription() - Method in class apollo.datamodel.AbstractSequence
getDescription() - Method in class apollo.datamodel.AnnotatedFeature
getDescription() - Method in interface apollo.datamodel.AnnotatedFeatureI
getDescription() - Method in class apollo.datamodel.DbXref
getDescription() - Method in class apollo.datamodel.Identifier
getDescription() - Method in interface apollo.datamodel.SequenceI
getDescription() - Method in class apollo.gui.GenericFileFilter: The description of this filter
getDescription() - Method in class apollo.util.ExampleFileFilter: Returns the human readable description of this filter.
getDescription() - Method in class apollo.util.FastaHeader
getDisplayId() - Method in class apollo.datamodel.Chromosome
getDisplayId() - Method in class apollo.datamodel.ChromosomeBand
getDisplayId() - Method in class apollo.datamodel.FeaturePair
getDisplayLabel() - Method in interface apollo.gui.drawable.Drawable
getDisplayLabel() - Method in class apollo.gui.drawable.DrawableSeqFeature
getDisplayName(RangeI) - Method in class apollo.config.DefaultDisplayPrefs
getDisplayName(RangeI) - Method in interface apollo.config.DisplayPrefsI
getDisplayName(RangeI) - Method in class apollo.config.FlyDisplayPrefs: This is used for making (short) labels in the display.
getDisplayName(RangeI) - Method in class apollo.config.ParameciumDisplayPrefs
getDisplayName(RangeI) - Method in class apollo.config.TigrAnnotDisplayPrefs
getDisplayPrefs() - Static method in class apollo.config.Config
getDisplayPrefs() - Method in class apollo.config.Style
getDisplayType() - Method in class apollo.config.FeatureProperty
getDistance(String, String) - Static method in class apollo.seq.ResidueProperties
getDitagFeatureCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDitagFeatureTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDitagFeatureTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDNA() - Method in interface apollo.dataadapter.das.DASSequence
getDNA() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getDnaDnaAlignmentCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDnaDnaAlignmentTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDnaDnaAlignTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDNALength() - Method in interface apollo.dataadapter.das.DASSequence
getDNALength() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getDnaProteinAlignmentCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDnaProteinAlignmentTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDnaProteinAlignTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getDNAUtilsValue() - Method in enum apollo.gui.detailviewers.sequencealigner.ReadingFrame
getDonor() - Method in class apollo.datamodel.Exon
getDragView() - Method in class apollo.gui.genomemap.ApolloPanel
getDragViews() - Method in class apollo.gui.genomemap.ApolloPanel
getDraw3D() - Static method in class apollo.config.Config
getDraw3D() - Method in class apollo.config.Style
getDrawableAt(int) - Method in class apollo.gui.drawable.DrawableFeatureSet: Returns a DrawableSeqFeature (not model SeqFeature)
getDrawableAt(int) - Method in interface apollo.gui.drawable.DrawableSetI
getDrawableAt(int) - Method in class apollo.gui.genomemap.FeatureTier
getDrawableColor() - Method in class apollo.gui.drawable.DrawableSeqFeature
getDrawables() - Method in class apollo.gui.drawable.DrawableFeatureSet: A Vector of DrawableSeqFeatures is returned, not model SeqFeatures.
getDrawables() - Method in interface apollo.gui.drawable.DrawableSetI
getDrawables() - Method in class apollo.gui.genomemap.FeatureTier
getDrawableSet() - Method in class apollo.gui.genomemap.FeatureView: Returns the DrawableFeatureSet that is the top(holder) of all the drawables in the view
getDrawBounds() - Method in class apollo.gui.genomemap.LinearView
getDrawCentre() - Method in class apollo.gui.Tier
getDrawHigh() - Method in class apollo.gui.Tier
getDrawIntrons() - Method in class apollo.gui.detailviewers.sequencealigner.overview.Overview: Gets the current value of drawIntrons
getDrawIntrons() - Method in class apollo.gui.detailviewers.sequencealigner.overview.TranscriptOverview
getDrawLevel() - Method in interface apollo.gui.drawable.Drawable: returns the number of levels in the hierarchy that this will draw
getDrawLevel() - Method in class apollo.gui.drawable.DrawableSeqFeature
getDrawLow() - Method in class apollo.gui.Tier
getDrawOutline() - Static method in class apollo.config.Config
getDrawOutline() - Method in class apollo.config.Style
getDrawSpace() - Method in class apollo.gui.Tier
getDriver() - Method in class apollo.dataadapter.ensj.EnsJAdapter
getDriver() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getDriverClass() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getDriverConf() - Method in class apollo.dataadapter.ensj19.EnsJAdapter: Get the value of driverConf.
getDriverProperties() - Method in class apollo.dataadapter.ensj.AlternateEnsJSequence
getDriverProperties() - Method in class apollo.dataadapter.ensj19.AlternateEnsJSequence
getDropSpaceSize() - Method in class apollo.gui.genomemap.ManagedView
getDsn() - Method in class apollo.dataadapter.das.DASLazySequence
getDSN() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getDSN() - Method in class apollo.dataadapter.das2.DAS2Adapter
getDSN(String) - Method in class apollo.dataadapter.das2.DAS2Request: Given a URI, return the DSN (if any) for that URI.
getDSNs() - Method in interface apollo.dataadapter.das.DASServerI
getDsns() - Method in class apollo.dataadapter.das.simple.DASDsnContentHandler
getDSNs() - Method in class apollo.dataadapter.das.simple.SimpleDASServer: I return all data-sources from the das server URL passed in when this instance was constructed.
getDSNs() - Method in class apollo.dataadapter.das2.DAS2Request: Gets a list of versioned sources from the server.
getDsns() - Method in class apollo.dataadapter.das2.SourceParser
getEasyRead() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.ResultRendererFactory
getEdgematchColor() - Static method in class apollo.config.Config
getEdgematchColor() - Method in class apollo.config.Style
getEdgematchWidth() - Static method in class apollo.config.Config
getEdgematchWidth() - Method in class apollo.config.Style
getEditedFeature() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getEditingComponent() - Method in class apollo.dataadapter.GuiTabPanel: Default editing component is JComboBox - override if need different
getEditType() - Method in class apollo.datamodel.SequenceEdit: phase out for getFeatureType? yes! same thing - although actually CLEAR_EDIT/NOP is really the deletion of the indel - hmmm
getElement(String) - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
getEnd() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getEnd() - Method in interface apollo.dataadapter.das.DASFeature
getEnd() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getEnd() - Method in class apollo.dataadapter.ensj.model.LocationModel
getEnd() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the end of the feature on the reference sequence
getEnd() - Method in class apollo.dataadapter.Region
getEnd() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getEnd() - Method in class apollo.datamodel.FeaturePair
getEnd() - Method in class apollo.datamodel.Protein: so the end is rather controversial.
getEnd() - Method in class apollo.datamodel.Range
getEnd() - Method in interface apollo.datamodel.RangeI
getEnd() - Method in class apollo.datamodel.StrandedFeatureSet
getEnd(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getEnd() - Method in interface apollo.gui.drawable.Drawable
getEnd() - Method in class apollo.gui.drawable.DrawableSeqFeature
getEnd() - Method in class apollo.gui.genomemap.Rubberband
getEnd1() - Method in class apollo.datamodel.SyntenyRegion
getEnd2() - Method in class apollo.datamodel.SyntenyRegion
getEndAsString() - Method in class apollo.datamodel.Range
getEndPhase() - Method in class apollo.datamodel.SeqFeature
getEndPhase() - Method in interface apollo.datamodel.SeqFeatureI
getEndPhase(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getEndTextBox() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getEnsemblDatabaseDropdown() - Method in class apollo.dataadapter.ensj.view.DatabasePanel
getEnsemblDatabaseDropdown() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getEnsemblDatabaseLabel() - Method in class apollo.dataadapter.ensj.view.DatabasePanel
getEnsemblDatabases() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getEnsemblDBDropdownSelectionListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getEnsemblSchema(Connection) - Static method in class apollo.dataadapter.ensj.EnsJConnectionUtil
getEntryPoints(DASDsn) - Method in interface apollo.dataadapter.das.DASServerI
getEntryPoints(DASDsn) - Method in class apollo.dataadapter.das.simple.SimpleDASServer: I return all entry-points from the input DASDsn instance passed in.
getEntryPoints(DASDsn) - Method in class apollo.dataadapter.das2.DAS2Request: I return all entry-points from the input SimpleDASDsn instance passed in.
getErrors() - Method in class apollo.config.Style
getEvidence() - Method in class apollo.datamodel.AnnotatedFeature
getEvidence() - Method in interface apollo.datamodel.AnnotatedFeatureI
getEvidence(String) - Method in class apollo.datamodel.EvidenceSet
getEvidence() - Method in class apollo.datamodel.EvidenceSet
getEvidence(int) - Method in class apollo.datamodel.EvidenceSet
getEvidence(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getEvidenceFinder() - Method in class apollo.datamodel.AnnotatedFeature
getEvidenceFinder() - Method in interface apollo.datamodel.AnnotatedFeatureI
getEvidenceFinder() - Method in class apollo.gui.genomemap.AnnotationView: i think evidence finder is pase now that theres edge matching - rip out?
getEvidencePanelHeight() - Method in class apollo.config.Style
getException(Transcript) - Method in class apollo.dataadapter.genbank.GenbankValidator
getExceptPos(PeptideNote) - Method in class apollo.dataadapter.genbank.GenbankValidator
getExecuteButton() - Method in class apollo.dataadapter.URLDiagnosticTool
getExistingCurationSet() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
getExonAt(int) - Method in class apollo.datamodel.Transcript
getExonDetailEditorBackgroundColor1() - Static method in class apollo.config.Config
getExonDetailEditorBackgroundColor2() - Static method in class apollo.config.Config
getExonDetailEditorFeatureColor1() - Static method in class apollo.config.Config
getExonDetailEditorFeatureColor2() - Static method in class apollo.config.Config
getExonDetailEditorSequenceFont() - Static method in class apollo.config.Config
getExonDetailEditorSequenceFont() - Method in class apollo.config.Style: Font for amino and dna sequence in EDE
getExonRangeIndex(int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getExonRangeIndex(int, int, int, boolean) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getExonRangeIndex(int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getExonRangeIndex(int, int, int, boolean) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getExonRank(Long, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getExons() - Method in class apollo.datamodel.Transcript
getExonSyntenyDir() - Static method in class apollo.config.Config
getExonTransRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getExplicitAlignment() - Method in class apollo.datamodel.FeaturePair: Explicitly set alignment.
getExplicitAlignment() - Method in class apollo.datamodel.SeqFeature: Explicitly set alignment.
getExplicitAlignment() - Method in interface apollo.datamodel.SeqFeatureI: Explicitly set alignment.
getExtension(File) - Method in class apollo.util.ExampleFileFilter: Return the extension portion of the file's name .
getExtension(File) - Static method in class apollo.util.FileUtil: Get the extension for a File
getExtension(String) - Static method in class apollo.util.FileUtil: Get the extension of a String filename
getExtensions() - Method in class apollo.gui.GenericFileFilter: Get the file extensions added to this filter
getExternalRefURL() - Static method in class apollo.config.Config: previously fban url - attempting to make more general
getFactor() - Method in class apollo.gui.ScoreCalculator
getFactorMultiplier() - Method in class apollo.gui.event.ZoomEvent
getFastDrawLimit() - Static method in class apollo.config.Config
getFeatNamesByType(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: This is a stripped down version of getAllChadoSequencesByType.
getFeatPropLeafFeatures(CurationSet, FeatureProperty) - Static method in class apollo.util.SeqFeatureUtil: Get all leaf features for the FeatureProperty.
getFeatPropLeafParentFeats(CurationSet, FeatureProperty) - Static method in class apollo.util.SeqFeatureUtil: return parent features of leaves (often these are transcript or transcript like feats) - the thin line that connects leaf feats/exons
getFeatSetForStrand(int) - Method in class apollo.datamodel.StrandedFeatureSet
getFeatSetForStrand(int) - Method in interface apollo.datamodel.StrandedFeatureSetI
getFeatsWithAlignments() - Method in class apollo.util.FeatureList: Filters FeatureList for features with hasAlignable==true and the Alignable hasAlignmentSequence
getFeatsWithinRefSeqRegion() - Method in class apollo.util.FeatureList
getFeature(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
getFeature() - Method in interface apollo.gui.drawable.Drawable: each drawable contains the actual datamodel for that feature and must support both setting and getting the actual datamodel
getFeature() - Method in class apollo.gui.drawable.DrawableSeqFeature
getFeature() - Method in class apollo.gui.event.BaseFocusEvent
getFeature() - Method in class apollo.gui.event.FeatureSelectionEvent: Returns fist feature - rename getFirstFeature
getFeature(int) - Method in class apollo.util.FeatureList
getFeatureAdaptor() - Method in class apollo.dataadapter.gbrowse.DBAdaptor
getFeatureAt(int) - Method in class apollo.datamodel.FeatureSet
getFeatureAt(int) - Method in class apollo.datamodel.SeqFeature: returns a seqfeature at the specified position
getFeatureAt(int) - Method in interface apollo.datamodel.SeqFeatureI: returns a seqfeature at the specified position - rename getChild(i) for clarity?
getFeatureAt(int) - Method in class apollo.datamodel.StrandedFeatureSet: This actually returns not forward feature set and reverse feature set, but the children of forward and reverse.
getFeatureAtIndex(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureAtIndex(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getFeatureAtPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureAtPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the SeqFeatureI at a position on a tier.
getFeatureBackground() - Static method in class apollo.config.Config
getFeatureBackground() - Method in class apollo.config.Style
getFeatureBox() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getFeatureColor(SeqFeatureI, FeatureProperty) - Static method in class apollo.gui.drawable.DrawableUtil
getFeatureContaining(int) - Method in class apollo.datamodel.FeatureSet: Returns the FIRST feature in the set containing the position return this if none of children contain pos but FS does (intron) return null if doesnt contain position.
getFeatureContaining(int) - Method in class apollo.datamodel.SeqFeature: returns self if self has position.
getFeatureContaining(int) - Method in interface apollo.datamodel.SeqFeatureI: Returns the FIRST child feature containing the position.
getFeatureCount(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureCount(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getFeatureCreateDatePropertyTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getFeatureCVName() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getFeatureCVName() - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance: Flybases feature cv is SO
getFeatureCVName() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance: Flybases feature cv is SO
getFeatureCVName() - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance: This should come from config
getFeatureDbXrefId(long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getFeatureEditorDialog() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getFeatureForPixelPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureForPixelPosition(int, int, boolean) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureForPixelPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the sequence feature that is shown at the given display coordinates.
getFeatureForPixelPosition(int, int, boolean) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the sequence feature that is shown at the given display coordinates.
getFeatureHeading(String, String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
getFeatureId(Connection, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve the Chado feature.feature_id for a specified feature.
getFeatureId(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve the Chado feature.feature_id for a specified feature.
getFeatureId() - Method in class apollo.datamodel.Evidence
getFeatureIdBySynonym(Connection, String, String, StringBuilder) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Get feature.feature_id by searching against synonyms.
getFeatureIndex(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet
getFeatureIndex(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature: By default SeqFeature has no kids so returns -1 be default.
getFeatureIndex(SeqFeatureI) - Method in interface apollo.datamodel.SeqFeatureI: Returns index of child if feat has child.
getFeatureItem(String, String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
getFeatureLabelColor() - Static method in class apollo.config.Config
getFeatureLabelColor() - Method in class apollo.config.Style
getFeatureLoadSize() - Method in class apollo.config.Style
getFeatureOwnerPropertyTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getFeaturePair(int) - Method in class apollo.util.FeatureList
getFeaturePosition(int) - Method in class apollo.datamodel.FeatureSet: This is an important method.
getFeaturePosition(int) - Method in class apollo.datamodel.SeqFeature: This needs to be fixed to account for edits to the genomic sequence, but I don't think it is urgent because this case is still so extremely rare
getFeaturePosition(int) - Method in interface apollo.datamodel.SeqFeatureI
getFeatureProperties() - Method in class apollo.config.TierProperty
getFeatureProperty(String, boolean) - Method in class apollo.config.PropertyScheme: Returns the FeatureProperty associated with analysis_type.
getFeatureProperty(String) - Method in class apollo.config.PropertyScheme: Returns the FeatureProperty associated with analysis_type.
getFeatureProperty(String) - Method in class apollo.config.TierProperty
getFeatureProperty() - Method in interface apollo.gui.drawable.Drawable: sets the FeatureProperty for the drawable, if it is is to be shown
getFeatureProperty() - Method in class apollo.gui.drawable.DrawableSeqFeature: features FeautureProperty.
getFeatureProperty() - Method in class apollo.gui.genomemap.FeatureTier
getFeatureRelationshipId(Long, Long, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getFeatures(DASDsn, DASSegment[]) - Method in interface apollo.dataadapter.das.DASServerI
getFeatures() - Method in class apollo.dataadapter.das.simple.DASFeatureContentHandler
getFeatures(DASDsn, DASSegment[]) - Method in class apollo.dataadapter.das.simple.SimpleDASServer: I am the call used by apollo to fetch annotations (features) from the input dsn, for the entry-points and ranges given by the input segments
getFeatures(DASDsn, HashMap, HashMap, long, long) - Method in class apollo.dataadapter.das.simple.SimpleDASServer: I am the getFeatures signature called internally by the DASFeatureContentHandler.
getFeatures(DASDsn, DASSegment[]) - Method in class apollo.dataadapter.das2.DAS2Request: I am the call used by apollo to fetch annotations (features) from the input dsn, for the entry-points and ranges given by the input segments
getFeatures(DASDsn, HashMap, HashMap, long, long) - Method in class apollo.dataadapter.das2.DAS2Request
getFeatures() - Method in class apollo.datamodel.FeatureSet
getFeatures() - Method in class apollo.datamodel.SeqFeature: returns a vector of all the child features belonging to this feature.
getFeatures() - Method in interface apollo.datamodel.SeqFeatureI: returns a vector of all the child features belonging to this feature.
getFeatures() - Method in class apollo.datamodel.StrandedFeatureSet: This actually returns not forward feature set and reverse feature set, but the children of forward and reverse.
getFeatures() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getFeatures(TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets a collection of all the top level features in the tier
getFeatures(TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getFeatures() - Method in class apollo.gui.event.FeatureSelectionEvent
getFeatures() - Method in class apollo.seq.io.GFFFile
getFeatureSequence() - Method in class apollo.datamodel.SeqFeature: Creates a Sequence object with Range.getResidues.
getFeatureSequence() - Method in interface apollo.datamodel.SeqFeatureI: Retrieve the SequenceI defined by this feature itself.
getFeatureSet() - Method in class apollo.analysis.SeqAnalysisBase
getFeatureSet() - Method in interface apollo.analysis.SeqAnalysisI
getFeatureSet() - Method in class apollo.gui.drawable.DrawableFeatureSet: returns the underlying FeatureSetI model.
getFeatureSet() - Method in interface apollo.gui.drawable.DrawableSetI
getFeatureSetAtPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeatureSetAtPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getFeaturesInRange(int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getFeaturesInRange(int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: XXX:Dont think this is in use Returns all of the sequence features within a given range on a tier.
getFeaturesOfClass(SeqFeatureI, Class, boolean) - Static method in class apollo.util.SeqFeatureUtil
getFeatureTreeFrame() - Method in class apollo.gui.featuretree.FeatureTreePanel
getFeatureTreeFrame() - Method in class apollo.gui.synteny.GuiCurationState
getFeatureType(String, String, String, String, String, String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return the Apollo type for a search hit feature.
getFeatureType(String, String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance: Flybase does feature type "program:sourcename", the rest of the params are ignored (used by tigr feat type)
getFeatureType(String, String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Tigr and fb assign feature type differently - config!
getFeatureType(String, String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance: Flybase does feature type "program:sourcename", the rest of the params are ignored (used by tigr feat type)
getFeatureType(String, String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance: tigrs feature type
getFeatureType(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature
getFeatureType() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getFeatureType() - Method in class apollo.datamodel.FeaturePair
getFeatureType() - Method in class apollo.datamodel.Protein: Returns "polypeptide" as that is the SO term for proteins
getFeatureType() - Method in class apollo.datamodel.Range: getType is not the "visual" type, ie the type one sees in the EvidencePanel.
getFeatureType() - Method in interface apollo.datamodel.RangeI: getType is not the "visual" type, ie the type one sees in the EvidencePanel.
getFeatureType(String) - Method in class apollo.gui.drawable.DrawableSeqFeature: Convenience fn.
getFeatureVector(CurationSet) - Static method in class apollo.util.SeqFeatureUtil
getFeatureVector(FeatureSetI) - Static method in class apollo.util.SeqFeatureUtil
getFeatWithName(String) - Method in class apollo.util.FeatureList: not recursive - just gets first feature with name - null if none
getFieldNames() - Method in class apollo.dataadapter.mysql.Table
getFieldNamesByTable(Table) - Method in class apollo.dataadapter.mysql.MySQLDatabase
getFieldsPanel() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getFileFilter() - Method in class apollo.gui.GenericFileAdapterGUI
getFileName() - Static method in class apollo.config.Config
getFileName() - Method in class apollo.config.Style
getFilename() - Method in class apollo.dataadapter.AbstractApolloAdapter: Returns null if not file
getFilename() - Method in class apollo.dataadapter.BaseGFFAdapter
getFilename() - Method in class apollo.dataadapter.DataInput
getFilename() - Method in class apollo.dataadapter.SerialDiskAdapter
getFiles() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getFilter() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getFilter() - Method in class apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction
getFilter() - Static method in class apollo.util.NumericKeyFilter
getFindButton() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getFindButton() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getFinishedColor() - Method in class apollo.config.FeatureProperty
getFirst() - Method in class apollo.util.Pair: Get the first value
getFirstAnnot(Selection) - Static method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor: Returns first AnnotatedFeatureI in Selection on strand clicked on, null if there is none.
getFirstAnnot(Selection) - Static method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame: Returns first AnnotatedFeatureI in Selection on strand clicked on, null if there is none.
getFlattenedTransactions() - Method in class apollo.editor.TransactionManager: Flattens out transactions.
getFMaxCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getFMinCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getFocus() - Method in class apollo.gui.event.BaseFocusEvent
getFocus() - Method in class apollo.gui.genomemap.ApolloPanel
getFocus() - Method in interface apollo.gui.genomemap.ApolloPanelI
getFont() - Method in class apollo.config.PeptideStatus
getFont() - Method in class apollo.gui.genomemap.FastClippingGraphics
getFont() - Method in class apollo.gui.genomemap.NavigationBar
getFontMetrics() - Method in class apollo.gui.genomemap.FastClippingGraphics
getFontMetrics(Font) - Method in class apollo.gui.genomemap.FastClippingGraphics
getForegroundColour() - Method in class apollo.gui.genomemap.LinearView
getForeignKeyConstraints(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Returns an array of the chado columns that reference a given table.
getForeignKeyReferenceMapping() - Static method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getForwardAnnotations() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getForwardResults() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getForwardSet() - Method in class apollo.datamodel.StrandedFeatureSet
getForwardSet() - Method in interface apollo.datamodel.StrandedFeatureSetI
getFragmentOffset() - Method in class apollo.datamodel.AssemblyFeature
getFragmentOffset() - Method in interface apollo.datamodel.AssemblyFeatureI
getFrame(long, boolean) - Method in class apollo.datamodel.AbstractSequence: This returns frame as 0, 1, or 2 (not 1,2,3)
getFrame() - Method in class apollo.datamodel.Exon: Overrides SeqFeature.getFrame.
getFrame() - Method in class apollo.datamodel.FeaturePair
getFrame() - Method in class apollo.datamodel.SeqFeature
getFrame() - Method in interface apollo.datamodel.SeqFeatureI
getFrame(long, boolean) - Method in interface apollo.datamodel.SequenceI
getFrame() - Static method in class apollo.gui.ApolloFrame
getFrame() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getFrame() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getFrame() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the frame that is currently being viewed
getFrame() - Method in class apollo.gui.FeaturePropertyPanel
getFrame() - Method in class apollo.gui.TypePanel
getFrameOrientation() - Static method in class apollo.config.Config
getFullName() - Method in class apollo.dataadapter.otter.parser.EvidenceNameTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.EvidenceTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.EvidenceTypeTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonEndTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonFrameTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonStableIdTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonStartTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonStrandTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ExonTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.GenericTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusAuthorEmailTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusAuthorTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusKnownTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusNameTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusRemarkTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusStableIdTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusSynonymTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.LocusTypeTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.OtterTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.ResponseTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAccessionTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyEndTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyStartTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorEmailTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentChromosomeTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOffsetTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOrientationTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentIdTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentKeywordTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentRemarkTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentVersionTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceSetAssemblyTypeTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceSetAuthorTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.SequenceSetTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorEmailTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptCdsEndNotFoundTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptCdsStartNotFoundTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptClassTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAEndNotFoundTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAStartNotFoundTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptNameTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptRemarkTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptStableIdTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationEndTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStableIdTagHandler
getFullName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStartTagHandler
getFullNameForUser(String) - Static method in class apollo.config.Config: Returns full name of user - if dont have full name just returns user
getGapExtendCost() - Method in class apollo.analysis.RemoteBlastNCBI.BlastOptions: Get the cost of extending a gap in an alignment.
getGapOpenCost() - Method in class apollo.analysis.RemoteBlastNCBI.BlastOptions: Get the cost of opening a gap in an alignment.
getGenbankType(String) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
getGenBankXref(AnnotatedFeatureI) - Method in class apollo.dataadapter.genbank.XrefUtil
getGene() - Method in class apollo.datamodel.Transcript
getGeneCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getGeneCountsByType(Model) - Method in class apollo.dataadapter.ensj.controller.ShowGeneCountsByTypeHandler
getGeneHolder() - Method in class apollo.gui.genomemap.AnnotationView: Returns the model(not drawable) of top of the model for the view.
getGeneName() - Method in class apollo.dataadapter.genbank.PeptideNote
getGeneNameField() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return the column in the chado feature table where the gene name can be found.
getGeneNameField() - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
getGeneNameField() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getGeneNameField() - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getGenePredictionPrograms() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getGeneProduct(AnnotatedFeatureI, Transcript, String, String, String, int) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getGeneticCode() - Method in class apollo.analysis.RemoteBlastNCBI.BlastOptions: Get the organism's genetic code.
getGeneticCodeNumber() - Method in class apollo.config.Style
getGeneTranscriptIds(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getGeneTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getGeneTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getGeneUrl() - Static method in class apollo.config.Config
getGeneUrl() - Method in class apollo.config.Style
getGeneWindow() - Static method in class apollo.config.Config
getGenomicErrors() - Method in class apollo.datamodel.AbstractSequence
getGenomicErrors() - Method in class apollo.datamodel.SeqFeature: first gets all of the genomic sequencing errors from the reference sequence and then eliminates any that are from outside the region of this feature.
getGenomicErrors() - Method in interface apollo.datamodel.SeqFeatureI
getGenomicErrors() - Method in interface apollo.datamodel.SequenceI
getGenomicLength(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getGenomicPosForPeptidePos(int) - Method in class apollo.datamodel.FeatureSet: For a position in peptide coordinates get the corresponding genomic position For now just do this in FeatureSet, I could imagine having a peptide object
getGenomicPosForPeptidePos(int) - Method in class apollo.datamodel.SeqFeature: For a position in peptide coordinates get the corresponding genomic position peptide object?
getGenomicPosForPeptidePos(int) - Method in interface apollo.datamodel.SeqFeatureI: For a position in peptide coordinates get the corresponding genomic position
getGenomicPosition(int) - Method in class apollo.datamodel.FeatureSet: Converts a transcript position (1 based without introns of course) to a genomic position
getGenomicPosition(int) - Method in class apollo.datamodel.SeqFeature
getGenomicPosition(int) - Method in interface apollo.datamodel.SeqFeatureI
getGenomicRange(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getGenomicSequence(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getGenotype() - Method in class apollo.dataadapter.genbank.GenbankValidator
getGFFFile() - Method in class apollo.dataadapter.BaseGFFAdapter
getGffFilename() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Get the GFF filename
getGFFSource() - Method in class apollo.dataadapter.chado.ChadoAdapter
getGFFSource() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter
getGPName() - Static method in class apollo.config.Config
getGraphFilename() - Method in class apollo.dataadapter.graph.GraphAdapter: Get the filename for the graph data
getGraphics() - Method in class apollo.gui.genomemap.LinearView
getGraphs() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getGraphView() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getGraphVisibility() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel: true if GraphView is visible
getGroupFlag() - Method in class apollo.config.FeatureProperty
getGroupFlagAsString() - Method in class apollo.config.FeatureProperty
getGroupId() - Method in interface apollo.dataadapter.das.DASFeature
getGroupId() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getGroupTargetStart() - Method in interface apollo.dataadapter.das.DASFeature
getGroupTargetStart() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getGroupTargetStop() - Method in interface apollo.dataadapter.das.DASFeature
getGroupTargetStop() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getGuiName() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getHalt() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel.AutoscrollThread
getHalt() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel.AutoscrollThread
getHandler() - Method in class apollo.dataadapter.ensj.controller.EventRouter
getHatchColor() - Method in class apollo.gui.detailviewers.exonviewer.AminoAcidRenderer
getHatchColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getHatchColor() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
getHatchColor() - Method in class apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD
getHatchColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getHatchColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getHatchColor() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
getHeader(RangeI) - Method in class apollo.config.DefaultDisplayPrefs
getHeader(RangeI) - Method in interface apollo.config.DisplayPrefsI
getHeader(RangeI) - Method in class apollo.config.FlyDisplayPrefs
getHeader() - Method in class apollo.datamodel.seq.GenbankSequence
getHeading() - Method in class apollo.config.ColumnProperty
getHeading(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
getHend() - Method in class apollo.datamodel.FeaturePair
getHend() - Method in class apollo.datamodel.SeqFeature
getHend() - Method in interface apollo.datamodel.SeqFeatureI
getHhigh() - Method in class apollo.datamodel.FeaturePair
getHhigh() - Method in class apollo.datamodel.SeqFeature
getHhigh() - Method in interface apollo.datamodel.SeqFeatureI
getHiddenTiers() - Method in class apollo.gui.genomemap.FeatureTierManager
getHiddenTiers() - Method in interface apollo.gui.genomemap.FeatureTierManagerI
getHigh() - Method in class apollo.datamodel.FeaturePair
getHigh() - Method in class apollo.datamodel.Range
getHigh() - Method in interface apollo.datamodel.RangeI
getHigh() - Method in class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange
getHigh(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getHigh(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getHigh() - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets the highest position on this tier
getHigh() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: the highest pixel position on the tier
getHigh(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: the highest pixel position on a feature
getHigh(SeqFeatureI) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getHigh() - Method in interface apollo.gui.drawable.Drawable
getHigh() - Method in class apollo.gui.drawable.DrawableSeqFeature
getHigh() - Method in class apollo.gui.genomemap.FeatureTier
getHigh() - Method in class apollo.util.interval.Interval
getHigh1() - Method in class apollo.datamodel.Link
getHigh2() - Method in class apollo.datamodel.Link
getHighestBase() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getHighestBase() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getHighlightColor() - Static method in class apollo.config.Config
getHighlightColor() - Method in class apollo.config.Style
getHistory() - Method in interface apollo.gui.ApolloLoaderI
getHistory() - Method in class apollo.test.ApolloLaundry
getHistory() - Method in class apollo.test.WashingLine
getHitChromosome() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHitCoordSystemString() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHitEnd() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHitFeature() - Method in class apollo.datamodel.FeaturePair
getHitFeature() - Method in class apollo.datamodel.SeqFeature: shoulnt this return null? yea it should - why is it returning this??
getHitFeature() - Method in interface apollo.datamodel.SeqFeatureI: if hasHitFeature true return hit, else return itself
getHitFeature(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getHitIndex(int) - Method in class apollo.datamodel.FeaturePair: Gets the index into the hit strings explicitAlignment for a genomic position
getHitIndex(int, String) - Method in class apollo.datamodel.FeaturePair
getHitSeqName(RangeI, boolean) - Method in class apollo.config.TigrAnnotDisplayPrefs
getHitSequence() - Method in class apollo.datamodel.FeaturePair: Returns hit.getFeatureSequence (which is start to end of hits ref seq),
getHitSequence() - Method in interface apollo.datamodel.FeaturePairI
getHitSequence() - Method in class apollo.datamodel.FeatureSet: if kids have hit feats then this is the hit seq associated with them This is a convenience for having to get hit seq from kids
getHitSequence() - Method in interface apollo.datamodel.FeatureSetI
getHitSequence() - Method in class apollo.datamodel.SeqFeature: returns null - FeaturePair and FeatureSet override
getHitSequence() - Method in interface apollo.datamodel.SeqFeatureI: If feat has hit feat, or children with hit feat, then this is the seq associated with the hit or kid hits
getHitSpecies() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHitStableId() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHitStart() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getHlow() - Method in class apollo.datamodel.FeaturePair
getHlow() - Method in class apollo.datamodel.SeqFeature
getHlow() - Method in interface apollo.datamodel.SeqFeatureI
getHname() - Method in class apollo.datamodel.FeaturePair
getHname() - Method in class apollo.datamodel.SeqFeature: Set explicit hit alignment - string with gaps.
getHname() - Method in interface apollo.datamodel.SeqFeatureI: convenience function for getHitFeature().getName()
getHost() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getHost() - Method in class apollo.dataadapter.mysql.Database
getHost() - Method in class apollo.dataadapter.mysql.MySQLInstance
getHostListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getHstart() - Method in class apollo.datamodel.FeaturePair
getHstart() - Method in class apollo.datamodel.SeqFeature
getHstart() - Method in interface apollo.datamodel.SeqFeatureI
getHstrand() - Method in class apollo.datamodel.FeaturePair
getHstrand() - Method in class apollo.datamodel.SeqFeature
getHstrand() - Method in interface apollo.datamodel.SeqFeatureI
getID() - Method in class apollo.dataadapter.chado.ChadoTransaction
getId() - Method in interface apollo.dataadapter.das.DASFeature
getId() - Method in interface apollo.dataadapter.das.DASSegment
getId() - Method in interface apollo.dataadapter.das.DASSequence
getId() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getId() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getId() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getId() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the feature ID
getId() - Method in class apollo.datamodel.Comment
getId() - Method in class apollo.datamodel.FeaturePair
getId() - Method in class apollo.datamodel.Protein: for now just a wrapper for prot seq - eventually id will migrate here
getId() - Method in class apollo.datamodel.SeqFeature
getId() - Method in interface apollo.datamodel.SeqFeatureI
getID(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getID() - Method in class apollo.gui.event.LazyLoadEvent
getIdentifier() - Method in interface apollo.datamodel.AnnotatedFeatureI
getIdentifier() - Method in class apollo.datamodel.SeqFeature
getIdFormat() - Method in class apollo.config.FeatureProperty: Regular expression that describes format for ID, null if not set
getIdForURL(SeqFeatureI) - Method in class apollo.config.DefaultDisplayPrefs
getIdForURL(SeqFeatureI) - Method in class apollo.config.EnsjDisplayPrefs
getIdForURL(SeqFeatureI) - Method in class apollo.config.FlyDisplayPrefs
getIdForURL(SeqFeatureI) - Method in class apollo.config.ParameciumDisplayPrefs
getIdGeneratedForFeature(SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter
getIDPrefix(SeqFeatureI) - Method in class apollo.config.ChadoJdbcNameAdapter: Returns the prefix of a SeqFeature's ID format (e.g.
getIdPrefix() - Method in class apollo.config.FeatureProperty: Get the id prefix
getIDPrefix(SeqFeatureI) - Method in class apollo.config.GmodNameAdapter: Returns the prefix of a SeqFeature's ID format (e.g.
getIds(AnnotatedFeatureI, Transcript) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getIdType() - Method in class apollo.datamodel.DbXref
getIdValue() - Method in class apollo.datamodel.DbXref
getIndex() - Method in enum apollo.gui.detailviewers.sequencealigner.ReadingFrame
getIndexContaining(int) - Method in class apollo.datamodel.FeatureSet
getIndexContaining(int) - Method in interface apollo.datamodel.FeatureSetI
getIndexForType(String) - Method in class apollo.gui.genomemap.FeatureTierManager
getIndicatorColor() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
getIndicatorColor() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
getIndicatorColor() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
getInitialSettings() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getInitialSitesVisibility() - Method in class apollo.config.Style: Initial state for sites visibility (view menu item)
getInnerPanel() - Method in class apollo.dataadapter.GuiTabPanel
getInput() - Method in class apollo.dataadapter.AbstractApolloAdapter: Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?
getInput() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?
getInput() - Method in class apollo.dataadapter.BaseGFFAdapter
getInput() - Method in class apollo.dataadapter.CGI
getInput() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter
getInput() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getInput() - Method in class apollo.dataadapter.das2.DAS2Adapter
getInput() - Method in class apollo.dataadapter.DummySequenceAdapter
getInput() - Method in class apollo.dataadapter.EfetchSequenceAdapter
getInput() - Method in class apollo.dataadapter.EnsCGIAdapter
getInput() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getInput() - Method in class apollo.dataadapter.GbrowseAdapter
getInput() - Method in class apollo.dataadapter.otter.OtterAdapter
getInput() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getInput() - Method in class apollo.dataadapter.SerialDiskAdapter
getInput() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getInputFileHistory() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getInputFilename() - Method in class apollo.datamodel.CurationSet
getInputSequence() - Method in class apollo.analysis.SeqAnalysisBase
getInputSequence() - Method in interface apollo.analysis.SeqAnalysisI: Retrieve the SequenceI that this analysis builds a CurationSet from
getInputSequenceCount() - Method in class apollo.analysis.SeqAnalysisBase
getInputSequenceCount() - Method in interface apollo.analysis.SeqAnalysisI: usually returns 1, but some programs (eg clustalw) require >1 input sequence
getInputSequences() - Method in class apollo.analysis.SeqAnalysisBase
getInputSequences() - Method in interface apollo.analysis.SeqAnalysisI: Retrieve the SequenceI list that this builds a curation set from
getInputServerHistory() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getInputStream() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
getInputStream() - Method in class apollo.dataadapter.otter.OtterAdapter
getInputStream() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getInputString() - Method in class apollo.dataadapter.DataInput
getInputType() - Method in class apollo.dataadapter.AbstractApolloAdapter: Returns the type of input data (gene,file,band...)
getInputType() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getInputType() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Returns the type of input data (gene,file,band...) I believe this is now contained in the DataInput object, so this should probably be phased out eventually
getInputType() - Method in class apollo.dataadapter.BaseGFFAdapter
getInputType() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getInputType() - Method in class apollo.dataadapter.das2.DAS2Adapter
getInputType() - Method in class apollo.dataadapter.DummySequenceAdapter
getInputType() - Method in class apollo.dataadapter.EfetchSequenceAdapter
getInputType() - Method in class apollo.dataadapter.EnsCGIAdapter
getInputType() - Method in class apollo.dataadapter.ensj.EnsJAdapter: This is queried by Apollo's FileMenu
getInputType() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter: This is an arcane requirement to get the File->Save menu to light up.
getInputType() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getInputType() - Method in class apollo.dataadapter.FileTabPanel
getInputType() - Method in class apollo.dataadapter.gamexml.GAMEAdapterGUI: need?
getInputType() - Method in class apollo.dataadapter.GbrowseAdapter
getInputType() - Method in class apollo.dataadapter.GuiTabPanel
getInputType() - Method in class apollo.dataadapter.otter.OtterAdapter
getInputType() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getInputType() - Method in class apollo.dataadapter.sample.SampleAdapter: This is queried by Apollo's FileMenu
getInputType() - Method in class apollo.dataadapter.SerialDiskAdapter
getInputType() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getInputType() - Method in class apollo.dataadapter.synteny.SyntenyAdapter: This is an arcane requirement to get the File->Save menu to light up.
getInsertionRange(int, String) - Method in class apollo.datamodel.FeaturePair
getInstance() - Static method in class apollo.gui.PreferenceWindow: Static method for retrieving singleton instance.
getInstance(Selection) - Static method in class apollo.gui.PreferenceWindow: Static method for retrieving singleton instance with selected type.
getInteractionListener() - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel: The default interaction listener will do nothing.
getInteractionListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getInterval(RbNode) - Method in class apollo.util.interval.IntervalTree
getInvertedScrollbarValue() - Method in class apollo.gui.genomemap.TierView
getJalviewController() - Method in class apollo.gui.ApolloJalviewEventBridge
getJavaWebStartVersion() - Static method in class apollo.config.Config: Get the Java Web Start version.
getJdbcUrl() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getJdbcUrl() - Method in class apollo.dataadapter.chado.ChadoDatabase
getJVM() - Static method in class apollo.config.Config
getKaryotypeAdapter() - Method in class apollo.dataadapter.GFFSyntenyAdapter
getKaryotypeAdapter() - Method in class apollo.dataadapter.SyntenyAdapter: This has to be stamped into me beforehand.
getKaryotypeAdapter() - Method in interface apollo.dataadapter.SyntenyAdapterI
getKaryotypeAdapter() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getKaryotypeBySpeciesName(String) - Method in class apollo.dataadapter.ChromosomeAdapter
getKaryotypeBySpeciesName(String) - Method in class apollo.dataadapter.KaryotypeAdapter
getKaryotypeBySpeciesName(String) - Method in interface apollo.dataadapter.KaryotypeAdapterI
getKaryotypeFile() - Static method in class apollo.config.Config
getKaryotypes() - Method in class apollo.dataadapter.ChromosomeAdapter
getKaryotypes() - Method in class apollo.dataadapter.KaryotypeAdapter
getKaryotypes() - Method in interface apollo.dataadapter.KaryotypeAdapterI
getKey() - Method in class apollo.dataadapter.ensj.controller.EventHandler
getKey() - Method in class apollo.dataadapter.ensj.controller.EventRouter
getKeyFromValue(Hashtable, Object) - Method in class apollo.config.FeatureProperty
getKeywords() - Method in class apollo.dataadapter.genbank.GenbankReport
getKeywords() - Method in class apollo.datamodel.AssemblyFeature
getLabel() - Method in class apollo.config.TierProperty
getLabel() - Method in interface apollo.dataadapter.das.DASFeature
getLabel() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getLast() - Method in class apollo.gui.genomemap.Rubberband
getLastBaseOfStopCodon() - Method in class apollo.datamodel.FeatureSet
getLastBaseOfStopCodon() - Method in interface apollo.datamodel.TranslationI
getLayoutIniFile() - Static method in class apollo.config.Config
getLayoutIniFile() - Method in class apollo.config.Style
getLeadSpaceSize() - Method in class apollo.gui.genomemap.ManagedView
getLeafFeatsOver(int) - Method in class apollo.datamodel.FeatureSet
getLeafFeatsOver(int) - Method in class apollo.datamodel.SeqFeature
getLeafFeatsOver(int) - Method in interface apollo.datamodel.SeqFeatureI: This is used in the base editor to find the sub features that overlap a base with a sequence edit on it
getLeafFeatsOver(int) - Method in class apollo.datamodel.StrandedFeatureSet
getLeafName() - Method in class apollo.dataadapter.otter.parser.EvidenceNameTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.EvidenceTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.EvidenceTypeTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonEndTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonFrameTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonStableIdTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonStartTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonStrandTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ExonTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.GenericTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusAuthorEmailTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusAuthorTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusKnownTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusNameTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusRemarkTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusStableIdTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusSynonymTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.LocusTypeTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.OtterTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.ResponseTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAccessionTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyEndTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyStartTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorEmailTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentChromosomeTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOffsetTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOrientationTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentIdTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentKeywordTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentRemarkTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceFragmentVersionTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceSetAssemblyTypeTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceSetAuthorTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.SequenceSetTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorEmailTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptCdsEndNotFoundTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptCdsStartNotFoundTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptClassTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAEndNotFoundTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAStartNotFoundTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptNameTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptRemarkTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptStableIdTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationEndTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStableIdTagHandler
getLeafName() - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStartTagHandler
getLeafTransactions() - Method in class apollo.editor.CompoundTransaction: returns list of all non-compound leaf descendants.
getLeafTransactions() - Method in class apollo.editor.Transaction: Return all descendant leaves of this transaction.
getLeft(Transformer) - Method in interface apollo.gui.drawable.Drawable
getLeft(Transformer) - Method in class apollo.gui.drawable.DrawableSeqFeature
getLeftmostVisible(Transformer) - Method in class apollo.gui.drawable.DrawableSeqFeature
getLeftOverlap(RangeI) - Method in class apollo.datamodel.Range
getLeftOverlap(RangeI) - Method in interface apollo.datamodel.RangeI
getLeftView() - Method in class apollo.gui.genomemap.SplitterView
getLength() - Method in interface apollo.dataadapter.das.DASSegment
getLength() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getLength() - Method in class apollo.datamodel.AbstractSequence
getLength() - Method in class apollo.datamodel.Chromosome
getLength() - Method in class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange
getLength() - Method in class apollo.datamodel.seq.DebugLazySequence
getLength() - Method in class apollo.datamodel.seq.PFetchSequence
getLength() - Method in class apollo.datamodel.seq.SRSSequence
getLength() - Method in class apollo.datamodel.Sequence
getLength() - Method in interface apollo.datamodel.SequenceI
getLength() - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent: Gets the length of this component
getLengthFromPFetch(String) - Static method in class apollo.datamodel.seq.DataUtil
getLengthFromSRS(String) - Static method in class apollo.datamodel.seq.DataUtil
getLimits() - Method in class apollo.gui.genomemap.LinearView: Limits not necasarily equal to seq start and end, Component.syncViewLimits pads out the limits beyond sequence
getLimits() - Method in interface apollo.gui.genomemap.ViewI: Gets the minimum and maximum limits
getLinearCentre() - Method in class apollo.gui.genomemap.ApolloPanel
getLinearMaximum() - Method in class apollo.gui.genomemap.ApolloPanel
getLinearMinimum() - Method in class apollo.gui.genomemap.ApolloPanel
getLineType(String) - Method in class apollo.dataadapter.genbank.GenbankRead: Return the embl line type of the line contained in the argument String.
getLink(int) - Method in class apollo.datamodel.LinkSet
getLinkedFeatProp(int) - Method in class apollo.config.PropertyScheme
getLinkedFeatPropsSize() - Method in class apollo.config.PropertyScheme
getLinkedSpeciesFeature(SeqFeatureI) - Method in class apollo.datamodel.Link: If feat is not part of link - neither species1 nor species2 feature - then return null.
getLinkedTierProp(int) - Method in class apollo.config.PropertyScheme
getLinkedTierProps() - Method in class apollo.config.PropertyScheme
getLinkPanels() - Method in class apollo.gui.synteny.SyntenyPanel
getLinkPanelSize() - Method in class apollo.config.Style
getLinkSet(int) - Method in class apollo.datamodel.CompositeDataHolder
getLinksMenu() - Static method in class apollo.gui.menus.LinksMenu: singleton access
getLinkSpecies1() - Method in class apollo.config.FeatureProperty
getLinkSpecies2() - Method in class apollo.config.FeatureProperty
getLinkType() - Method in class apollo.config.FeatureProperty: Return LinkType - default LinkType.NO_LINK (not linked) LinkType describes how FeatureProperty links to other species
getListDescendedFromModel(SeqFeatureI, boolean) - Method in class apollo.gui.Selection
getListener() - Method in class apollo.gui.ProgressFrame
getListeners() - Method in class apollo.gui.Controller
getLocation() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getLocation() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getLocation(Drawable) - Method in class apollo.gui.genomemap.FeatureTier
getLocationHistory() - Method in class apollo.dataadapter.ensj.model.LocationModel
getLocationModel() - Method in class apollo.dataadapter.ensj.model.Model
getLocationPanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getLocationSeqType() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Returns seq type that has location
getLockScrolling() - Method in class apollo.gui.menus.SyntenyChoiceMenu
getLocus(AnnotatedFeatureI, String) - Method in class apollo.dataadapter.genbank.GenbankAdapter: Change the flag that is passed if Genbank decides that some feature does/doesn't get the locus_tag field
getLocus() - Method in class apollo.dataadapter.genbank.GenbankReport: Properties that were saved from the GenBank-format input were saved verbatim, including newlines, and we don't need to add the keyword to the first line because it's there already.
getLogDirectory() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getLoggingFile() - Method in class apollo.dataadapter.ensj19.EnsJAdapter: Get the value of loggingFile.
getLoggingFile() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getLogin() - Method in class apollo.dataadapter.chado.ChadoDatabase
getLongestSeq() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getLow() - Method in class apollo.datamodel.FeaturePair
getLow() - Method in class apollo.datamodel.Range
getLow() - Method in interface apollo.datamodel.RangeI
getLow() - Method in class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange
getLow(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getLow(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getLow() - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets the lowest position on this tier
getLow() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: the lowest pixel position on the tier
getLow(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: the lowest pixel position on a feature
getLow(SeqFeatureI) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getLow() - Method in interface apollo.gui.drawable.Drawable
getLow() - Method in class apollo.gui.drawable.DrawableSeqFeature
getLow() - Method in class apollo.util.interval.Interval
getLow1() - Method in class apollo.datamodel.Link
getLow2() - Method in class apollo.datamodel.Link
getLowestBase() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getLowestBase() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getLowestVisible() - Method in class apollo.gui.TierManager
getLowestVisible() - Method in interface apollo.gui.TierManagerI
getLowestVisibleTier() - Method in class apollo.gui.genomemap.TierView
getLowestVisibleTier() - Method in interface apollo.gui.genomemap.TierViewI: Get the lowest visible tier.
getMainAdapterGUI(String) - Method in class apollo.dataadapter.synteny.builder.Model
getMainAdapterModel(String) - Method in class apollo.dataadapter.synteny.builder.Model
getMainWindowWidth() - Static method in class apollo.config.Config
getMapID() - Method in class apollo.dataadapter.TransactionOutputAdapter
getMapMaster() - Method in interface apollo.dataadapter.das.DASDsn
getMapMaster() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getMapType() - Method in class apollo.dataadapter.TransactionOutputAdapter
getMasterController() - Static method in class apollo.gui.Controller: static master controller - should be renamed master listener.
getMatchCount() - Method in class apollo.gui.SequenceSelector: Returns the number of matches to the query string found in the sequence
getMatches() - Method in class apollo.gui.SequenceSelector: Returns a vector of SeqFeatures for the find display
getMatchLength(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getMatchRange(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getMatchSequence(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getMax(RbNode) - Method in class apollo.util.interval.IntervalTree
getMaxAlignGap() - Method in class apollo.analysis.filter.AnalysisInput
getMaxCover() - Method in class apollo.analysis.filter.AnalysisInput
getMaxExons() - Method in class apollo.analysis.filter.AnalysisInput
getMaxExpect() - Method in class apollo.analysis.filter.AnalysisInput
getMaxHistoryLength() - Static method in class apollo.config.Config
getMaxHistoryLength() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getMaxHistoryLength() - Method in class apollo.dataadapter.GuiTabPanel
getMaximum() - Method in class apollo.gui.genomemap.LinearView
getMaximum() - Method in interface apollo.gui.genomemap.ViewI: Get the maximum limit.
getMaximumVisibleTransformCoord(int) - Method in class apollo.gui.TierManager
getMaxRatio() - Method in class apollo.analysis.filter.AnalysisInput
getMaxRow() - Method in class apollo.config.TierProperty
getMaxScore() - Method in class apollo.config.FeatureProperty
getMaxScore() - Method in class apollo.gui.StoredScoreCalculator: Get the maximum score for this set
getMaxScrollbarValue() - Method in class apollo.gui.genomemap.TierView
getMaxTierUserHeight() - Method in class apollo.gui.TierManager
getMaxTierUserHeight() - Method in interface apollo.gui.TierManagerI
getMaxUserCoord() - Method in class apollo.gui.TierManager
getMaxUserCoord() - Method in interface apollo.gui.TierManagerI
getMaxVisibleTierNumber() - Method in class apollo.gui.TierManager: Returns the maximum visible tier number - The highest tier number can be greater than the number of tiers.
getMaxVisibleTierNumber() - Method in interface apollo.gui.TierManagerI
getMemoryAllocation() - Static method in class apollo.config.Config
getMenu() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getMenu() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getMenu() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the Menu object
getMenuBar() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Method for easy access to MenuBar
getMessage() - Method in class apollo.dataadapter.synteny.builder.Model
getMessageWStackTrace() - Method in exception apollo.dataadapter.exception.BopException
getMethodId() - Method in interface apollo.dataadapter.das.DASFeature
getMethodId() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getMethodLabel() - Method in interface apollo.dataadapter.das.DASFeature
getMethodLabel() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getMin(RbNode) - Method in class apollo.util.interval.IntervalTree
getMinIdentity() - Method in class apollo.analysis.filter.AnalysisInput
getMinimum() - Method in class apollo.gui.genomemap.LinearView
getMinimum() - Method in interface apollo.gui.genomemap.ViewI: Get the minimum limit.
getMinimumSize() - Method in class apollo.gui.evidencepanel.EvidencePanelContainer: Min size 0,0 - allow the user to shrink the ev panel down to 0
getMinimumSize() - Method in class apollo.gui.synteny.SyntenyPanel: Min size 0,0 - allow the user to shrink the syn panel down to 0
getMinimumThumbSize() - Method in class apollo.gui.ApolloMetalScrollBarUI
getMinimumVisibleTransformCoord() - Method in class apollo.gui.TierManager
getMinimumVisibleTransformCoord() - Method in interface apollo.gui.TierManagerI
getMinLength() - Method in class apollo.analysis.filter.AnalysisInput
getMinScore() - Method in class apollo.analysis.filter.AnalysisInput
getMinScore() - Method in class apollo.config.FeatureProperty
getMinScore() - Method in class apollo.gui.StoredScoreCalculator: Get the minimum score for this set
getMinScrollbarValue() - Method in class apollo.gui.genomemap.TierView
getMinWidth() - Method in class apollo.config.FeatureProperty
getMismatchRegionLength() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getMode() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getMode() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getModel() - Method in class apollo.dataadapter.ensj.controller.Controller
getModel() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
getModel() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getModel() - Method in class apollo.dataadapter.synteny.builder.Controller
getModel() - Method in class apollo.gui.ScoreCalculator: By default returns null.
getModel() - Method in class apollo.gui.WindowScoreCalculator
getModelName() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getModelWithName(String, String) - Method in class apollo.dataadapter.synteny.builder.Model
getModeStack() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getModifiers() - Method in class apollo.gui.genomemap.Rubberband
getMultiSequenceAlignerPanel() - Method in class apollo.gui.detailviewers.sequencealigner.ResultMouseListener: Gets the scrollable object that will be affected
getMultiSequenceAlignerPanel() - Method in class apollo.gui.detailviewers.sequencealigner.ResultRightClickMenu: Gets the MultiSequenceAlignerPanel object for this menu
getNaiveCrossSpeciesDataLoading() - Method in class apollo.config.Style: This indicates whether a composite adapter UI is to load cross-species data simply - that is, just read the adapters for each species & the compara sets in turn, and not propagate information from one read to the other.
getName() - Method in class apollo.analysis.SeqAnalysisBase
getName() - Method in class apollo.analysis.SeqAnalysisBDGP
getName() - Method in interface apollo.analysis.SeqAnalysisI
getName() - Method in class apollo.analysis.SeqAnalysisLocal
getName() - Method in class apollo.analysis.SeqAnalysisNCBI
getName() - Method in class apollo.analysis.SeqAnalysisRemote
getName() - Method in class apollo.dataadapter.AbstractApolloAdapter: Name label for use in Data Adapter Chooser.
getName() - Method in class apollo.dataadapter.chado.ChadoDatabase
getName() - Method in class apollo.dataadapter.chado.SeqType
getName() - Method in class apollo.dataadapter.ChromosomeAdapter
getName() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getName() - Method in class apollo.dataadapter.das2.DAS2Adapter
getName() - Method in class apollo.dataadapter.DummySequenceAdapter
getName() - Method in class apollo.dataadapter.EfetchSequenceAdapter
getName() - Method in class apollo.dataadapter.EnsCGIAdapter
getName() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
getName() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getName() - Method in class apollo.dataadapter.GbrowseAdapter
getName() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the feature name
getName() - Method in class apollo.dataadapter.GFFSyntenyAdapter
getName() - Method in class apollo.dataadapter.KaryotypeAdapter
getName() - Method in interface apollo.dataadapter.KaryotypeAdapterI
getName() - Method in class apollo.dataadapter.mysql.Database
getName() - Method in class apollo.dataadapter.mysql.Table
getName() - Method in class apollo.dataadapter.otter.OtterAdapter
getName() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getName() - Method in class apollo.dataadapter.synteny.builder.AdapterModel
getName() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getName() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getName() - Method in class apollo.dataadapter.SyntenyAdapter
getName() - Method in interface apollo.dataadapter.SyntenyAdapterI
getName() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getName() - Method in class apollo.datamodel.AbstractSequence
getName() - Method in interface apollo.datamodel.ApolloDataI: unclear if name is really needed.
getName() - Method in class apollo.datamodel.CompositeDataHolder
getName() - Method in class apollo.datamodel.FeaturePair
getName() - Method in class apollo.datamodel.FeatureSet
getName() - Method in class apollo.datamodel.LinkSet
getName() - Method in class apollo.datamodel.Protein
getName() - Method in class apollo.datamodel.Range
getName() - Method in interface apollo.datamodel.RangeI: In the case where the range is chromosomal the name is the chromosome name
getName() - Method in class apollo.datamodel.Score
getName() - Method in interface apollo.datamodel.SequenceI
getName() - Method in class apollo.datamodel.Synonym
getName(SeqFeatureI) - Static method in class apollo.gui.DetailInfo: The whole logic of this section has been put into the individual getDisplayName() methods of the various classes
getName() - Method in interface apollo.gui.drawable.Drawable
getName() - Method in class apollo.gui.drawable.DrawableSeqFeature
getName() - Method in class apollo.gui.genomemap.ApolloPanel: Returns the name of the panel.
getName() - Method in class apollo.gui.genomemap.LinearView
getName() - Method in interface apollo.gui.genomemap.ViewI: Returns the name of the view.
getName() - Method in class apollo.gui.tweeker.RestrictionEnzyme
getName1() - Method in class apollo.datamodel.Link
getName2() - Method in class apollo.datamodel.Link
getNameAdapter() - Method in class apollo.config.Style
getNameAdapter(AnnotatedFeatureI) - Method in class apollo.dataadapter.AbstractApolloAdapter
getNameAdapter(AnnotatedFeatureI) - Method in class apollo.dataadapter.CurationState: A style/property scheme can be used by multiple curations (which is often the case) BUT the name adapters proscribed by its feature properties are curation specific in that they require the curations transaction manager, as the TM is checked for past ids in making new temp ids.
getNameAdapter(AnnotatedFeatureI) - Method in class apollo.gui.annotinfo.FeatureEditorDialog
getNameAdapter() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getNameAdapter(AnnotatedFeatureI) - Method in class apollo.gui.synteny.GuiCurationState
getNameAdapterString() - Method in class apollo.config.FeatureProperty
getNameField() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getNameGeneratedForFeature(SeqFeatureI) - Method in class apollo.config.TigrAnnotNameAdapter
getNames() - Method in class apollo.gui.event.NamedFeatureSelectionEvent
getNavigationAction() - Method in class apollo.gui.genomemap.NavigationBar: apollo.gui.menu.ViewMenu uses this
getNavigationBar() - Method in class apollo.gui.synteny.GuiCurationState: navigation bar on top of szap - should this be multi cur set?
getNewActiveCurState() - Method in class apollo.gui.event.SetActiveCurStateEvent
getNewAdapterModel(Model) - Method in class apollo.dataadapter.synteny.builder.View
getNewChadoDbUniquename(String, long) - Method in class apollo.config.GmodNameAdapter
getNewChadoDbUniquename(SeqFeatureI, long) - Method in class apollo.config.GmodNameAdapter
getNewConnection() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Opens and return a new Connection to the database specified in the arguments to init.
getNewConnection() - Method in class apollo.dataadapter.chado.jdbc.SybaseChadoAdapter
getNewId() - Method in class apollo.editor.Transaction
getNewIdFromTypeChange(String, String, String) - Method in interface apollo.config.ApolloNameAdapterI
getNewIdFromTypeChange(String, String, String) - Method in class apollo.config.ChadoJdbcNameAdapter
getNewIdFromTypeChange(String, String, String) - Method in class apollo.config.DefaultNameAdapter
getNewIdFromTypeChange(String, String, String) - Method in class apollo.config.GmodNameAdapter: convert oldId to a new id in new type format
getNewIdFromTypeChange(String, String, String) - Method in class apollo.config.ParameciumNameAdapter
getNewIdFromTypeChange(String, String, String) - Method in class apollo.config.TigrAnnotNameAdapter
getNewSequencingErrorPosition() - Method in class apollo.editor.AnnotationUpdateEvent
getNewSequencingErrorPosition() - Method in interface apollo.editor.UpdateDetailsI
getNewSetName() - Method in class apollo.dataadapter.synteny.builder.View
getNewSplitFeature() - Method in class apollo.editor.CompoundTransaction: If split compound transaction (isSplit == true), this returns the new split off feature.
getNewSplitFeature() - Method in class apollo.editor.Transaction: If split compound transaction, this returns the new split off feature.
getNewSubpartValue() - Method in class apollo.editor.Transaction
getNextFeature(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel: Given a pixel position return the next feature
getNextFeature(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: gets the next feature in the 3' direction
getNextFeature(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getNextFeature(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: Given a pixel position return the next feature on the tier
getNextFeature(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getNextOverlap(Vector, int, int[], Vector[], int[], Vector) - Method in class apollo.gui.genomemap.FeatureTierManager
getNextPrimaryKeyId(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Run a SELECT(MAX()) + 1 query to get the next available primary key value for a chado table.
getNextPrimaryKeyId(String) - Method in class apollo.dataadapter.chado.jdbc.PostgresChadoAdapter
getNonConsensusAcceptorNum() - Method in class apollo.datamodel.AnnotatedFeature: Returns transcript exon number with non consensus acceptor.
getNonConsensusAcceptorNum() - Method in interface apollo.datamodel.AnnotatedFeatureI: Returns transcript exon number with non consensus acceptor.
getNonConsensusAcceptorNum() - Method in class apollo.datamodel.Transcript: This returns the exon index of the non-consensus acceptor (if any), or -1 if there aren't any non-consensus acceptors.
getNonConsensusDonorNum() - Method in class apollo.datamodel.AnnotatedFeature: Returns transcript exon number with non consensus donor.
getNonConsensusDonorNum() - Method in interface apollo.datamodel.AnnotatedFeatureI: Returns transcript exon number with non consensus donor.
getNonConsensusDonorNum() - Method in class apollo.datamodel.Transcript
getNoStripes() - Static method in class apollo.config.Config
getNoStripes() - Method in class apollo.config.Style
getNote() - Method in interface apollo.dataadapter.das.DASFeature
getNote() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getNote() - Method in class apollo.dataadapter.genbank.PeptideNote
getNullCVTermId(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getNumberOfChildAdapters() - Method in class apollo.dataadapter.AbstractApolloAdapter: Returns 0 by default.
getNumberOfChildAdapters() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Returns number of child adapters.
getNumberOfChildAdapters() - Method in class apollo.dataadapter.synteny.SyntenyAdapter: From ApolloDataAdapterI
getNumberOfChildren() - Method in class apollo.datamodel.SeqFeature: Returns the number of direct children (not all descendants) this feature has.
getNumberOfChildren() - Method in interface apollo.datamodel.SeqFeatureI: Returns the number of features (not all descnedants) this feature has.
getNumberOfChildren() - Method in class apollo.editor.AnnotationChangeEvent: If compound event return # of child events, default 0
getNumberOfChildren() - Method in class apollo.editor.AnnotationCompoundEvent
getNumberOfDescendents() - Method in class apollo.datamodel.FeatureSet
getNumberOfDescendents() - Method in class apollo.datamodel.SeqFeature: The number of descendants (direct and indirect) in this FeatureSetI.
getNumberOfDescendents() - Method in interface apollo.datamodel.SeqFeatureI: The number of descendants (direct and indirect) in this FeatureSetI.
getNumberOfHits() - Method in class apollo.analysis.RemoteBlastNCBI.BlastOptions: Get the maximum number of hits to calculate.
getNumberOfLevels() - Method in class apollo.config.FeatureProperty
getNumberOfLinkSets() - Method in class apollo.datamodel.CompositeDataHolder
getNumberOfSpecies() - Method in class apollo.config.Style: How many species to display in synteny - default is 1
getNumberOfSpecies() - Method in class apollo.datamodel.CompositeDataHolder: I keep forgetting numberOfSpecies has no 'get' in front of it, so I'm inserting this standard accessor for my own sanity.
getNumberOfSyntenySpecies() - Method in class apollo.config.Style
getNumTiers() - Method in class apollo.gui.TierManager
getNumTiers() - Method in interface apollo.gui.TierManagerI
getNumVisible() - Method in class apollo.gui.TierManager
getNumVisible() - Method in interface apollo.gui.TierManagerI
getObjectClass() - Method in class apollo.editor.ResultChangeEvent: can object class be figured automatically from feature type? this works for annots
getObjectClass() - Method in class apollo.editor.Transaction
getObjectStack() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getObjFeatCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getOccurance() - Method in class apollo.analysis.filter.HuffNode
getOffset() - Method in class apollo.analysis.filter.AnalysisInput
getOffset(int, TierI) - Static method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getOldActiveCurState() - Method in class apollo.gui.event.SetActiveCurStateEvent
getOldComment() - Method in class apollo.editor.AnnotationChangeEvent
getOldComment() - Method in class apollo.editor.AnnotationUpdateEvent
getOldComment() - Method in class apollo.editor.Transaction: Convenience method for getting old comment
getOldComment() - Method in interface apollo.editor.UpdateDetailsI
getOldId() - Method in class apollo.editor.AnnotationChangeEvent: A parent update for transcripts will change the transcript id and make it impossible to update the db.
getOldId() - Method in class apollo.editor.Transaction
getOldInt() - Method in class apollo.editor.AnnotationUpdateEvent
getOldInt() - Method in interface apollo.editor.UpdateDetailsI
getOldParent() - Method in class apollo.editor.AnnotationUpdateEvent
getOldParent() - Method in interface apollo.editor.UpdateDetailsI
getOldRange() - Method in class apollo.editor.AnnotationUpdateEvent
getOldRange() - Method in interface apollo.editor.UpdateDetailsI
getOldString() - Method in class apollo.editor.AnnotationChangeEvent
getOldString() - Method in class apollo.editor.Transaction
getOldString() - Method in interface apollo.editor.UpdateDetailsI
getOldSubpartValue() - Method in class apollo.editor.Transaction: Get the previous value.
getOneLevelAnnotTypes() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Get a list of annotation types that are saved in the Chado database as one-level features.
getOneLevelResultPrograms() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: for simple results that are only 1 level deep
getOperation() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getOperation() - Method in class apollo.dataadapter.chado.ChadoTransaction
getOperation(String) - Static method in class apollo.dataadapter.chado.ChadoTransaction.Operation
getOperation() - Method in class apollo.dataadapter.chado.ChadoUpdateTransaction
getOperation() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getOperation() - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI
getOperation() - Method in class apollo.editor.FeatureChangeEvent
getOperation() - Method in class apollo.editor.Transaction
getOperationAsString() - Method in class apollo.editor.AnnotationAddEvent
getOperationAsString() - Method in class apollo.editor.AnnotationDeleteEvent
getOperationAsString() - Method in class apollo.editor.AnnotationUpdateEvent
getOperationAsString() - Method in class apollo.editor.FeatureChangeEvent
getOperationString() - Method in class apollo.editor.AddTransaction
getOperationString() - Method in class apollo.editor.Transaction
getOperationString() - Method in class apollo.editor.UpdateTransaction
getOpposite() - Method in enum apollo.gui.detailviewers.sequencealigner.Orientation
getOpposite() - Method in enum apollo.gui.detailviewers.sequencealigner.Strand
getOptionPanelToShow() - Method in class apollo.dataadapter.ensj.model.OptionsModel
getOptionsModel() - Method in class apollo.dataadapter.ensj.model.Model
getOrganism() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getOrganism() - Method in class apollo.dataadapter.ensj19.EnsJAdapter: An ugly hack to tease the organism name from the database name Ignore it if this doesn't parse out
getOrganism() - Method in class apollo.dataadapter.genbank.GenbankReport
getOrganism() - Method in class apollo.dataadapter.genbank.GenbankValidator
getOrganism() - Method in class apollo.datamodel.AbstractSequence
getOrganism() - Method in class apollo.datamodel.GenomicRange
getOrganism() - Method in interface apollo.datamodel.SequenceI
getOrganism() - Method in class apollo.util.FastaHeader
getOrganismLabel() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel: A label that's stamped with a curation set's organism name and range whenever I'm informed of a new curation set.
getOrganismLike() - Method in class apollo.dataadapter.chado.ChadoDatabase
getOrientation() - Method in interface apollo.dataadapter.das.DASFeature
getOrientation() - Method in interface apollo.dataadapter.das.DASSegment
getOrientation() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getOrientation() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getOrientation() - Method in class apollo.datamodel.SyntenyRegion
getOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.PanelFactory
getOrientation() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getOrientation() - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getOriginalStackTrace() - Method in exception apollo.dataadapter.exception.BopException
getOriginPosition() - Method in class apollo.gui.genomemap.DragView
getOriginPosition() - Method in interface apollo.gui.genomemap.DragViewI
getOriginView() - Method in class apollo.gui.genomemap.DragView
getOriginView() - Method in interface apollo.gui.genomemap.DragViewI
getOutlineColor() - Static method in class apollo.config.Config
getOutlineColor() - Method in class apollo.config.Style: Edgematch color is also used for generic outlines around features
getOutlineColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getOutlineColor() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer: Checks if selected or selected refs feature is the feature set at current pos, so an exon as well as a transcript will have an outline color
getOutlineColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getOutlineColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
getOutlineColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getOutlineColor() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer: Checks if selected or selected refs feature is the feature set at current pos, so an exon as well as a transcript will have an outline color
getOutlineType() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getOutlineType() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer: Checks if selected or selected refs feature is the current feature set, so an exon as well as a transcript will have an outline type
getOutlineType() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getOutlineType() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
getOutlineType() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getOutlineType() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer: Checks if selected or selected refs feature is the current feature set, so an exon as well as a transcript will have an outline type
getOutputFileHistory() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getOutputStream() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
getOutputStream() - Method in class apollo.dataadapter.otter.OtterAdapter
getOutputStream() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getOverlapDefinition() - Method in class apollo.config.Style
getOverlapper(SeqFeatureI) - Static method in class apollo.config.Config
getOverlapper() - Method in class apollo.config.FeatureProperty
getOverview() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getOverview() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getOverview() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the overview object for the panel
getOwner() - Method in class apollo.datamodel.AnnotatedFeature
getOwner() - Method in interface apollo.datamodel.AnnotatedFeatureI: Get owner of annotation.
getOwner() - Method in class apollo.datamodel.Synonym
getOwnerId() - Method in class apollo.datamodel.Synonym
getPadLeftURLField() - Method in class apollo.config.Style: Field in url to replace with padding int
getPadRightURLField() - Method in class apollo.config.Style
getPanel() - Method in class apollo.dataadapter.GuiTabPanel
getPanel() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame
getPanel(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getPanel() - Method in class apollo.gui.GenericFileAdapterGUI
getPanels() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getPanels() - Method in class apollo.gui.synteny.SyntenyPanel
getParameter(String) - Method in class apollo.config.Style: Returns the last value (even if there are many)
getParameterMulti(String) - Method in class apollo.config.Style: Returns the whole vector of values for this parameter
getParameters() - Method in class apollo.config.Style: Returns hash with only one string for each key.
getParametersMulti() - Method in class apollo.config.Style: Returns hash of Parameter vectors.
getParent() - Method in class apollo.analysis.filter.HuffNode
getParent() - Method in class apollo.datamodel.SeqFeature: Returns refFeature as FeatureSetI which I believe it is always the case that the refFeature is a FeatureSetI
getParent() - Method in interface apollo.datamodel.SeqFeatureI: Returns refFeature as FeatureSetI which I believe it is always the case that the refFeature is a FeatureSetI
getParentException() - Method in exception apollo.dataadapter.ApolloAdapterException
getParentFeature() - Method in class apollo.editor.AnnotationChangeEvent
getParentFeature() - Method in class apollo.editor.FeatureChangeEvent
getParentFeature() - Method in class apollo.editor.Transaction
getParentFeatureClone() - Method in class apollo.editor.Transaction
getParentFile(File) - Static method in class apollo.config.Config
getParents() - Method in class apollo.util.FeatureList: Returns unique list of parents
getParentTransaction() - Method in class apollo.editor.Transaction: If this is a child of a compound transactions, return compound transaction parent return null if have no parent.
getParser() - Method in class apollo.dataadapter.analysis.AnalysisPanel
getPartOfCvTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: return string for "part_of" relationship (tigr part_of, fb partof)
getPass() - Method in class apollo.dataadapter.mysql.Database
getPass() - Method in class apollo.dataadapter.mysql.MySQLInstance
getPassword() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getPassword() - Method in class apollo.dataadapter.chado.ChadoDatabase
getPassword() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getPath() - Method in class apollo.dataadapter.mysql.Database
getPathListWidth() - Method in class apollo.gui.GenericFileAdapterGUI
getPeptide(String) - Method in class apollo.dataadapter.genbank.PeptideNote
getPeptideId() - Method in class apollo.dataadapter.genbank.PeptideNote
getPeptidePosForGenomicPos(int) - Method in class apollo.datamodel.FeatureSet
getPeptideSequence() - Method in class apollo.datamodel.Protein: transcripts peptide sequence should be moved here eventually
getPeptideSequence() - Method in class apollo.datamodel.SeqFeature: If SeqFeatureI has a peptide sequence returns it, otherwise returns null.
getPeptideSequence() - Method in interface apollo.datamodel.SeqFeatureI: If SeqFeatureI.hasPeptideSequence()==true returns pep seq, otherwise returns null
getPeptideSequence() - Method in class apollo.datamodel.Transcript: creates peptide sequence if dont have one && prot coding gene - also if pep is invalid retranslates
getPeptideStates() - Static method in class apollo.config.Config
getPeptideStatus(String) - Static method in class apollo.config.Config
getPeptideSuffixRoot() - Method in class apollo.config.FlyNameAdapter: returns "-P", The peptide suffix minus the ordinal
getPeptideSuffixRoot() - Method in class apollo.config.GmodNameAdapter: The root of the suffix is the non changing part of the suffix - the suffix\ minus the ordinal.
getPeptideValidity() - Method in class apollo.datamodel.Transcript
getPercentIdentity() - Method in class apollo.datamodel.Link
getPerson() - Method in class apollo.datamodel.Comment
getPFetchServer() - Static method in class apollo.config.Config
getPhase() - Method in interface apollo.dataadapter.das.DASFeature
getPhase() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getPhase() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the feature phase
getPhase() - Method in class apollo.datamodel.SeqFeature
getPhase() - Method in interface apollo.datamodel.SeqFeatureI: Phase is the internal offset from feature start for translation.
getPhase(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getPickViewFocus() - Method in class apollo.gui.genomemap.ApolloPanel: If focus is a pick focus, returns the PickViewI
getPickViews(Rectangle) - Method in class apollo.gui.genomemap.ApolloPanel: find pick views which are at least partly within a specified rectangle
getPixelBounds() - Method in class apollo.gui.Transformer
getPixelForPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getPixelForPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: Gets a pixel in the tier panel for a given (pixel) position in the tier panel
getPixelForPosition(int) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getPixelHigh() - Method in class apollo.gui.genomemap.FeatureTier
getPixelLocForColAndRow(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getPixelLocForColAndRow(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getPixelLocForPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getPixelLocForPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: The pixel coordinates for the position at a particular tier
getPKeyCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getPlength() - Method in class apollo.datamodel.Chromosome
getPlotColour() - Method in class apollo.gui.genomemap.GraphView
getPolypeptideCdsRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPolypeptideTransRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPolypeptideTransRelationTerm() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getPolypeptideType() - Method in class apollo.dataadapter.chado.ChadoTransactionTransformer
getPolypeptideType() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Old SO/SOFA uses "protein", new uses "polypeptide" (default)
getPopup() - Method in class apollo.dataadapter.ensj.view.UpdateWorkRoundComboBox
getPort() - Method in class apollo.dataadapter.CGI
getPort() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getPort() - Method in class apollo.dataadapter.mysql.Database
getPort() - Method in class apollo.dataadapter.mysql.MySQLInstance
getPos() - Method in class apollo.gui.detailviewers.sequencealigner.ResultMouseListener: Gets the current (pixel) position
getPosition() - Method in class apollo.datamodel.SequenceEdit
getPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Translates a base pair coordinate into a position on the tier
getPosition(int) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getPositionForPixel(Point) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getPositionForPixel(Point) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: Gets the (pixel) position in the tierPanel for a given pixel
getPositionForPixel(Point) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getPositionFrom(int, int) - Method in class apollo.datamodel.FeatureSet
getPositionFrom(int, int) - Method in interface apollo.datamodel.FeatureSetI
getPositions(String) - Method in class apollo.analysis.HashDB
getPosRectangleForPixels(Rectangle) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: Converts a pixel rectangle to a pos(row/col) rectangle
getPosRectangleForPixels(Rectangle) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Converts a pixel rectangle to a pos(row/col) rectangle
getPreambleString() - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
getPrecedence() - Method in class apollo.config.PeptideStatus
getPredictedCdsSql(FeatureLocImplementation, ChadoProgram[]) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: A variant of getCdsSql that returns an SQL query that only fetches a CDS feature if it was predicted by one of the programs in chadoPrgs for which isRetrieveCDS() is true.
getPredictedCdsSql(FeatureLocImplementation, ChadoProgram[]) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance: Returns only the cds linked to a transcript predicted by a program of chadoPrgs which isRetrieveCDS is true
getPredictedCdsSql(FeatureLocImplementation, ChadoProgram[]) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance: Returns only the cds linked to a transcript predicted by a program of chadoPrgs which isRetrieveCDS is true
getPredictedCdsSql(FeatureLocImplementation, ChadoProgram[]) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getPredictionTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getPreferredFrameHeight() - Method in class apollo.gui.ApolloFrame
getPreferredScrollableViewportSize() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getPreferredScrollableViewportSize() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel: These Are the methods needed to implement the Scrollable interface.
getPreferredScrollableViewportSize() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getPreferredScrollableViewportSize() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: These Are the methods needed to implement the Scrollable interface.
getPreferredScrollableViewportSize() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader: These Are the methods needed to implement the Scrollable interface.
getPreferredSize() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI: Need a height of 200 to accomodate different UI's for each db.
getPreferredSize() - Method in class apollo.gui.evidencepanel.EvidencePanelContainer
getPreferredSize() - Method in class apollo.gui.genomemap.ApolloPanel
getPreferredSize() - Method in class apollo.gui.genomemap.FeatureView: This only sets the height to a sensible value.
getPreferredSize() - Method in class apollo.gui.genomemap.LinearView
getPreferredSize() - Method in class apollo.gui.genomemap.ScrollAdjustedView
getPreferredSize() - Method in class apollo.gui.genomemap.SiteView
getPreferredSize() - Method in interface apollo.gui.genomemap.ViewI: Get the preferred size for the view
getPreferredSize() - Method in class apollo.gui.synteny.SyntenyPanel
getPreferredWidth() - Method in class apollo.config.ColumnProperty
getPrefix(String) - Method in class apollo.config.FlyNameAdapter: Given a format string (e.g.
getPrefix(String) - Method in class apollo.config.GmodNameAdapter: Given a format string (e.g.
getPrefix() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel: Prefix is used to 'namespace' a group of settings.
getPrefixedProperties(Properties, String) - Static method in class apollo.dataadapter.ensj.EnsJAdapterUtil
getPrefixedProperties() - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel: Return properties from all choosers, prefixing each with its key
getPrefixedProperties(Properties, String, boolean) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI: Construct a vector containing all the values of properties with a key that begins with _prefix_.
getPrettyNameForProperty(Integer) - Static method in class apollo.gui.DetailInfo
getPrettyNameForString(String) - Static method in class apollo.gui.DetailInfo
getPrettyNamesFromStrings(Vector) - Static method in class apollo.gui.DetailInfo
getPrevFeature(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel: Given a pixel position return the previous feature
getPrevFeature(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.Tier: gets the next feature in the 5' direction
getPrevFeature(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getPrevFeature(int, TierI.Level) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel: Given a pixel position return the previous feature on the tier
getPrevFeature(int, TierI.Level) - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getPrimaryColor() - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent
getPrimaryDbXref() - Method in class apollo.datamodel.SeqFeature: Return the DbXref, if any, that has isPrimary==true
getPrimaryKeyColumn(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Returns the name of the (single) primary key column for a chado table.
getPrimaryKeyColumnMapping() - Static method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getPrimer3End() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions: Get the reverse primer end genomic coordinate.
getPrimer3endSpecificityMismatch() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimer3Start() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions: Get the reverse primer start genomic coordinate.
getPrimer5End() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions: Get the forward primer end genomic coordinate.
getPrimer5Start() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions: Get the forward primer start genomic coordinate.
getPrimerLeftInput() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerMaxDiffTm() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerMaxTm() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerMinTm() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerNumReturn() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerOptTm() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerProductMax() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerProductMin() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerRightInput() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrimerSpecificityDatabase() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getPrintStream() - Method in class apollo.dataadapter.genbank.GenbankReport
getProblematicColor() - Method in class apollo.config.FeatureProperty
getProductSizeDeviation() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getProgram() - Method in class apollo.bop.JobOutput
getProgram() - Method in class apollo.dataadapter.analysis.AbstractParser
getProgram() - Method in class apollo.dataadapter.analysis.BlastParser
getProgram() - Method in class apollo.dataadapter.analysis.BlatParser
getProgram() - Method in class apollo.dataadapter.analysis.GeneFinderParser
getProgram() - Method in class apollo.dataadapter.analysis.RpMaskerParser
getProgram() - Method in class apollo.dataadapter.analysis.Sim4Parser
getProgram() - Method in class apollo.dataadapter.analysis.tRNA_Parser
getProgram() - Method in class apollo.dataadapter.chado.jdbc.ChadoProgram
getProgramDirectory() - Method in class apollo.analysis.SeqAnalysisLocal
getProgramHandler(SeqAnalysisI) - Method in class apollo.analysis.ProgramHandlerFactory
getProgramName() - Method in class apollo.analysis.SeqAnalysisBase
getProgramName() - Method in interface apollo.analysis.SeqAnalysisI
getProgramName() - Method in class apollo.datamodel.FeaturePair
getProgramName() - Method in class apollo.datamodel.SeqFeature
getProgramName() - Method in interface apollo.datamodel.SeqFeatureI
getProgramParams() - Method in class apollo.analysis.SeqAnalysisBase
getProgramPath() - Method in class apollo.analysis.SeqAnalysisLocal: programPath = programDirectory / programName
getProgramShellCommand() - Method in class apollo.analysis.SeqAnalysisLocal: programShellCommand = programPath programArgs
getProgramversion() - Method in class apollo.dataadapter.chado.jdbc.ChadoProgram
getProjectName(String) - Static method in class apollo.config.Config
getProjectName(String) - Method in class apollo.config.Style
getProperties() - Method in class apollo.analysis.filter.BlastFilterPanel: add on the hit-information to the query-information already in there.
getProperties() - Method in class apollo.analysis.filter.FilterPanel
getProperties() - Method in interface apollo.analysis.filter.FilterPanelI
getProperties() - Method in class apollo.analysis.filter.GenscanFilterPanel: add on the hit-information to the query-information already in there.
getProperties() - Method in class apollo.analysis.filter.NoFilterPanel: add on the hit-information to the query-information already in there.
getProperties() - Method in class apollo.analysis.filter.Sim4FilterPanel: add on the hit-information to the query-information already in there.
getProperties() - Method in class apollo.analysis.SeqAnalysisBase
getProperties() - Method in class apollo.analysis.SeqAnalysisGUI
getProperties() - Method in interface apollo.analysis.SeqAnalysisI: all set properties (should this be public????)
getProperties() - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI: Retrieve history and return in Properties.
getProperties() - Method in class apollo.dataadapter.analysis.AnalysisPanel: Puts the size of history and all the history items into Properties prop
getProperties() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getProperties() - Method in class apollo.dataadapter.chado.ChadoTransaction
getProperties() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI: This must run after the server successfully finishes the doOperation() method - i.e.
getProperties() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI: This must run after the server successfully finishes the doOperation() method - i.e.
getProperties() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getProperties() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI: Create the property list which is written to the history file
getProperties() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI: This method is run to capture the state of the GUI.
getProperties() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel: Returns the properties described in setProperties().
getProperties() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getProperties() - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI: Retrieve history and return in Properties.
getProperties() - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI: Retrieve history and return in Properties.
getProperties() - Method in class apollo.dataadapter.GbrowseAdapterGUI
getProperties() - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI: Retrieve history and return in Properties.
getProperties() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI: Returns Properties with history items of all the files in filePaths Vector, puts currently selected path at front of list
getProperties() - Method in class apollo.dataadapter.GFFAdapterGUI: Returns Properties with history items of all the files in filePaths Vector, puts currently selected path at front of list
getProperties() - Method in class apollo.dataadapter.otter.OtterAdapterGUI
getProperties() - Method in class apollo.dataadapter.sample.SampleAdapterGUI
getProperties() - Method in class apollo.dataadapter.synteny.builder.AdapterModel
getProperties() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
getProperties() - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI: Gather properties for each child adapter - prefix each gathered property with the name of the species (so, "myProp" -> "Homo_sapiens:myProp") and then glue all child Properties into one big Properties.
getProperties() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI: Returns the state of the database config panel, pretty much.
getProperties() - Method in class apollo.datamodel.FeaturePair
getProperties() - Method in class apollo.datamodel.seq.GenbankSequence
getProperties() - Method in class apollo.datamodel.SeqFeature
getProperties() - Method in interface apollo.datamodel.SeqFeatureI
getProperties() - Method in class apollo.datamodel.Synonym
getProperties() - Method in class apollo.gui.GenericFileAdapterGUI: Returns Properties with history items of all the files in filePaths Vector, puts currently selected path at front of list
getPropertiesMulti() - Method in class apollo.datamodel.SeqFeature
getPropertiesMulti() - Method in interface apollo.datamodel.SeqFeatureI
getPropertiesMulti() - Method in class apollo.datamodel.Synonym
getProperty(String) - Method in class apollo.analysis.SeqAnalysisBase
getProperty(String) - Method in interface apollo.analysis.SeqAnalysisI: get the value of a property
getProperty(String) - Method in class apollo.dataadapter.synteny.builder.AdapterModel
getProperty(String) - Method in class apollo.datamodel.FeaturePair
getProperty(String) - Method in class apollo.datamodel.seq.GenbankSequence
getProperty(String) - Method in class apollo.datamodel.SeqFeature
getProperty(String) - Method in interface apollo.datamodel.SeqFeatureI
getProperty(String) - Method in class apollo.datamodel.Synonym
getProperty(String, int) - Method in class apollo.editor.Transaction: Return a single property for name.
getProperty() - Method in class apollo.gui.FeaturePropertyPanel
getProperty() - Method in class apollo.gui.PropertyPanel
getPropertyDescription(String) - Method in class apollo.analysis.SeqAnalysisBase
getPropertyDescription(String) - Method in interface apollo.analysis.SeqAnalysisI: get the description of a property; this gives metadata to the GUI/front end
getPropertyForFeature(String, SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getPropertyForString(String) - Static method in class apollo.gui.DetailInfo
getPropertyList() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getPropertyMulti(String) - Method in class apollo.datamodel.SeqFeature
getPropertyMulti(String) - Method in interface apollo.datamodel.SeqFeatureI
getPropertyMulti(String) - Method in class apollo.datamodel.Synonym
getPropertyScheme() - Static method in class apollo.config.Config: When multi-curations have multi-propSchemes this method will become pase.
getPropertyScheme() - Method in class apollo.config.PropSchemeChangeEvent
getPropertyScheme() - Method in class apollo.config.Style
getPropertyScheme() - Method in class apollo.dataadapter.CurationState
getPropertyScheme() - Method in class apollo.gui.synteny.GuiCurationState
getPropertyType(String) - Method in class apollo.analysis.SeqAnalysisBase
getPropertyType(String) - Method in interface apollo.analysis.SeqAnalysisI: get the type of a property (optional).
getPropertyType(SeqFeatureI) - Static method in class apollo.gui.DetailInfo: Changed return from Object to String since FeatureProperty.getDisplayType is a String - rename this getVisualType?
getPropertyTypeCVName() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPropertyValueWithPrefix(Properties, String, String) - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI
getProteinAnnotationCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getProteinDesc(AnnotatedFeatureI, Transcript) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
getProteinFeat() - Method in class apollo.datamodel.SeqFeature
getProteinFeat() - Method in interface apollo.datamodel.SeqFeatureI: getProteinFeature().getReferenceSequence() should replace getPeptideSeq()
getProteinFeat() - Method in class apollo.datamodel.Transcript: first cut - eventually grow into full fledged protein feat that has a pep seq - which will replace Transcripts peptide Seq probably will require a Protein class.
getPublicDbList() - Static method in class apollo.config.Config
getPublicName(SeqFeatureI) - Method in class apollo.config.DefaultDisplayPrefs
getPublicName(SeqFeatureI) - Method in interface apollo.config.DisplayPrefsI
getPureJDBCCopyOnWrite() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPureJDBCNoCommit() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPureJDBCUseCDS() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPureJDBCWriteMode() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getPValCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getQlength() - Method in class apollo.datamodel.Chromosome
getQueryFeature() - Method in class apollo.datamodel.FeaturePair
getQueryFeature() - Method in interface apollo.datamodel.FeaturePairI
getQueryFeatureIdWithName() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getQueryFeatureIdWithUniquename() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getQueryField() - Method in class apollo.dataadapter.URLDiagnosticTool
getQuerySequence() - Method in class apollo.bop.JobOutput
getQuerySpecies() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getQueryStableId() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getRange() - Method in class apollo.datamodel.AbstractSequence
getRange() - Method in class apollo.datamodel.seq.AbstractLazySequence: CacheSequenceLoader requires a Range - getRange will set one up from 1 to length if there has not been a range set yet - should this go in AbstractSeq?
getRange() - Method in class apollo.datamodel.seq.PFetchSequence
getRange() - Method in interface apollo.datamodel.SequenceI
getRangeAtPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRangeAtPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRangeClone() - Method in class apollo.datamodel.Range: returns clone of self
getRangeClone() - Method in interface apollo.datamodel.RangeI: Returns clone of self
getRangeEnd() - Method in class apollo.gui.event.BaseFocusEvent
getRangeIndex(int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRangeIndex(int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRangeLimits() - Method in class apollo.gui.event.BaseFocusEvent
getRangeOfWholeList() - Method in class apollo.util.FeatureList: Assumes feats on same strand
getRangeStart() - Method in class apollo.gui.event.BaseFocusEvent
getRangeUrl() - Static method in class apollo.config.Config
getRangeUrl() - Method in class apollo.config.Style
getRank() - Method in class apollo.editor.Transaction
getRawAnalysisResults(String) - Method in class apollo.dataadapter.AbstractApolloAdapter
getRawAnalysisResults(String) - Method in interface apollo.dataadapter.ApolloDataAdapterI
getRawAnalysisResults(String) - Method in class apollo.dataadapter.BaseGFFAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.chado.ChadoAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.das2.DAS2Adapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.EnsCGIAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.GbrowseAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.otter.OtterAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getRawAnalysisResults(String) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getRawOutput() - Method in class apollo.bop.JobOutput
getRawResultHashtable() - Method in class apollo.analysis.SeqAnalysisBase
getRawResultHashtable() - Method in interface apollo.analysis.SeqAnalysisI
getRawResultVector() - Method in class apollo.analysis.SeqAnalysisBase
getRawResultVector() - Method in interface apollo.analysis.SeqAnalysisI: all the raw results - usually Vector of main output and error (if any) as Strings these Strings should *NOT* be parsed; it is up to the SeqAnalysisI implementation object to do any parsing and return the results as a CurationSet or similar object
getRawResultVector() - Method in class apollo.analysis.SeqAnalysisLocal
getReadingFrame() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getReadingFrame() - Method in class apollo.gui.detailviewers.sequencealigner.PanelFactory
getReadingFrame() - Method in class apollo.gui.detailviewers.sequencealigner.Tier
getReadingFrame() - Method in class apollo.gui.detailviewers.sequencealigner.TierFactory
getReadingFrame() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getRealException(ApolloAdapterException) - Static method in exception apollo.dataadapter.ApolloAdapterException
getRealException(InvocationTargetException) - Static method in exception apollo.dataadapter.ApolloAdapterException
getRecentDate() - Method in class apollo.config.FeatureProperty
getRecognisedPrograms() - Method in class apollo.analysis.ProgramHandlerFactory
getRectangleForCharPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRectangleForCharPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRectangleForTierPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRectangleForTierPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRefDrawable() - Method in interface apollo.gui.drawable.Drawable
getRefDrawable() - Method in class apollo.gui.drawable.DrawableSeqFeature
getReference() - Method in class apollo.dataadapter.genbank.GenbankReport
getReference() - Method in class apollo.dataadapter.genbank.PeptideNote
getReference(Strand) - Method in class apollo.gui.detailviewers.sequencealigner.ReferenceFactory
getReference(Strand, ReadingFrame) - Method in class apollo.gui.detailviewers.sequencealigner.ReferenceFactory
getReference(Strand) - Method in interface apollo.gui.detailviewers.sequencealigner.ReferenceFactoryI
getReference(Strand, ReadingFrame) - Method in interface apollo.gui.detailviewers.sequencealigner.ReferenceFactoryI
getReference() - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Returns the sequence which is used as a reference for this tier.
getReference() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getReferenceId() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the reference sequence ID
getReferenceNumber() - Method in class apollo.dataadapter.genbank.PeptideNote
getReferencePanel() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getReferencePanel() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getReferencePanel() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the reference panel (the one in between the annotation and result)
getReferenceSequence() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getReferenceSequence() - Method in class apollo.dataadapter.GbrowseAdapter
getReferenceSequence(Strand, ReadingFrame) - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getReferenceSequence(Strand, ReadingFrame) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getReferenceSequence(Strand, ReadingFrame) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Creates a Sequence object which can be used as a reference for the given strand/frame pair
getReferenceSequence() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getReferencingRowIds(String, String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: TODO - this is actually a generic method; all it's doing is evaluating a single equijoin (modulo quoting) and returning the row ids
getRefFeature() - Method in class apollo.datamodel.FeaturePair
getRefFeature() - Method in class apollo.datamodel.SeqFeature
getRefFeature(String) - Method in class apollo.datamodel.SeqFeature
getRefFeature() - Method in interface apollo.datamodel.SeqFeatureI: Retrieve the parent SeqFeatureI for this SeqFeatureI, or null if it is a tree root.
getRefId() - Method in class apollo.datamodel.FeaturePair
getRefId() - Method in class apollo.datamodel.SeqFeature
getRefId() - Method in interface apollo.datamodel.SeqFeatureI
getRefreshPeptides() - Static method in class apollo.config.Config
getRefSequence() - Method in class apollo.datamodel.FeaturePair
getRefSequence() - Method in class apollo.datamodel.Protein
getRefSequence() - Method in class apollo.datamodel.Range
getRefSequence() - Method in interface apollo.datamodel.RangeI: Retrieve the SequenceI that this feature annotates.
getRefSequence() - Method in class apollo.datamodel.SequenceEdit
getRefSequence() - Method in class apollo.gui.tweeker.RestrictionEnzyme
getRegion() - Method in class apollo.dataadapter.DataInput
getRegion() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getRegion() - Method in class apollo.dataadapter.GbrowseAdapter
getRegionEnd() - Method in interface apollo.gui.detailviewers.sequencealigner.RegionSelectableI
getRegionEnd() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getRegionHigh() - Method in interface apollo.gui.detailviewers.sequencealigner.RegionSelectableI
getRegionHigh() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getRegionLow() - Method in interface apollo.gui.detailviewers.sequencealigner.RegionSelectableI
getRegionLow() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getRegionStart() - Method in interface apollo.gui.detailviewers.sequencealigner.RegionSelectableI
getRegionStart() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getRelatedFeatureIds(Long, boolean, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getRelatedFeatureRank(Long, Long, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getRelationshipCVName() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getRelationshipCVTermId(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getRemarks() - Method in class apollo.datamodel.AssemblyFeature
getRenderer() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getRenderer() - Method in class apollo.gui.detailviewers.sequencealigner.PanelFactory
getRenderer() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getRenderer() - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getRendererAt(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRendererAt(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRepeatCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getReplacedFeature() - Method in class apollo.editor.FeatureChangeEvent: Returns feature replaced for replace event.
getResidue() - Method in class apollo.datamodel.SequenceEdit
getResidues() - Method in class apollo.datamodel.AbstractSequence
getResidues(int, int) - Method in class apollo.datamodel.AbstractSequence: returns substring of sequence residues, all of this apollo stuff is counting from 1 -not- 0
getResidues() - Method in class apollo.datamodel.FeaturePair
getResidues() - Method in class apollo.datamodel.Range
getResidues() - Method in interface apollo.datamodel.RangeI
getResidues(int, int) - Method in class apollo.datamodel.seq.CacheSeqIdLoader
getResidues(int, int) - Method in class apollo.datamodel.seq.CacheSequenceLoader
getResidues() - Method in class apollo.datamodel.Sequence
getResidues() - Method in interface apollo.datamodel.SequenceI
getResidues(int, int) - Method in interface apollo.datamodel.SequenceI
getResidues() - Method in class apollo.editor.AddTransaction: Seq errors insertion & substition include residues that need to be inserted with feature
getResiduesFromSource(int, int) - Method in class apollo.datamodel.seq.AbstractLazySequence
getResiduesFromSource(int, int) - Method in class apollo.datamodel.seq.GAMESequence
getResiduesFromSource(int, int) - Method in interface apollo.datamodel.seq.LazySequenceI
getResiduesFromSourceImpl(int, int) - Method in class apollo.dataadapter.das.DASLazySequence: Returns the sequence string
getResiduesFromSourceImpl(int, int) - Method in class apollo.dataadapter.ensj.AlternateEnsJSequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.dataadapter.ensj19.AlternateEnsJSequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.dataadapter.ensj19.EnsJSequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.AbstractLazySequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.DebugLazySequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.EnsCGISequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.GAMESequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.PFetchSequence
getResiduesFromSourceImpl(int, int) - Method in class apollo.datamodel.seq.SRSSequence
getResiduesImpl(int, int) - Method in class apollo.datamodel.AbstractSequence
getResiduesImpl(int) - Method in class apollo.datamodel.AbstractSequence
getResiduesImpl(int, int) - Method in class apollo.datamodel.seq.AbstractLazySequence
getResiduesImpl(int) - Method in class apollo.datamodel.seq.AbstractLazySequence
getResiduesImpl(int, int) - Method in class apollo.datamodel.seq.GenbankSequence
getResiduesImpl(int, int) - Method in class apollo.datamodel.Sequence: this does a plus one to the end which i assume is to be inclucsive, the only problem i think is AbstractSequence.getResudes calls pegLimits which sutracts one from start to convert from one based to zero based, but one is not subtracted from the end which i think is also an act of inclusivity.
getResiduesImpl(int) - Method in class apollo.datamodel.Sequence
getResidueType() - Method in class apollo.datamodel.AbstractSequence: Returns null if never set.
getResidueType() - Method in interface apollo.datamodel.SequenceI
getResponseField() - Method in class apollo.dataadapter.URLDiagnosticTool
getRestrictionEnzyme() - Method in class apollo.gui.tweeker.CutSite
getResultComparator() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getResultComparator() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getResultComparator() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the comparator used to order results
getResultFilter() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getResultFilter() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getResultFilter() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the filter used to decide which results to display
getResultHeader() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getResultHeader() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getResultHeader() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the header for the result panel
getResultPanel() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getResultPanel() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getResultPanel() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the Result Panel
getResults() - Method in class apollo.datamodel.CurationSet
getResults() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getResults() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getResults() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the list of results.
getResults(String, SeqFeatureI) - Static method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets all the results from a particular feature set Don't think this is used...
getResults(SeqFeatureI, Filter) - Static method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets all the results from a particular feature set that pass the filter
getResults() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getResultStrandedFeatSet() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getResultTag(String) - Method in class apollo.config.Style
getResultTags() - Method in class apollo.config.Style
getResultView() - Method in class apollo.gui.genomemap.AnnotationView
getResultView() - Method in class apollo.gui.genomemap.SiteView
getReturnBuffer() - Method in class apollo.dataadapter.otter.parser.OtterXMLRenderingVisitor
getReturnButton() - Method in class apollo.dataadapter.URLDiagnosticTool
getReturnedObjects() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getRevCompListener() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getReverseAnnotations() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getReverseComplement() - Method in class apollo.datamodel.AbstractSequence
getReverseComplement() - Method in interface apollo.datamodel.SequenceI
getReverseResults() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getReverseSet() - Method in class apollo.datamodel.StrandedFeatureSet
getReverseSet() - Method in interface apollo.datamodel.StrandedFeatureSetI
getReverseSort() - Method in class apollo.config.FeatureProperty
getReverseSort() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getReverseStrand() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getReverseStrand() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRight(Transformer) - Method in interface apollo.gui.drawable.Drawable
getRight(Transformer) - Method in class apollo.gui.drawable.DrawableSeqFeature
getRightOverlap(RangeI) - Method in class apollo.datamodel.Range
getRightOverlap(RangeI) - Method in interface apollo.datamodel.RangeI
getRightView() - Method in class apollo.gui.genomemap.SplitterView
getRootDir() - Static method in class apollo.config.Config
getRootDir() - Static method in class apollo.util.IOUtil: Apollo root directory is defined by system property APOLLO_ROOT; if that's not defined, try .
getRootElement() - Method in class apollo.dataadapter.gamexml.XMLParser
getRootEndTag() - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
getRootStartTag() - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
getRow(Vector, SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getRow(int) - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getRowCount() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRowCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRowCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel: For now the only row will be the name
getRowCount() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getRowCount() - Method in class apollo.gui.SeqSelectorTable.SequenceMatchModel
getRowCountForTable(String, Connection) - Method in class apollo.dataadapter.ensj.controller.EventHandler
getRowForPixelPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRowForPixelPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRowForPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRowForPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRowHeight() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRowHeight() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRowMargin() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getRowMargin() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getRowMargin() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getRowMargin() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: FIXME: Returns the row margin property value, whatever that is...
getRowWidth() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getRubberband() - Method in class apollo.gui.genomemap.ApolloPanel: Rubberband related methods
getRunDate() - Method in class apollo.analysis.filter.AnalysisInput
getRunDate() - Method in class apollo.bop.JobOutput
getSaveClonedFeaturesInTransactions() - Static method in class apollo.config.Config
getScaffoldUrl() - Static method in class apollo.config.Config
getScaffoldUrl() - Method in class apollo.config.Style
getScaleView() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getScore() - Method in interface apollo.dataadapter.das.DASFeature
getScore() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getScore() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the feature score
getScore() - Method in class apollo.datamodel.FeaturePair
getScore(String) - Method in class apollo.datamodel.FeaturePair
getScore() - Method in class apollo.datamodel.FeatureSet
getScore() - Method in class apollo.datamodel.SeqFeature
getScore(String) - Method in class apollo.datamodel.SeqFeature
getScore() - Method in interface apollo.datamodel.SeqFeatureI
getScore(String) - Method in interface apollo.datamodel.SeqFeatureI
getScore(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getScoreCalculator() - Method in class apollo.gui.genomemap.GraphView
getScoreForPosition(int) - Method in class apollo.gui.ScoreCalculator: Get the score for a given position
getScoreForPosition(int) - Method in class apollo.gui.StoredScoreCalculator
getScores() - Method in class apollo.datamodel.FeaturePair
getScores() - Method in class apollo.datamodel.SeqFeature
getScores() - Method in interface apollo.datamodel.SeqFeatureI
getScoresForPositions(int[]) - Method in class apollo.gui.GCScoreCalculator
getScoresForPositions(int[]) - Method in class apollo.gui.ScoreCalculator
getScoresForPositions(int[]) - Method in class apollo.gui.StoredScoreCalculator: Get the scores for an array of positions
getScoresString(SeqFeatureI) - Static method in class apollo.dataadapter.debug.DisplayTool
getScoresString(SeqFeatureI) - Static method in class apollo.gui.drawable.DrawableDisplayTool
getScrollableBlockIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getScrollableObject() - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener: Gets the scrollable object that will be affected
getScrollableObject() - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu: Gets the scrollable object for this menu
getScrollableTracksViewportHeight() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getScrollableTracksViewportHeight() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getScrollableTracksViewportHeight() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getScrollableTracksViewportHeight() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getScrollableTracksViewportHeight() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getScrollableTracksViewportWidth() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getScrollableTracksViewportWidth() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getScrollableTracksViewportWidth() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getScrollableTracksViewportWidth() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getScrollableTracksViewportWidth() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getScrollableUnitIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getScrollBar() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getScrollBar() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getScrollBar() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the main horizontal scrollbar for the window
getScrollbarValue() - Method in class apollo.gui.genomemap.TierView
getScrollPane() - Method in class apollo.gui.TypePanel
getSearchHitPrograms() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Set array of strings for all search hit programs.
getSecond() - Method in class apollo.util.Pair: Get the second value
getSegment() - Method in class apollo.dataadapter.das.DASLazySequence
getSegment() - Method in interface apollo.dataadapter.das.DASSegment
getSegment() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getSegments() - Method in class apollo.dataadapter.das.simple.DASEntryPointContentHandler: I return a list of DASSegments.
getSegments() - Method in class apollo.dataadapter.das2.SegmentParser: I return a list of DASSegments.
getSelected(SeqFeatureI) - Method in class apollo.gui.evidencepanel.TablePanel.RowSelectionListener
getSelected() - Method in class apollo.gui.Selection: Vector of SelectionItems
getSelectedAdapterIndex(String) - Method in class apollo.dataadapter.synteny.builder.Model
getSelectedAdapterModel() - Method in class apollo.dataadapter.synteny.builder.Model
getSelectedAdapterSet() - Method in class apollo.dataadapter.synteny.builder.Model
getSelectedChooser() - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
getSelectedChr() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedChr() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedChr() - Method in class apollo.dataadapter.GbrowseAdapterGUI
getSelectedChrStartEnd() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedChrStartEnd() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedChrStartEnd() - Method in class apollo.dataadapter.GbrowseAdapterGUI
getSelectedCloneFragment() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedCoordSystem() - Method in class apollo.dataadapter.ensj.model.LocationModel
getSelectedData() - Method in class apollo.gui.Selection: Returns vector of selection items data of selection (SeqFeatureI's) change this to return FeatureList
getSelectedData(int) - Method in class apollo.gui.Selection: The data of the selection items is a SeqFeatureI, model not drawable
getSelectedDataSet() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getSelectedDitagFeatureTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedDnaDnaAlignTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedDnaProteinAlignTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedDSN() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI: This returns an actual DASDsn - either the source id or the MapMaster attribute will give the URL of the annotated source.
getSelectedDSN() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI: This returns an actual DASDsn - either the source id or the MapMaster attribute will give the URL of the annotated source.
getSelectedEnd() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedEnd() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedEnd() - Method in class apollo.dataadapter.GbrowseAdapterGUI
getSelectedEnsemblDatabase() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSelectedEnsemblDatabase() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel
getSelectedFeature() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getSelectedFeature() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getSelectedFeature() - Method in class apollo.gui.featuretree.FeatureTreePanel
getSelectedFeature(TreePath) - Method in class apollo.gui.featuretree.FeatureTreePanel
getSelectedFile() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getSelectedGeneTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedGFFPath() - Method in class apollo.dataadapter.otter.OtterXMLAdapterGUI
getSelectedHistory() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
getSelectedHistory() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
getSelectedHistoryLocation() - Method in class apollo.dataadapter.ensj.model.LocationModel
getSelectedInputDataSetName() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedInputFileName() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedInputServerName() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedNode() - Method in class apollo.dataadapter.synteny.builder.View
getSelectedNode() - Method in class apollo.gui.featuretree.FeatureTreePanel
getSelectedOutputDataSetName() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedOutputFileName() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedPath() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedPath() - Method in class apollo.gui.GenericFileAdapterGUI
getSelectedPredictionTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedRectangle() - Method in class apollo.gui.genomemap.ScaleView
getSelectedRegion() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedSegment() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
getSelectedSegment() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
getSelectedSeqPath() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI
getSelectedSeqPath() - Method in class apollo.dataadapter.GFFAdapterGUI
getSelectedSeqPath() - Method in class apollo.dataadapter.otter.OtterXMLAdapterGUI
getSelectedSeqRegion() - Method in class apollo.dataadapter.ensj.model.LocationModel
getSelectedSeqType() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getSelectedSequenceEnsemblDatabase() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSelectedServer() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
getSelectedServer() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
getSelectedServerPort() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
getSelectedSetName() - Method in class apollo.dataadapter.synteny.builder.View
getSelectedSimpleFeatureTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSelectedSource() - Method in class apollo.dataadapter.ensj19.SourceChooserWithHistory
getSelectedStableID() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedStart() - Method in class apollo.dataadapter.EnsCGIAdapterGUI
getSelectedStart() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getSelectedStart() - Method in class apollo.dataadapter.GbrowseAdapterGUI
getSelectedTier() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getSelectedTier() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getSelectedTreePath() - Method in class apollo.dataadapter.synteny.builder.View
getSelectedVector() - Method in class apollo.gui.Selection
getSelectedVisualTypes() - Method in class apollo.gui.Selection: Returns a HashSet of Strings that is the unique set of visual types for the selection.
getSelection() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the currently sellected annotation
getSelection() - Method in class apollo.gui.event.FeatureSelectionEvent
getSelection() - Method in class apollo.gui.genomemap.ApolloPanel
getSelection() - Method in interface apollo.gui.genomemap.ApolloPanelI
getSelection() - Method in class apollo.gui.genomemap.DragView
getSelection() - Method in class apollo.gui.SelectionManager
getSelectionBoxColor() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getSelectionBoxColor() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getSelectionColor() - Static method in class apollo.config.Config
getSelectionColor() - Method in class apollo.config.Style
getSelectionDescendedFromModel(SeqFeatureI) - Method in class apollo.gui.Selection: Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model.
getSelectionDescendedFromModel(SeqFeatureI, boolean) - Method in class apollo.gui.Selection: Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model.
getSelectionItem(int) - Method in class apollo.gui.Selection
getSelectionItem(SeqFeatureI) - Method in class apollo.gui.Selection
getSelectionManager() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
getSelectionManager() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
getSelectionManager() - Method in class apollo.gui.evidencepanel.TablePanel
getSelectionManager() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getSelectionManager() - Method in class apollo.gui.synteny.GuiCurationState
getSelectionRectangle(Point) - Method in class apollo.gui.genomemap.LinearView
getSeqAnalysis(Hashtable) - Method in class apollo.analysis.SeqAnalysisFactory
getSeqAnalysisTypes() - Method in class apollo.analysis.SeqAnalysisFactory
getSeqDescriptionCVName() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getSeqDescriptionTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getSeqEditRefFeature(SequenceEdit) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
getSeqErrorColor() - Method in class apollo.config.Style: Return color for showing genomic sequencing errors or frameshifts
getSeqFeat(int, String) - Method in class apollo.datamodel.StrandedFeatureSet: Returns seq feat grandchildren (tier level) of type & strand.
getSeqFeature() - Method in class apollo.editor.Transaction: Get the touched SeqFeatureI object.
getSeqFeatureClone() - Method in class apollo.editor.Transaction: Return a clone of the touched SeqFeatureI object; it should reflect the state of the SeqFeatureI when the transaction actually ocurred.
getSeqFile() - Method in class apollo.analysis.SeqAnalysisLocal: writes input sequence as a fasta file
getSeqFilename() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Get the sequence filename
getSeqGapColor() - Static method in class apollo.config.Config
getSeqGapColor() - Method in class apollo.config.Style
getSeqId() - Method in class apollo.dataadapter.DataInput: So for all input types except BASEPAIR_RANGE/regions the "seqId" is the input string itself.
getSeqId() - Method in class apollo.util.FastaHeader
getSeqLengthForFeatureId(Connection, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve the Chado feature.seqlen for a specified feature.
getSeqRegions() - Method in class apollo.dataadapter.ensj.model.LocationModel
getSeqRegionToLengthsMap() - Method in class apollo.dataadapter.ensj.model.LocationModel
getSeqs() - Method in class apollo.seq.io.FastaFile
getSeqSelectColor() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getSeqSelectColor() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getSeqString() - Method in class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange
getSeqType(int) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return ith SeqType
getSeqType(String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: SeqType for name
getSeqTypesSize() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return number of seq types for instance
getSequence(String) - Method in class apollo.dataadapter.AbstractApolloAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.AbstractApolloAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.AbstractApolloAdapter
getSequence(String) - Method in interface apollo.dataadapter.ApolloDataAdapterI: Strings for input types
getSequence(DbXref) - Method in interface apollo.dataadapter.ApolloDataAdapterI
getSequence(DbXref, int, int) - Method in interface apollo.dataadapter.ApolloDataAdapterI
getSequence(String) - Method in class apollo.dataadapter.BaseGFFAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.BaseGFFAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.BaseGFFAdapter
getSequence() - Method in class apollo.dataadapter.BaseGFFAdapter
getSequence(String) - Method in class apollo.dataadapter.chado.ChadoAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.chado.ChadoAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.chado.ChadoAdapter
getSequence(long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Retrieve a sequence from Chado and convert it into an instance of apollo.dataadapter.Sequence.
getSequence(long, boolean, String, int) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getSequence(String) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter: The dbxref passed into this argument is only checked to make sure that the the IdValue it contains is the same as the Id for the DASSegment that this adapter is poised on.
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getSequence(String) - Method in class apollo.dataadapter.das2.DAS2Adapter
getSequence(DbXref) - Method in class apollo.dataadapter.das2.DAS2Adapter: The dbxref passed into this argument is only checked to make sure that the the IdValue it contains is the same as the Id for the DASSegment that this adapter is poised on.
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.das2.DAS2Adapter
getSequence(String) - Method in class apollo.dataadapter.DummySequenceAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.DummySequenceAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.DummySequenceAdapter
getSequence(String) - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSequence(String) - Method in class apollo.dataadapter.EnsCGIAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.EnsCGIAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.EnsCGIAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.ensj.EnsJAdapter: There is no longer a notion of a 'sequence' database - it is now assumed to come from the standard db (use the BuilderAdapter to stack up results from different db's).
getSequence(DbXref) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter: We will either draw our sequence from the main database, or from another sequence database, if it was passed in.
getSequence(String) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getSequence(String) - Method in class apollo.dataadapter.GbrowseAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.GbrowseAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.GbrowseAdapter
getSequence(String) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSequence(String) - Method in class apollo.dataadapter.otter.OtterAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.otter.OtterAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.otter.OtterAdapter
getSequence(String) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSequence(String) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSequence(DbXref) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSequence(DbXref, int, int) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSequence(String) - Method in class apollo.datamodel.CurationSet
getSequence(CompositeDataHolder) - Method in class apollo.main.DataLoader: This should have the simgle species cdh or cur set passed in
getSequenceColor() - Static method in class apollo.config.Config
getSequenceColor() - Method in class apollo.config.Style
getSequenceCount() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getSequenceCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getSequenceEnsemblDatabaseDropdown() - Method in class apollo.dataadapter.ensj.view.DatabasePanel
getSequenceEnsemblDatabaseLabel() - Method in class apollo.dataadapter.ensj.view.DatabasePanel
getSequenceEnsemblDatabases() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSequenceFilename() - Method in class apollo.dataadapter.BaseGFFAdapter
getSequenceFilename() - Method in class apollo.dataadapter.DataInput
getSequenceForTier(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getSequenceForTier(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getSequenceHost() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSequenceId() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getSequenceList(String, Vector, Vector) - Method in class apollo.dataadapter.chado.ChadoAdapter: Read a list of sequence IDs and descriptions into two parallel Vectors.
getSequenceName(AnnotatedFeatureI, SequenceI, Transcript) - Static method in class apollo.dataadapter.genbank.GenbankAdapter
getSequencePassword() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSequencePort() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSequences(DbXref[]) - Method in class apollo.dataadapter.AbstractApolloAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.AbstractApolloAdapter
getSequences(DbXref[]) - Method in interface apollo.dataadapter.ApolloDataAdapterI
getSequences(DbXref[], int[], int[]) - Method in interface apollo.dataadapter.ApolloDataAdapterI
getSequences(DbXref[]) - Method in class apollo.dataadapter.BaseGFFAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.BaseGFFAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.chado.ChadoAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.chado.ChadoAdapter
getSequences(DASDsn, DASSegment[]) - Method in interface apollo.dataadapter.das.DASServerI
getSequences() - Method in class apollo.dataadapter.das.simple.DASSequenceContentHandler
getSequences(DbXref[]) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getSequences(DASDsn, DASSegment[]) - Method in class apollo.dataadapter.das.simple.SimpleDASServer: I am the call used by apollo to fetch dna (sequence) from the input dsn, for the entry-points and ranges given by the input segments
getSequences(DbXref[]) - Method in class apollo.dataadapter.das2.DAS2Adapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.das2.DAS2Adapter
getSequences(DASDsn, DASSegment[]) - Method in class apollo.dataadapter.das2.DAS2Request: I am the call used by apollo to fetch dna (sequence) from the input dsn, for the entry-points and ranges given by the input segments
getSequences(DbXref[]) - Method in class apollo.dataadapter.DummySequenceAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.DummySequenceAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.EnsCGIAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.EnsCGIAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.GbrowseAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.GbrowseAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.otter.OtterAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.otter.OtterAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSequences(DbXref[]) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSequences() - Method in class apollo.datamodel.CurationSet
getSequenceUser() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getSequencingErrorAtPosition(int) - Method in class apollo.datamodel.AbstractSequence
getSequencingErrorAtPosition(int) - Method in class apollo.datamodel.FeatureSet: any errors in the genomic sequence will apply to all of the transcripts for the gene
getSequencingErrorAtPosition(int) - Method in interface apollo.datamodel.FeatureSetI
getSequencingErrorAtPosition(int) - Method in interface apollo.datamodel.SequenceI
getSeqUrl() - Static method in class apollo.config.Config
getSeqUrl() - Method in class apollo.config.Style
getSeqWrapperForTier(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getSeqWrapperForTier(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getServer() - Method in class apollo.dataadapter.CGI
getServer() - Method in class apollo.dataadapter.das.DASLazySequence
getServer() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getServerPort() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
getSetId() - Method in class apollo.datamodel.Evidence
getShadeByPercId() - Method in class apollo.gui.menus.SyntenyChoiceMenu
getShadeByPercId() - Method in class apollo.gui.synteny.SyntenyLinkPanel
getSharedData() - Method in class apollo.dataadapter.synteny.SyntenyAdapterGUI: Data common to all adapters should have a place to live - this is it.
getShowAnnotations() - Static method in class apollo.config.Config
getShowAnnotations() - Method in class apollo.config.Style
getShowHitZones() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getShowHitZones() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getShowHitZones() - Method in class apollo.gui.detailviewers.sequencealigner.FindDialog
getShowResults() - Static method in class apollo.config.Config
getShowResults() - Method in class apollo.config.Style
getShowSaveAsOptionInFileMenu() - Static method in class apollo.config.Config
getShowSaveOptionInFileMenu() - Static method in class apollo.config.Config
getShowSyntenyEvidencePanels() - Static method in class apollo.config.Config
getSimpleFeatureCount() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSimpleFeatureTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSimpleFeatureTypes() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSimpleOverlap() - Static method in class apollo.config.SimpleOverlap
getSimplePeptideTypeCounts() - Method in class apollo.dataadapter.ensj.model.TypesModel
getSingleSpeciesPanelSize() - Method in class apollo.config.Style
getSingleton() - Static method in class apollo.gui.evidencepanel.EvidencePanelContainer
getSingleton() - Static method in class apollo.gui.evidencepanel.EvidencePanelOrientationManager
getSiteCodon(SeqFeatureI) - Method in class apollo.gui.genomemap.Sites
getSiteCodon(String) - Method in class apollo.gui.genomemap.Sites
getSiteCodon(int, int, String, int, String) - Method in class apollo.gui.genomemap.Sites: low is not start.
getSiteShowLimit() - Static method in class apollo.config.Config
getSiteView() - Method in class apollo.gui.genomemap.AnnotationView
getSiteViewVisibleOnZoom() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel: This does not return whther the sites are actually visible but whether they are capable of being visible.
getSize(Transformer, TierManagerI) - Method in interface apollo.gui.drawable.Drawable
getSize(Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
getSizeByScore() - Method in class apollo.config.FeatureProperty
getSoOboFilename() - Static method in class apollo.config.Config
getSortedKids(SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil
getSortKey() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getSortProperty() - Method in class apollo.config.FeatureProperty
getSoType() - Method in class apollo.dataadapter.DataInput
getSoType() - Method in class apollo.dataadapter.DataInputType
getSource() - Method in class apollo.config.PropSchemeChangeEvent
getSource() - Method in interface apollo.dataadapter.das.DASDsn
getSource() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getSource() - Method in class apollo.dataadapter.genbank.GenbankReport
getSource() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the source for the feature
getSource() - Method in class apollo.editor.FeatureChangeEvent
getSource() - Method in class apollo.gui.event.FeatureSelectionEvent
getSource() - Method in class apollo.gui.event.NamedFeatureSelectionEvent
getSource() - Method in class apollo.gui.event.OrientationEvent
getSource() - Method in class apollo.gui.event.ReverseComplementEvent
getSource() - Method in class apollo.gui.event.RubberbandEvent
getSource() - Method in class apollo.gui.event.ScrollEvent
getSource() - Method in class apollo.gui.event.SetActiveCurStateEvent
getSource() - Method in class apollo.gui.event.TierManagerEvent
getSource() - Method in class apollo.gui.event.ViewEvent
getSource() - Method in class apollo.gui.event.ZoomEvent
getSource() - Method in class apollo.gui.SelectionItem
getSourceActions(JComponent) - Method in class apollo.gui.ArrayListTransferHandler
getSourceHistory() - Method in class apollo.dataadapter.ensj19.SourceChooserWithHistory
getSourceHistoryList() - Method in class apollo.dataadapter.ensj19.SourceChooserWithHistory
getSourceId() - Method in interface apollo.dataadapter.das.DASDsn
getSourceId() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getSourcename() - Method in class apollo.dataadapter.chado.jdbc.ChadoProgram
getSourceVersion() - Method in interface apollo.dataadapter.das.DASDsn
getSourceVersion() - Method in class apollo.dataadapter.das.simple.SimpleDASDsn
getSpecies() - Method in class apollo.dataadapter.AbstractApolloAdapter
getSpecies() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Synteny gives a species to each adapter to help keep track of them
getSpecies(int) - Method in class apollo.datamodel.CompositeDataHolder
getSpecies1() - Method in class apollo.datamodel.LinkSet
getSpecies1() - Method in class apollo.datamodel.SpeciesComparison
getSpecies2() - Method in class apollo.datamodel.LinkSet
getSpecies2() - Method in class apollo.datamodel.SpeciesComparison
getSpeciesAdapter(String) - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSpeciesComparison(int) - Method in class apollo.datamodel.CompositeDataHolder
getSpeciesController(int) - Method in class apollo.gui.MultiController
getSpeciesFeature1() - Method in class apollo.datamodel.Link
getSpeciesFeature2() - Method in class apollo.datamodel.Link
getSpeciesName() - Method in class apollo.datamodel.Chromosome
getSpeciesName() - Method in class apollo.datamodel.Karyotype
getSplashURL(String) - Static method in class apollo.main.Apollo
getSpliceColor(Graphics, int, int, int, String, int, Color) - Method in class apollo.gui.genomemap.ScaleView
getSplicedLength() - Method in class apollo.datamodel.FeatureSet
getSplicedLength(int, int) - Method in class apollo.datamodel.FeatureSet: This needs to be fixed to account for edits to the genomic sequence
getSplicedLength() - Method in interface apollo.datamodel.FeatureSetI
getSplicedTranscript(int, int) - Method in class apollo.datamodel.FeatureSet
getSplitFract() - Method in class apollo.gui.genomemap.SplitterView
getSplitPane() - Method in class apollo.gui.ApolloFrame: Returns split pane between evidence panel(s) and syntenyPanel(szaps), creates one on first call.
getSRSServer() - Static method in class apollo.config.Config
getStableID() - Method in class apollo.dataadapter.ensj.model.LocationModel
getStableId() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getStableIdButton() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getStableIDHistory() - Method in class apollo.dataadapter.ensj.model.LocationModel
getStackObject() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getStackTraceString() - Method in exception apollo.dataadapter.exception.BopException
getStain() - Method in class apollo.datamodel.ChromosomeBand
getStanza(String, int) - Method in class apollo.config.TiersIO
getStart() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getStart() - Method in interface apollo.dataadapter.das.DASFeature
getStart() - Method in interface apollo.dataadapter.das.DASSegment
getStart() - Method in interface apollo.dataadapter.das.DASSequence
getStart() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getStart() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getStart() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getStart() - Method in class apollo.dataadapter.ensj.model.LocationModel
getStart() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the start of the feature on the reference sequence
getStart() - Method in class apollo.dataadapter.Region
getStart() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getStart() - Method in class apollo.datamodel.FeaturePair
getStart() - Method in class apollo.datamodel.Protein
getStart() - Method in class apollo.datamodel.Range
getStart() - Method in interface apollo.datamodel.RangeI
getStart() - Method in class apollo.datamodel.StrandedFeatureSet
getStart(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getStart() - Method in interface apollo.gui.drawable.Drawable: these are for ease of use and pass through to the actual datamodel for the feature
getStart() - Method in class apollo.gui.drawable.DrawableSeqFeature
getStart1() - Method in class apollo.datamodel.SyntenyRegion
getStart2() - Method in class apollo.datamodel.SyntenyRegion
getStartAA() - Method in class apollo.datamodel.FeatureSet
getStartAA() - Method in interface apollo.datamodel.FeatureSetI
getStartAsString() - Method in class apollo.datamodel.Range
getStartCodon() - Method in class apollo.datamodel.FeatureSet
getStartCodon() - Method in interface apollo.datamodel.FeatureSetI
getStartCodonColor(FeatureSetI) - Static method in class apollo.gui.drawable.DrawableUtil
getStartTextBox() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
getStateInformation() - Method in class apollo.dataadapter.AbstractApolloAdapter
getStateInformation() - Method in class apollo.dataadapter.analysis.AnalysisAdapter
getStateInformation() - Method in interface apollo.dataadapter.ApolloDataAdapterI: State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput.
getStateInformation() - Method in class apollo.dataadapter.BaseGFFAdapter
getStateInformation() - Method in class apollo.dataadapter.chado.ChadoAdapter
getStateInformation() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter
getStateInformation() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter: The adapter is characterised by dsn (e.g.
getStateInformation() - Method in class apollo.dataadapter.das2.DAS2Adapter: The adapter is characterised by dsn (e.g.
getStateInformation() - Method in class apollo.dataadapter.EnsCGIAdapter
getStateInformation() - Method in class apollo.dataadapter.ensj.EnsJAdapter
getStateInformation() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getStateInformation() - Method in class apollo.dataadapter.gamexml.GAMEAdapter
getStateInformation() - Method in class apollo.dataadapter.GbrowseAdapter
getStateInformation() - Method in class apollo.dataadapter.genbank.GenbankAdapter
getStateInformation() - Method in class apollo.dataadapter.otter.OtterAdapter
getStateInformation() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getStateInformation() - Method in class apollo.dataadapter.sample.SampleAdapter: When the data load is done, this adapter is queried for any state information: this information is then written to a text file which stores a history of this adapter's state (see ApolloRunner.writeAdapterHistory).
getStateInformation() - Method in class apollo.dataadapter.SerialDiskAdapter
getStateInformation() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getStatusBar() - Method in class apollo.gui.genomemap.ApolloPanel
getStatusBar() - Method in class apollo.gui.synteny.CurationManager
getStatusBar() - Method in class apollo.gui.synteny.SyntenyPanel
getStop() - Method in interface apollo.dataadapter.das.DASSegment
getStop() - Method in interface apollo.dataadapter.das.DASSequence
getStop() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getStop() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getStrand() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the strand of the feature on the reference sequence
getStrand() - Method in class apollo.datamodel.FeaturePair
getStrand() - Method in class apollo.datamodel.Range
getStrand() - Method in interface apollo.datamodel.RangeI
getStrand(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the strand of the annotations currently being viewed
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.PanelFactory
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.Tier: Gets the strand of this tier.
getStrand() - Method in class apollo.gui.detailviewers.sequencealigner.TierFactory
getStrand() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getStrand() - Method in interface apollo.gui.drawable.Drawable
getStrand() - Method in class apollo.gui.drawable.DrawableSeqFeature
getStrand() - Method in class apollo.gui.genomemap.LinearView
getStrand1() - Method in class apollo.datamodel.Link
getStrand2() - Method in class apollo.datamodel.Link
getStrandedFeatSetAncestor() - Method in class apollo.datamodel.SeqFeature
getStrandedFeatSetAncestor() - Method in interface apollo.datamodel.SeqFeatureI
getStrandedFeatSetAncestor() - Method in class apollo.datamodel.StrandedFeatureSet
getStrandedZoomableApolloPanel() - Method in class apollo.gui.genomemap.ApolloPanel
getStrandedZoomableApolloPanel() - Method in interface apollo.gui.genomemap.ApolloPanelI
getStreamFromUrl(URL, String, String) - Static method in class apollo.util.IOUtil: Makes InputStream from URL - throws DataAdapterException with badUrlMessage if URL is not found, or with notFoundMessage if stream is empty (i.e., requested region is not found).
getStreamFromUrl(URL, String) - Static method in class apollo.util.IOUtil
getStretched() - Method in class apollo.gui.genomemap.Rubberband
getString(int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditorRowHeader
getString(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditorRowHeader
getStringForDrawable(Drawable) - Static method in class apollo.gui.drawable.DrawableDisplayTool
getStringForSeqFeature(SeqFeatureI) - Static method in class apollo.dataadapter.debug.DisplayTool
getStripeWidth() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the number of bases that will be included in a stripe
getStyle(String) - Static method in class apollo.config.Config: Returns Style for adapter class string, null if non existent
getStyle() - Static method in class apollo.config.Config
getStyle() - Method in class apollo.config.FeatureProperty
getStyle() - Method in class apollo.dataadapter.AbstractApolloAdapter: By default return style associated with the adapter in apollo.cfg.
getStyle() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Return style associated with data adapter - at the moment synteny overrides all its child adapters with its own style - this may change in the future
getStyle() - Method in class apollo.dataadapter.chado.ChadoAdapter: A chado database can set its own style.
getStyle() - Method in class apollo.gui.annotinfo.FeatureEditPanel
getStyle() - Method in class apollo.gui.synteny.GuiCurationState: does the data adapter have the right style? check this
getStyleFileName() - Method in class apollo.dataadapter.chado.ChadoDatabase
getStyleForDb(String) - Method in class apollo.config.Style: Returns null if cant make style for db
getSubHeading(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter
getSubjFeatCol() - Method in class apollo.dataadapter.chado.jdbc.SchemaVersion
getSubpart() - Method in class apollo.editor.FeatureChangeEvent: Returns null if no subpart
getSubpart() - Method in class apollo.editor.Transaction
getSubpartRank() - Method in class apollo.editor.AnnotationChangeEvent
getSubpartRank() - Method in class apollo.editor.Transaction
getSubpartRank() - Method in interface apollo.editor.UpdateDetailsI: More details that are needed
getSubparts() - Method in interface apollo.dataadapter.das.DASSegment
getSubparts() - Method in class apollo.dataadapter.das.simple.SimpleDASSegment
getSubpartString() - Method in class apollo.editor.Transaction
getSubSequence(int, int) - Method in class apollo.dataadapter.das.DASLazySequence
getSubSequence(int, int) - Method in class apollo.dataadapter.ensj.AlternateEnsJSequence
getSubSequence(int, int) - Method in class apollo.dataadapter.ensj19.AlternateEnsJSequence
getSubSequence(int, int) - Method in class apollo.dataadapter.ensj19.EnsJSequence
getSubSequence(int, int) - Method in class apollo.datamodel.AbstractSequence
getSubSequence(int, int) - Method in class apollo.datamodel.seq.AbstractLazySequence: Clean up dangling reference as listener to controller that will make old instances persist - no longer needed as doesnt listen to controller anymore
getSubSequence(int, int) - Method in class apollo.datamodel.seq.DebugLazySequence
getSubSequence(int, int) - Method in class apollo.datamodel.seq.EnsCGISequence
getSubSequence(int, int) - Method in class apollo.datamodel.seq.GAMESequence
getSubSequence(int, int) - Method in class apollo.datamodel.seq.PFetchSequence
getSubSequence(int, int) - Method in class apollo.datamodel.seq.SRSSequence
getSubSequence(String, int, int) - Method in class apollo.datamodel.SeqFeature: This has nothing to do with translation starts, it merely obtains the string between the 2 positions.
getSubSequence(int, int) - Method in class apollo.datamodel.Sequence: this method actually isnt used at all - take out of SequenceI? calls AbstractSequence.getResidues which calls getResiduesImpl
getSubSequence(int, int) - Method in interface apollo.datamodel.SequenceI: I can see this being a handy method but its actually not used at all - delete?
getSuffixDelimiter() - Method in interface apollo.config.ApolloNameAdapterI
getSuffixDelimiter() - Method in class apollo.config.ChadoJdbcNameAdapter
getSuffixDelimiter() - Method in class apollo.config.DefaultNameAdapter
getSuffixDelimiter() - Method in class apollo.config.ParameciumNameAdapter
getSuffixDelimiter() - Method in class apollo.config.TigrAnnotNameAdapter
getSupportedOperations() - Method in class apollo.analysis.SeqAnalysisBase
getSupportedOperations() - Method in class apollo.dataadapter.analysis.AnalysisAdapter
getSupportedOperations() - Method in class apollo.dataadapter.BaseGFFAdapter
getSupportedOperations() - Method in class apollo.dataadapter.chado.ChadoAdapter
getSupportedOperations() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: From org.bdgp.io.DataAdapter interface
getSupportedOperations() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getSupportedOperations() - Method in class apollo.dataadapter.das2.DAS2Adapter
getSupportedOperations() - Method in class apollo.dataadapter.DummySequenceAdapter
getSupportedOperations() - Method in class apollo.dataadapter.EfetchSequenceAdapter
getSupportedOperations() - Method in class apollo.dataadapter.EnsCGIAdapter
getSupportedOperations() - Method in class apollo.dataadapter.ensj.EnsJAdapter: From bdgp DataAdapter.
getSupportedOperations() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter
getSupportedOperations() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getSupportedOperations() - Method in class apollo.dataadapter.gamexml.GAMEAdapter
getSupportedOperations() - Method in class apollo.dataadapter.GbrowseAdapter
getSupportedOperations() - Method in class apollo.dataadapter.genbank.GenbankAdapter
getSupportedOperations() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Get supported operations (read / write)
getSupportedOperations() - Method in class apollo.dataadapter.graph.GraphAdapter: Get supported operations (append)
getSupportedOperations() - Method in class apollo.dataadapter.otter.OtterAdapter
getSupportedOperations() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getSupportedOperations() - Method in class apollo.dataadapter.sample.SampleAdapter: From bdgp DataAdapter.
getSupportedOperations() - Method in class apollo.dataadapter.SerialDiskAdapter
getSupportedOperations() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getSupportedOperations() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getSupportedOperations() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getSupportedOperations() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getSynonym(int) - Method in class apollo.datamodel.AnnotatedFeature
getSynonym(int) - Method in interface apollo.datamodel.AnnotatedFeatureI
getSynonymId(String, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getSynonymPropertyTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getSynonyms() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getSynonyms() - Method in class apollo.datamodel.AnnotatedFeature
getSynonyms(boolean) - Method in class apollo.datamodel.AnnotatedFeature
getSynonyms() - Method in interface apollo.datamodel.AnnotatedFeatureI
getSynonyms(boolean) - Method in interface apollo.datamodel.AnnotatedFeatureI
getSynonyms() - Method in class apollo.datamodel.Identifier: this returns all synonyms, both internal and external.
getSynonyms(boolean) - Method in class apollo.datamodel.Identifier: This used to return a clone, for no good reason that anyone can recall, so now it doesn't.
getSynonymSize() - Method in class apollo.datamodel.AnnotatedFeature
getSynonymSize() - Method in interface apollo.datamodel.AnnotatedFeatureI
getSyntenyChoiceMenu() - Method in class apollo.gui.menus.MenuManager
getSyntenyDatabaseForSpecies(String) - Static method in class apollo.config.Config
getSyntenyDatabaseForSpecies(String) - Method in class apollo.config.Style: Database species maps to as proscribed by SpeciesToDatabase entries.
getSyntenyDir() - Static method in class apollo.config.Config
getSyntenyLinkedFeatProps() - Method in class apollo.config.PropertyScheme: Retrieves all feature props that are synteny links At some point we may want to include species as a parameter and only retrieve links between specified species.
getSyntenyLinkInfo() - Method in class apollo.datamodel.SeqFeature
getSyntenyLinkInfo() - Method in interface apollo.datamodel.SeqFeatureI
getSyntenyLinkOrder() - Method in class apollo.config.Style
getSyntenyPanel() - Method in class apollo.gui.ApolloFrame
getSyntenyPanelRelativeSize() - Static method in class apollo.config.Config
getSyntenyRegions(String) - Method in class apollo.dataadapter.GFFSyntenyAdapter
getSyntenyRegions() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getSyntenyRegionsByChromosome(Chromosome) - Method in class apollo.dataadapter.GFFSyntenyAdapter
getSyntenyRegionsByChromosome(Chromosome) - Method in class apollo.dataadapter.SyntenyAdapter: Returns a vector's worth of Apollo.datamodel.SyntenyRegion objects for the input chromosome.
getSyntenyRegionsByChromosome(Chromosome) - Method in interface apollo.dataadapter.SyntenyAdapterI
getSyntenyRegionsByChromosome(String) - Method in class apollo.dataadapter.SyntenyGFFAdapter
getSyntenyRelationshipType() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getSyntenySpeciesAndLinkOrder() - Method in class apollo.config.Style: List of Strings which are the species/names/tags of sub-adapters.
getSyntenySpeciesNames() - Method in class apollo.config.Style: Maps names (Name.Mouse) to adapter label/logical name (Mus Musculus).
getSyntenySpeciesOrder() - Method in class apollo.config.Style: Same as syntenySpeciesAndLinkOrder(Strings) minus links(denoted by "Compara") eg "Name.Mouse", "Name.Human" If synteny species names not explicitly set(ensj,gff), and useGenericSyntenySpecies is true, make a generic list up to getNumberOfSpecies (Species1,Species2,...SpeciesN) (game)
getSyntenySpeciesProperties() - Method in class apollo.config.Style: This maps these kinds of strings from the style file: "Species.Mouse.DataAdapter" -> "apollo.dataadapter.ensj.AnnotationEnsJAdapter" So basically its where the dataadapter is
getSyntenySpeciesString(int) - Method in class apollo.config.Style
getSZAP() - Method in class apollo.gui.synteny.GuiCurationState
getTable() - Method in class apollo.gui.SeqSelectorTable
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class apollo.gui.DisabledEditor
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class apollo.gui.evidencepanel.TablePanel.CellRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class apollo.gui.evidencepanel.TablePanel.TypeCellRenderer
getTableName() - Method in class apollo.dataadapter.chado.ChadoTransaction
getTables() - Method in class apollo.dataadapter.mysql.Database
getTables() - Method in class apollo.dataadapter.mysql.MySQLDatabase
getTaggedColor() - Method in class apollo.config.Style: Return color for boxing tagged results
getTagMap() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler
getTagValues() - Method in class apollo.dataadapter.genbank.PublicDbFeature
getTarget() - Method in class apollo.dataadapter.TransactionOutputAdapter
getTargetId() - Method in interface apollo.dataadapter.das.DASFeature
getTargetId() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTargetName(String, String, String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return the name to use for a target sequence in a search hit.
getTargetName(String, String, String) - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance: just returns chadoName - cant add species as fb doesnt record species of target
getTargetName(String, String, String) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance: just returns chadoName - cant add species as fb doesnt record species of target
getTargetName(String, String, String) - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance: returns target name as species + targetChadoName, unless align type is SNP, where query name is used for target name
getTargetStart() - Method in interface apollo.dataadapter.das.DASFeature
getTargetStart() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTargetStop() - Method in interface apollo.dataadapter.das.DASFeature
getTargetStop() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTech() - Method in class apollo.dataadapter.genbank.GenbankValidator
getTermById(String) - Method in class apollo.util.OBOParser: Get a term IdentifiedObject by ID
getTermByName(String) - Method in class apollo.util.OBOParser: Get a term IdentifiedObject by name
getText() - Method in class apollo.config.PeptideStatus
getText() - Method in class apollo.datamodel.Comment
getText() - Method in class apollo.gui.PrefsPanel: It's only ever relevant to get text from the personal text area
getTextAvoidLimit() - Static method in class apollo.config.Config
getTextColor() - Method in class apollo.gui.detailviewers.exonviewer.AminoAcidRenderer
getTextColor() - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
getTextColor() - Method in class apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidBaseRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRendererSpaced
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
getTextColor() - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
getTextEnd() - Method in class apollo.gui.genomemap.FeatureTier
getTextEnd(Drawable, int) - Method in class apollo.gui.genomemap.FeatureTierManager
getTextEnd() - Method in class apollo.gui.Tier
getTextStart(Drawable) - Method in class apollo.gui.genomemap.FeatureTierManager
getThis() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
getThreeLevelAnnotTypes() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Get a list of features that are stored in the chado db as three-level features (gene-namedFeature-exon).
getThreshold() - Method in class apollo.config.FeatureProperty
getTier() - Method in class apollo.analysis.filter.AnalysisInput
getTier() - Method in class apollo.config.FeatureProperty
getTier(String) - Method in class apollo.config.TiersIO
getTier(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getTier() - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener: Gets the current tier
getTier(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getTier() - Method in class apollo.gui.detailviewers.sequencealigner.ResultMouseListener: Gets the current tier
getTier() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getTier() - Method in interface apollo.gui.detailviewers.sequencealigner.TierPanelI
getTier(int) - Method in class apollo.gui.TierManager
getTier(int) - Method in interface apollo.gui.TierManagerI
getTierCount() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getTierCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns the number of sequence tiers in the panel
getTierForFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: Returns tier number that SeqFeatureI is in.
getTierForFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Returns tier number that SeqFeatureI is in.
getTierForPixelPosition(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getTierForPixelPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getTierInd(String) - Method in class apollo.config.PropertyScheme
getTierIndex(TierManagerI) - Method in interface apollo.gui.drawable.Drawable: Get the tier on which this Drawable resides
getTierIndex(TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature: This returns the variable called tier_index so i renamed to getTierIndex - hope thats ok.
getTierLabel() - Method in class apollo.gui.genomemap.FeatureTier
getTierLabel(int) - Method in interface apollo.gui.genomemap.FeatureTierManagerI
getTierLabel() - Method in class apollo.gui.genomemap.SiteTier
getTierLabel() - Method in class apollo.gui.Tier
getTierLabel(int) - Method in class apollo.gui.TierManager
getTierManager() - Method in class apollo.gui.genomemap.ManagedView
getTierManager() - Method in interface apollo.gui.genomemap.ManagedViewI
getTierManagerSource() - Method in class apollo.gui.event.TierManagerEvent
getTierName() - Method in class apollo.config.FeatureProperty
getTierProperties() - Method in class apollo.gui.genomemap.FeatureTierManager: This is actually for testing - doesnt otherwise need to be exposed to outside world
getTierProperty(String, boolean) - Method in class apollo.config.PropertyScheme: Returns the TierProperty associated with either label or analysis_type.
getTierProperty(String) - Method in class apollo.config.PropertyScheme
getTiers() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getTiers() - Method in class apollo.gui.TierManager
getTiers() - Method in interface apollo.gui.TierManagerI
getTiersFile() - Static method in class apollo.config.Config
getTiersFile() - Method in class apollo.config.Style
getTierYCentre(Drawable) - Method in class apollo.gui.genomemap.FeatureView
getTierYCentrePixel(int, Transformer, TierManagerI) - Static method in class apollo.gui.drawable.DrawableUtil: Return y value for middle of tier, not feature.
getTigrAnnotNameAdapterNewNameCommand() - Static method in class apollo.config.Config
getTimeout() - Method in class apollo.dataadapter.CGI
getTimestamp() - Static method in class apollo.config.Config
getTimeStamp() - Method in class apollo.datamodel.Comment
getTitle(CurationSet) - Method in class apollo.config.DefaultDisplayPrefs
getTitle(CurationSet) - Method in interface apollo.config.DisplayPrefsI: generate a title for this curation
getTitle(CurationSet) - Method in class apollo.config.FlyDisplayPrefs
getTitle() - Method in class apollo.gui.detailviewers.seqexport.SeqExport: String that appears in window menus list
getTopFeatLoc() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTopLevelFeat(SeqFeatureI) - Method in class apollo.editor.AnnotationEditor: Return the top level feature for a given SeqFeatureI object
getTopLevelFeatType() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Top level feature type is needed for saving back to chado.
getTopLevelType() - Method in class apollo.datamodel.Exon: Exon has the same biotype as its gene
getTopLevelType() - Method in class apollo.datamodel.FeaturePair
getTopLevelType() - Method in class apollo.datamodel.SeqFeature: If biotype is null, returns type
getTopLevelType() - Method in interface apollo.datamodel.SeqFeatureI
getTopLevelType() - Method in class apollo.datamodel.Transcript: Transcript has the same biotype as its gene
getTopModel() - Method in class apollo.gui.genomemap.AnnotationView
getTopModel() - Method in class apollo.gui.genomemap.FeatureView: Returns the topmost model object of the result view, the FeatureSet that holds all of the tiers, (just dfset.getFeatureSet())
getTopModel() - Method in class apollo.gui.genomemap.ResultView: Returns the topmost model object of the result view, the FeatureSet that holds all of the tiers, (just dfset.getFeatureSet())
getTotalHeight() - Method in class apollo.gui.TierManager
getTotalHeight() - Method in interface apollo.gui.TierManagerI
getTotalPrimerSpecificityMismatch() - Method in class apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
getTotalSpace() - Method in class apollo.gui.Tier
getTransaction(int) - Method in class apollo.editor.AnnotationChangeLog
getTransaction(int) - Method in class apollo.editor.CompoundTransaction
getTransaction(int) - Method in class apollo.editor.Transaction: Default return null.
getTransaction(int) - Method in class apollo.editor.TransactionManager
getTransactionManager() - Method in class apollo.config.DefaultNameAdapter
getTransactionManager() - Method in class apollo.dataadapter.CurationState: Get the TransactionManager used by the embed curationSet.
getTransactionManager() - Method in class apollo.datamodel.CurationSet
getTransactionManager() - Method in class apollo.gui.synteny.GuiCurationState
getTransactions() - Method in class apollo.editor.AnnotationChangeLog: Returns list of Transactions
getTransactions() - Method in class apollo.editor.CompoundTransaction: Return list of transactions
getTransactions() - Method in class apollo.editor.TransactionManager: Get the list of Transaction instances managed by this object.
getTransactionSize() - Method in class apollo.editor.AnnotationChangeLog
getTranscript() - Method in class apollo.datamodel.Exon
getTranscript() - Method in interface apollo.datamodel.ExonI
getTranscript() - Method in class apollo.gui.annotinfo.FeatureEditorDialog
getTranscript() - Method in class apollo.gui.detailviewers.sequencealigner.overview.Overview
getTranscriptCdsIds(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getTranscriptComments() - Static method in class apollo.config.Config
getTranscriptComments() - Method in class apollo.config.Style
getTranscriptCvTermId() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTranscriptCvTermId() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getTranscriptExonIds(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getTranscriptName(FeatureSet, String) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTranscriptName(FeatureSet, String) - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getTranscriptNameField() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance: Return the column in the chado feature table where the transcript name can be found.
getTranscriptNameField() - Method in class apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
getTranscriptNameField() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getTranscriptNameField() - Method in class apollo.dataadapter.chado.jdbc.TigrChadoInstance
getTranscriptNamePattern() - Method in interface apollo.config.ApolloNameAdapterI: Returns expected pattern (if any) for transcript names
getTranscriptNamePattern() - Method in class apollo.config.ChadoJdbcNameAdapter: Returns expected pattern (if any) for transcript names
getTranscriptNamePattern() - Method in class apollo.config.DefaultNameAdapter
getTranscriptNamePattern() - Method in class apollo.config.GmodNameAdapter: This is used as a check if transcript suffix editing is allowed in the annot info editor.
getTranscriptNamePattern() - Method in class apollo.config.ParameciumNameAdapter: Returns expected pattern (if any) for transcript names
getTranscriptNamePattern() - Method in class apollo.config.TigrAnnotNameAdapter
getTranscriptOrdinalPattern() - Method in class apollo.config.GmodNameAdapter
getTranscriptPolypeptideIds(Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getTranscriptRank(Long, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
getTranscripts(CurationSet) - Static method in class apollo.util.SeqFeatureUtil: Returns a list of all transcripts in cur set - both strands
getTranscriptSuffix(SeqFeatureI, AnnotatedFeatureI) - Method in class apollo.config.GmodNameAdapter
getTranscriptSuffixRoot() - Method in class apollo.config.FlyNameAdapter
getTranscriptSuffixRoot() - Method in class apollo.config.GmodNameAdapter: This needs some explaining.
getTranscriptSymbolEditable() - Method in class apollo.config.Style: Whether transcript symbol/name is editable in annot info, default true
getTranscriptTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTranscriptTerm() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getTransferData(DataFlavor) - Method in class apollo.gui.ArrayListTransferHandler.ArrayListTransferable
getTransferDataFlavors() - Method in class apollo.gui.ArrayListTransferHandler.ArrayListTransferable
getTransform() - Method in class apollo.gui.genomemap.LinearView
getTransform() - Method in interface apollo.gui.genomemap.ViewI: Get the tranform object to convert between View and component coordinates.
getTransformer() - Method in class apollo.dataadapter.TransactionOutputAdapter
getTransformer() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getTransGeneRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTransGeneRelationTerm() - Method in class apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
getTranslatedHitZones(int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
getTranslatedHitZones(int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
getTranslation() - Method in class apollo.datamodel.FeatureSet: FeatureSetI itself implements TranslationI so just return self - in future this may be done with a separate translation object
getTranslation() - Method in class apollo.datamodel.SeqFeature: By default seqfeature has no translation - returns null
getTranslation() - Method in interface apollo.datamodel.SeqFeatureI
getTranslation(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getTranslationEnd() - Method in class apollo.datamodel.FeatureSet
getTranslationEnd() - Method in interface apollo.datamodel.TranslationI
getTranslationLength(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getTranslationRange() - Method in class apollo.datamodel.FeatureSet: TranslationI interface
getTranslationRange() - Method in interface apollo.datamodel.TranslationI
getTranslationShowLimit() - Static method in class apollo.config.Config
getTranslationStart() - Method in class apollo.datamodel.FeatureSet: Returns start of translation in genomic coords
getTranslationStart() - Method in interface apollo.datamodel.TranslationI
getTranslExcept(Transcript, int) - Method in class apollo.dataadapter.genbank.GenbankValidator
getTransOrOneLevelAnn(AnnotatedFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: AssemblyFeature is the only GAI at the moment that has no relation to // a transcript.
getTransProtRelationTerm() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getTwilightLower() - Method in class apollo.analysis.filter.AnalysisInput
getTwilightUpper() - Method in class apollo.analysis.filter.AnalysisInput
getType() - Method in class apollo.analysis.filter.AnalysisInput
getType() - Method in class apollo.analysis.SeqAnalysisBase
getType() - Method in class apollo.analysis.SeqAnalysisBDGP
getType() - Method in class apollo.analysis.SeqAnalysisLocal
getType() - Method in class apollo.analysis.SeqAnalysisNCBI
getType() - Method in class apollo.analysis.SeqAnalysisRemote
getType() - Method in class apollo.dataadapter.AbstractApolloAdapter: From org.bdgp.io.DataAdapter.
getType() - Method in class apollo.dataadapter.analysis.AnalysisAdapter: org.bdgp.io.DataAdapter method
getType() - Method in class apollo.dataadapter.BaseGFFAdapter
getType() - Method in class apollo.dataadapter.chado.ChadoAdapter
getType() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: Used by GenericFileAdapterGUI
getType() - Method in class apollo.dataadapter.ChromosomeAdapter
getType() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getType() - Method in class apollo.dataadapter.das2.DAS2Adapter
getType() - Method in class apollo.dataadapter.DataInput
getType() - Method in class apollo.dataadapter.DummySequenceAdapter
getType() - Method in class apollo.dataadapter.EfetchSequenceAdapter
getType() - Method in class apollo.dataadapter.EnsCGIAdapter
getType() - Method in class apollo.dataadapter.ensj.EnsJAdapter: From bdgp DataAdapter.
getType() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
getType() - Method in class apollo.dataadapter.gamexml.GAMEAdapter: org.bdgp.io.DataAdapter method
getType() - Method in class apollo.dataadapter.GbrowseAdapter
getType() - Method in class apollo.dataadapter.genbank.GenbankAdapter: Doesn't seem to be used
getType() - Method in class apollo.dataadapter.gff3.GFF3Entry: Get the type of feature
getType() - Method in class apollo.dataadapter.GFFSyntenyAdapter
getType() - Method in class apollo.dataadapter.KaryotypeAdapter
getType() - Method in interface apollo.dataadapter.KaryotypeAdapterI
getType() - Method in class apollo.dataadapter.otter.OtterAdapter
getType() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getType() - Method in class apollo.dataadapter.sample.SampleAdapter: From bdgp DataAdapter.
getType() - Method in class apollo.dataadapter.SerialDiskAdapter
getType() - Method in class apollo.dataadapter.synteny.builder.AdapterModel
getType() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getType() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
getType() - Method in class apollo.dataadapter.SyntenyAdapter
getType() - Method in interface apollo.dataadapter.SyntenyAdapterI
getType() - Method in class apollo.dataadapter.SyntenyGFFAdapter
getType() - Method in class apollo.datamodel.Evidence
getType() - Method in class apollo.datamodel.Link: return null if no type
getType(SeqFeatureI) - Static method in class apollo.gui.DetailInfo
getType() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel: Gets the type (always AA)
getType() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
getType() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Gets the type
getType() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getType() - Method in class apollo.gui.detailviewers.sequencealigner.Tier
getType() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI
getType() - Method in interface apollo.gui.drawable.Drawable
getType() - Method in class apollo.gui.drawable.DrawableSeqFeature
getType() - Method in class apollo.gui.event.FeatureSelectionEvent
getType() - Method in class apollo.gui.event.LazyLoadEvent
getType() - Method in class apollo.gui.event.TierManagerEvent
getType() - Method in class apollo.gui.event.ViewEvent
getType() - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
getType() - Method in class apollo.gui.SelectionType
getTypeAsString() - Method in class apollo.datamodel.Evidence
getTypeAtPosition(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getTypeAtPosition(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getTypeCategory() - Method in interface apollo.dataadapter.das.DASFeature
getTypeCategory() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTypeId() - Method in interface apollo.dataadapter.das.DASFeature
getTypeId() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTypeLabel() - Method in interface apollo.dataadapter.das.DASFeature
getTypeLabel() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTypePanelInstance() - Static method in class apollo.gui.TypePanel: for now there is only one types panel for all species, as there is presently only one tiers/style for multi species.
getTypePanelToShow() - Method in class apollo.dataadapter.ensj.model.TypesModel
getTypeReference() - Method in interface apollo.dataadapter.das.DASFeature
getTypeReference() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getTypes() - Method in class apollo.config.PropertyScheme
getTypesAsString() - Method in class apollo.config.TierProperty
getTypesModel() - Method in class apollo.dataadapter.ensj.model.Model
getTypeStrings() - Static method in class apollo.dataadapter.DataInputType
getTypeSubparts() - Method in interface apollo.dataadapter.das.DASFeature
getTypeSubparts() - Method in class apollo.dataadapter.das.simple.SimpleDASFeature
getUI(IOOperation) - Method in class apollo.analysis.SeqAnalysisBDGP
getUI(IOOperation) - Method in class apollo.analysis.SeqAnalysisLocal
getUI(IOOperation) - Method in class apollo.analysis.SeqAnalysisNCBI
getUI(IOOperation) - Method in class apollo.analysis.SeqAnalysisRemote
getUI(IOOperation) - Method in class apollo.dataadapter.analysis.AnalysisAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.BaseGFFAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.chado.ChadoAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter: From org.bdgp.io.VisualDataAdapter interface
getUI(IOOperation) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.das2.DAS2Adapter
getUI(IOOperation) - Method in class apollo.dataadapter.DummySequenceAdapter: No UI for this adapter
getUI(IOOperation) - Method in class apollo.dataadapter.EfetchSequenceAdapter: No UI for this adapter
getUI(IOOperation) - Method in class apollo.dataadapter.EnsCGIAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.ensj.EnsJAdapter: This method traditionally creates a new UI for the adapter, based on the operation - read or write (each creates a different UI instance).
getUI(IOOperation) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter: need to cache guis.
getUI(IOOperation) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter: From org.bdgp.io.VisualDataAdapter interface
getUI(IOOperation) - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.gamexml.GAMEAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.GbrowseAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.genbank.GenbankAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.gff3.GFF3Adapter: Get the UI for the data adapter
getUI(IOOperation) - Method in class apollo.dataadapter.graph.GraphAdapter: Get the UI for the data adapter
getUI(IOOperation) - Method in class apollo.dataadapter.otter.OtterAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.otter.OtterXMLAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.sample.SampleAdapter: From bdgp DataAdapter.
getUI(IOOperation) - Method in class apollo.dataadapter.SerialDiskAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
getUI(IOOperation) - Method in class apollo.dataadapter.synteny.SyntenyAdapter: gets ui for op from cache.
getUI(IOOperation) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter: BEWARE: this method creates a brand-new instance of this adapter's UI and hands it back!
getUI(IOOperation) - Method in class apollo.dataadapter.SyntenyGFFAdapter
getUniqueHitNames() - Method in class apollo.util.FeatureList
getUniqueKeyProps() - Method in class apollo.dataadapter.chado.ChadoTransaction: Return the properties that are part of the unique key, needed for LOOKUP as you only want to lookup on the unique key.
getUnpaddedAlignment() - Method in class apollo.datamodel.SeqFeature: Alignment without padding.
getUnpaddedAlignment() - Method in interface apollo.datamodel.SeqFeatureI: Alignment without padding.
getUpdateDetails() - Method in class apollo.editor.AnnotationUpdateEvent: generic way to get details of update
getUpdateDetails() - Method in class apollo.editor.FeatureChangeEvent: Update event has a bunch of stuff - need to be able to acces this from superclass - separate UpdateDetail class with update stuff? EventDetail? for now just get the update event
getUpdatedSeqFeature() - Method in class apollo.editor.UpdateTransaction: Get the updated SeqFeatureI
getUpdatedSeqFeatureClone() - Method in class apollo.editor.UpdateTransaction
getUpdateProperies() - Method in class apollo.dataadapter.chado.ChadoUpdateTransaction
getURL() - Method in interface apollo.dataadapter.das.DASServerI
getURL() - Method in class apollo.dataadapter.das.simple.SimpleDASServer
getURL() - Method in class apollo.dataadapter.das2.DAS2Request
getURL() - Method in class apollo.dataadapter.das2.SourceParser
getURL() - Method in class apollo.dataadapter.mysql.MySQLInstance
getURL(String, String) - Static method in class apollo.gui.URLQueryGenerator
getURLForBand(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter
getURLForGene(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter
getURLForRange(Region) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter: parse range string "Chr 2L 10000 20000" -> "2L:10000:20000"
getURLForScaffold(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter
getURLPrefix(FeatureProperty, SeqFeatureI, String) - Method in class apollo.config.DefaultDisplayPrefs
getURLPrefix(FeatureProperty, SeqFeatureI, String) - Method in class apollo.config.EnsjDisplayPrefs
getURLPrefix(FeatureProperty, SeqFeatureI, String) - Method in class apollo.config.FlyDisplayPrefs
getURLString() - Method in class apollo.config.FeatureProperty
getUseOpaqueLinks() - Method in class apollo.gui.menus.SyntenyChoiceMenu
getUseOpaqueLinks() - Method in class apollo.gui.synteny.SyntenyLinkPanel
getUser() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
getUser() - Method in class apollo.dataadapter.mysql.Database
getUser() - Method in class apollo.dataadapter.mysql.MySQLInstance
getUserAlignChoice(HashMap) - Static method in class apollo.dataadapter.synteny.AlignBlockChooser
getUserChoice(HashMap) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter
getUsername() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI
getUserName() - Static method in class apollo.editor.UserName: This is the sole public method.
getUserObject() - Method in class apollo.datamodel.SeqFeature: ADDED BY TAIR Return the user object or null if none exists
getUserObject() - Method in interface apollo.datamodel.SeqFeatureI: ADDED BY TAIR Return the user object or null if none exists
getUsersFullName() - Static method in class apollo.config.Config
getUseSynonyms() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getUtrColor() - Method in class apollo.config.FeatureProperty: For DrawableGeneSeqFeature that colors utrs
getValue(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature
getValue() - Method in class apollo.datamodel.Score
getValue() - Method in class apollo.gui.event.ScrollEvent
getValue() - Method in class apollo.gui.SwingWorker: Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValueAt(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
getValueAt(int, int) - Method in class apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel: Retrieve Object to be displayed at row,column.
getValueAt(int, int) - Method in class apollo.gui.SeqSelectorTable.SequenceMatchModel
getValues(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature
getVersion() - Method in class apollo.dataadapter.analysis.BlastParser
getVersion() - Method in interface apollo.dataadapter.das.DASSequence
getVersion() - Method in class apollo.dataadapter.das.simple.SimpleDASSequence
getVersion() - Method in class apollo.dataadapter.genbank.GenbankReport
getVersion() - Method in class apollo.datamodel.AssemblyFeature
getVersion() - Method in class apollo.datamodel.DbXref
getVersion() - Static method in class apollo.main.Version
getVersionedSources() - Method in class apollo.dataadapter.das2.DAS2Request
getView() - Method in class apollo.dataadapter.ensj.controller.Controller
getView() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI
getView() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI
getView() - Method in class apollo.dataadapter.synteny.builder.Controller
getView() - Method in class apollo.gui.TierManager
getView() - Method in interface apollo.gui.TierManagerI
getViewAt(Point) - Method in class apollo.gui.genomemap.ApolloPanel: Get the View at a specified location in the Panel
getViewForFeature(SeqFeatureI) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
getViewGraphics() - Method in class apollo.gui.genomemap.ApolloPanel: Get the Graphics to draw to.
getViewHeight() - Method in class apollo.gui.TierManager
getViewportAncestor(Component) - Static method in class apollo.util.SwingMissingUtil
getViews() - Method in class apollo.gui.genomemap.ApolloPanel: get the views Vector
getViews(Rectangle) - Method in class apollo.gui.genomemap.ApolloPanel: find non drag views which are at least partly within a specified rectangle
getViews(Rectangle, Vector) - Method in class apollo.gui.genomemap.ApolloPanel
getViews() - Method in class apollo.gui.genomemap.ContainerView
getViews() - Method in interface apollo.gui.genomemap.ContainerViewI
getViewSelection(Selection) - Method in class apollo.gui.genomemap.FeatureTierManager: For features that are instantiated as drawables the easiest way to find out if the view contains these is by rolling through the tiers and seeing if the selected item is present.
getViewSelection(Selection) - Method in interface apollo.gui.genomemap.FeatureTierManagerI: Searches through the tiers to find all drawables that have features in the current selection
getViewSelection(Selection) - Method in class apollo.gui.genomemap.FeatureView: given the entirety of what is currently selected, remove anything that doesn't belong to this view and return the remaining selections.
getViewSelection(Selection) - Method in class apollo.gui.genomemap.SiteView
getViewSelection(Selection) - Method in class apollo.gui.genomemap.TierView: given the entirety of what is currently selected, remove anything that doesn't belong to this view and return the remaining selections.
getViewSelection(Selection) - Method in interface apollo.gui.genomemap.TierViewI: Returns only those selection items that are presented in this view
getViewsOfClass(Class) - Method in class apollo.gui.genomemap.ContainerView
getViewsOfClass(Class) - Method in interface apollo.gui.genomemap.ContainerViewI
getViewSource() - Method in class apollo.gui.event.ViewEvent
getVisibleBase() - Method in interface apollo.gui.BaseScrollable
getVisibleBase() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel: From BaseScrollable interface.
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel: Gets the base pair position for the all the bases visible on the left side of the viewable window
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: From BaseScrollable interface.
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getVisibleBase() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getVisibleBase() - Method in class apollo.gui.genomemap.GuideLine
getVisibleBaseCount() - Method in interface apollo.gui.BaseScrollable
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel: Gets the number of bases that are visable on a single row
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
getVisibleBaseCount() - Method in class apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
getVisibleBaseCount() - Method in class apollo.gui.genomemap.GuideLine
getVisibleBasepairWidth() - Method in class apollo.gui.genomemap.ApolloPanel: This returns the width of the panel in base pairs NOT pixels.
getVisibleDrawables(int[]) - Method in class apollo.gui.genomemap.DrawableTierManager: int[] limits is an array of 2 ints corresponding to low and high limits Returns a Vector of Vectors, each Vector within the outer Vector contains DrawableSeqFeatures that are the visible Features for a given tier Each DrawableSeqFeature is assigned a tier index corresponding to vertical placement.
getVisibleDrawables(int[]) - Method in interface apollo.gui.genomemap.DrawableTierManagerI
getVisibleDrawables() - Method in class apollo.gui.genomemap.ManagedView
getVisibleDrawables() - Method in interface apollo.gui.genomemap.TierViewI: Returns Vector of visible features
getVisibleRange() - Method in class apollo.gui.genomemap.LinearView: visible range in base pairs
getVisibleRange() - Method in interface apollo.gui.genomemap.ViewI: Get the range on the linear axis that is visible
getVisibleScrollbarValue() - Method in class apollo.gui.genomemap.TierView
getVisibleUserCoord() - Method in class apollo.gui.TierManager
getVisibleUserCoord() - Method in interface apollo.gui.TierManagerI
getWidth() - Method in class apollo.gui.Transformer.PixelRange
getWindowAncestor(Component) - Static method in class apollo.util.SwingMissingUtil
getWindowExtents(int, int[], int, int) - Method in class apollo.gui.WindowScoreCalculator
getWindowList() - Method in class apollo.gui.Controller
getWindowList(Window) - Method in class apollo.gui.Controller
getWindowList(Window) - Method in class apollo.gui.MultiController
getWinSize() - Method in class apollo.gui.WindowScoreCalculator
getWord() - Method in class apollo.analysis.filter.HuffNode
getWordSize() - Method in class apollo.analysis.filter.AnalysisInput
getWordSize() - Method in class apollo.analysis.HashDB
getWritebackTemplateFile() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance
getXCentre() - Method in class apollo.gui.Transformer
getXCoordsPerPixel() - Method in class apollo.gui.Transformer
getXMaximum() - Method in class apollo.gui.Transformer
getXMinimum() - Method in class apollo.gui.Transformer
getXOrientation() - Method in class apollo.gui.Transformer: This can be Transformer.LEFT and Transformer.RIGHT.
getXPixelsPerCoord() - Method in class apollo.gui.Transformer
getXRange() - Method in class apollo.gui.GCScoreCalculator
getXRange() - Method in class apollo.gui.ScoreCalculator
getXRange() - Method in class apollo.gui.StoredScoreCalculator: Get the position range covered by the scores [lowestPosition, highestPosition]
getXRange() - Method in class apollo.gui.Transformer
getXrefs() - Method in class apollo.dataadapter.genbank.GenbankValidator
getXVisibleRange() - Method in class apollo.gui.Transformer
getYCentre(Rectangle) - Method in class apollo.gui.drawable.DrawableSeqFeature
getYCentre() - Method in class apollo.gui.Transformer
getYCoordsPerPixel() - Method in class apollo.gui.Transformer
getYMaximum() - Method in class apollo.gui.Transformer
getYMinimum() - Method in class apollo.gui.Transformer
getYOrientation() - Method in class apollo.gui.Transformer
getYPixelsPerCoord() - Method in class apollo.gui.Transformer
getYRange() - Method in class apollo.gui.genomemap.ManagedView
getYRange() - Method in class apollo.gui.ScoreCalculator
getYRange() - Method in class apollo.gui.StoredScoreCalculator: Gets the score range for all scores [minScore, maxScore]
getYRange() - Method in class apollo.gui.TierManager
getYRange() - Method in interface apollo.gui.TierManagerI
getYRange() - Method in class apollo.gui.Transformer
getYSpace(Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
getYVisibleRange() - Method in class apollo.gui.Transformer
getZones() - Method in class apollo.gui.SequenceSelector: Returns a simple vector of match positions to BaseEditorPanel.
getZoomFactor() - Method in class apollo.gui.event.ZoomEvent
GFF3Adapter - Class in apollo.dataadapter.gff3
GFF3Adapter() - Constructor for class apollo.dataadapter.gff3.GFF3Adapter: Constructor
GFF3AdapterGUI - Class in apollo.dataadapter.gff3
GFF3AdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.gff3.GFF3AdapterGUI
GFF3AdapterTest - Class in apollo.dataadapter.gff3
GFF3AdapterTest(String) - Constructor for class apollo.dataadapter.gff3.GFF3AdapterTest
GFF3Entry - Class in apollo.dataadapter.gff3: This class represents a GFF3 entry
GFF3Entry(String) - Constructor for class apollo.dataadapter.gff3.GFF3Entry: Constructs a GFF3Entry
GFF3Entry(SeqFeatureI) - Constructor for class apollo.dataadapter.gff3.GFF3Entry: Constructs a GFF3Entry
GFF3EntryTest - Class in apollo.dataadapter.gff3
GFF3EntryTest(String) - Constructor for class apollo.dataadapter.gff3.GFF3EntryTest
GFFAdapter - Class in apollo.dataadapter
GFFAdapter() - Constructor for class apollo.dataadapter.GFFAdapter
GFFAdapterGUI - Class in apollo.dataadapter
GFFAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.GFFAdapterGUI
GFFFile - Class in apollo.seq.io
GFFFile(DataInputStream) - Constructor for class apollo.seq.io.GFFFile
GFFFile(String) - Constructor for class apollo.seq.io.GFFFile
GFFFile(String, String) - Constructor for class apollo.seq.io.GFFFile
GFFSyntenyAdapter - Class in apollo.dataadapter
GFFSyntenyAdapter(String, String, KaryotypeAdapterI, String, String) - Constructor for class apollo.dataadapter.GFFSyntenyAdapter
Gln - Static variable in class apollo.seq.ResidueProperties
Glu - Static variable in class apollo.seq.ResidueProperties
Gly - Static variable in class apollo.seq.ResidueProperties
GlyphChooser - Class in apollo.gui
GlyphChooser(FeatureProperty) - Constructor for class apollo.gui.GlyphChooser
GmodNameAdapter - Class in apollo.config: This has a lot of stuff that needs to go in FlyNameAdapter subclass.
GmodNameAdapter() - Constructor for class apollo.config.GmodNameAdapter
goodEvidence(Vector, Vector) - Method in class apollo.editor.AnnotationEditor
goodUser - Variable in class apollo.gui.annotinfo.FeatureEditPanel
goToButton - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
goToButton - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
GoToDialog - Class in apollo.gui.detailviewers.sequencealigner
GoToDialog(BaseScrollable) - Constructor for class apollo.gui.detailviewers.sequencealigner.GoToDialog
goToMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
grabAlignment(int, FeatureSetI, FeaturePairI) - Method in class apollo.dataadapter.analysis.Sim4Parser
grabDatabase() - Method in class apollo.dataadapter.analysis.Sim4Parser
grabDate(FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.FgeneshGFFParser
grabDate(FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenieParser
grabDate(FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenscanParser
grabDNA() - Method in class apollo.dataadapter.analysis.FgeneshGFFParser
grabDNA() - Method in class apollo.dataadapter.analysis.GenieParser
grabDNA() - Method in class apollo.dataadapter.analysis.GenscanParser
grabGenes(CurationSet, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.FgeneshGFFParser
grabGenes(CurationSet, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.FgeneshParser
grabGenes(CurationSet, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GeneFinderParser
grabGenes(CurationSet, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenieParser
grabGenes(CurationSet, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenscanParser
grabMatrix(FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenscanParser
grabSequence(FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GenscanParser
GraphAdapter - Class in apollo.dataadapter.graph: This is the adapter class for handling graph data
GraphAdapter() - Constructor for class apollo.dataadapter.graph.GraphAdapter: Constructor
GraphAdapterGUI - Class in apollo.dataadapter.graph
GraphAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.graph.GraphAdapterGUI: Construct a GraphAdapterGUI object
GraphAdapterGUI.ColorActionListener - Class in apollo.dataadapter.graph
GraphAdapterGUI.ColorActionListener() - Constructor for class apollo.dataadapter.graph.GraphAdapterGUI.ColorActionListener
graphics - Variable in class apollo.gui.genomemap.LinearView
GraphMenu - Class in apollo.gui.menus
GraphMenu(ApolloPanel, GraphView, Point) - Constructor for class apollo.gui.menus.GraphMenu
GraphView - Class in apollo.gui.genomemap
GraphView(JComponent, String) - Constructor for class apollo.gui.genomemap.GraphView
groupFlag - Variable in class apollo.config.FeatureProperty
groupFlagSet - Variable in class apollo.config.FeatureProperty
groupId - Variable in class apollo.dataadapter.das.simple.SimpleDASFeature
groupTargetStart - Variable in class apollo.dataadapter.das.simple.SimpleDASFeature
groupTargetStop - Variable in class apollo.dataadapter.das.simple.SimpleDASFeature
groupTypes - Static variable in class apollo.config.FeatureProperty
GRP_GENE - Static variable in class apollo.config.FeatureProperty
GRP_HOMOLOGY - Static variable in class apollo.config.FeatureProperty
GRP_SINGLE - Static variable in class apollo.config.FeatureProperty
guessResidueTypeFromFeatureLength(int, int) - Static method in class apollo.util.SeqFeatureUtil: Calculates residue type by comparing seq length to feat length.
guessSchemaVersion(Connection) - Static method in class apollo.dataadapter.chado.jdbc.SchemaVersion: Attempt to determine the version of a chado schema by interrogating one or two key fields or tables.
GuiCurationState - Class in apollo.gui.synteny: Holds stuff needed for each curation-set/apollo-panel/szap/"species".
GuideLine - Class in apollo.gui.genomemap
GuideLine(ScaleView) - Constructor for class apollo.gui.genomemap.GuideLine
GuiTabPanel - Class in apollo.dataadapter: This is only used by GAMEAdapterGUI.
GuiTabPanel(String, String, Color) - Constructor for class apollo.dataadapter.GuiTabPanel
GuiTabPanel(String, String, DataInputType, Color) - Constructor for class apollo.dataadapter.GuiTabPanel
GuiTabPanel(String, String, DataInputType, String, Color) - Constructor for class apollo.dataadapter.GuiTabPanel
GuiTabPanel.ApolloGridBagConstraints - Class in apollo.dataadapter
GuiUtil - Class in apollo.util
GuiUtil() - Constructor for class apollo.util.GuiUtil

H

halt() - Method in class apollo.gui.AutoSaveThread
halt() - Method in class apollo.gui.CheckMemoryThread
halt - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel.AutoscrollThread
halt() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel.AutoscrollThread
halt - Variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel.AutoscrollThread
halt() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel.AutoscrollThread
haltThread(SeqAlignPanel.AutoscrollThread) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
haltThread(SeqAlignPanel.AutoscrollThread) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
handleAbout(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handleAlignViewportEvent(AlignViewportEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in interface apollo.editor.AnnotationChangeListener
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.editor.AnnotationChangeLog
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.editor.TransactionManager: Implements the method from AnnotationChangeListener.
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.annotinfo.FeatureEditorDialog: Calls setFeature with new annotation.
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.Controller
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.ControllerDebugListener
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.detailviewers.sequencealigner.Tier
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.detailviewers.sequencealigner.TierPanel
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.featuretree.FeatureTreeFrame
handleAnnotationChangeEvent(AnnotationChangeEvent) - Method in class apollo.gui.genomemap.AnnotationView
handleAutoscroll(int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
handleAutoscroll(int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.Controller
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.ControllerDebugListener
handleBaseFocusEvent(BaseFocusEvent) - Method in interface apollo.gui.event.BaseFocusListener
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.featuretree.FeatureTreeFrame
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.genomemap.ApolloPanel
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleBaseFocusEvent(BaseFocusEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel
handleChainedRepaint(ChainedRepaintEvent) - Method in interface apollo.gui.event.ChainedRepaintListener
handleChainedRepaint(ChainedRepaintEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel
handleChainedRepaintEvent(ChainedRepaintEvent) - Method in class apollo.gui.Controller
handleCharacters(OtterContentHandler, char[], int, int) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorEmailTagHandler
handleCharacters(OtterContentHandler, char[], int, int) - Method in class apollo.dataadapter.otter.parser.TagHandler
handleColumnSelectionEvent(ColumnSelectionEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleCreateNode() - Method in class apollo.dataadapter.synteny.builder.Controller
handleCreateSet() - Method in class apollo.dataadapter.synteny.builder.Controller
handleDataLoadEvent(DataLoadEvent) - Method in interface apollo.dataadapter.DataLoadListener
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.annotinfo.FeatureEditorDialog
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.ApolloFrame: This method got inadvertently disabled with composite frame merging (AF was listening to a unused Controller).
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.Controller
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.ControllerDebugListener
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.detailviewers.seqexport.SeqExport: Region changing means a new data set is being loaded.
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.featuretree.FeatureTreeFrame: DataLoadListener method.
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.FindPanel
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.genomemap.ApolloPanel
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.genomemap.NavigationBar
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.MultiController
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.PreferencesDialog
handleDataLoadEvent(DataLoadEvent) - Method in class apollo.gui.TypePanel: DataLoadListener method.
handleDeleteNode() - Method in class apollo.dataadapter.synteny.builder.Controller
handleDeleteSet() - Method in class apollo.dataadapter.synteny.builder.Controller
handleDropDownKeyPress() - Method in class apollo.dataadapter.synteny.builder.Controller
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.EvidenceNameTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.EvidenceTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.EvidenceTypeTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonEndTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonFrameTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonStableIdTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonStartTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonStrandTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ExonTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusAuthorEmailTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusAuthorTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusKnownTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusNameTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusRemarkTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusStableIdTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusSynonymTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.LocusTypeTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.ResponseTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAccessionTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyEndTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAssemblyStartTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorEmailTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentAuthorTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentChromosomeTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOffsetTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentFragmentOrientationTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentIdTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentKeywordTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentRemarkTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentVersionTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceSetAssemblyTypeTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceSetAuthorTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.SequenceSetTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorEmailTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptAuthorTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptCdsEndNotFoundTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptCdsStartNotFoundTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptClassTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAEndNotFoundTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptMRNAStartNotFoundTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptNameTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptRemarkTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptStableIdTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationEndTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStableIdTagHandler
handleEndElement(OtterContentHandler, String, String, String) - Method in class apollo.dataadapter.otter.parser.TranscriptTranslationStartTagHandler
handleEvent(String) - Method in class apollo.dataadapter.synteny.builder.Controller
handleEventForKey(String) - Method in class apollo.dataadapter.ensj.controller.Controller
handleFeatureChangeEvent(FeatureChangeEvent) - Method in interface apollo.editor.FeatureChangeListener
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.external.IgbBridge
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.annotinfo.FeatureEditorDialog
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.Controller
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.ControllerDebugListener
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor: Handle the selection event (feature was selected in another window--select it here) This is also where selections from BaseFineEditor come in which are really internal selections.
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor: Handle the selection event (feature was selected in another window--select it here) This is also where selections from BaseFineEditor come in which are really internal selections.
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in interface apollo.gui.event.FeatureSelectionListener
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.featuretree.FeatureTreeFrame
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.genomemap.ApolloPanel: FeatureSelectionListener - should this scroll to the selection? YES This sets Selection selection to the features in the selection event that are found in the views.
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel: If we had a FeatureSelectionEvent fired AT us, then we
handleFeatureSelectionEvent(FeatureSelectionEvent) - Method in class apollo.gui.TypePanel
handleLazyLoadEvent(LazyLoadEvent) - Method in class apollo.gui.ApolloFrame: woops - this is currently disabled as apollo frame is no longer listening to the controller - to reenable this should either be moved or made an inner class that does its own listening to the controller but it sounds like maybe this dialog was annoying and we may not want to reenable it.
handleLazyLoadEvent(LazyLoadEvent) - Method in class apollo.gui.Controller
handleLazyLoadEvent(LazyLoadEvent) - Method in class apollo.gui.ControllerDebugListener
handleLazyLoadEvent(LazyLoadEvent) - Method in interface apollo.gui.event.LazyLoadListener
handleMouseLeftClickOnTree() - Method in class apollo.dataadapter.synteny.builder.Controller
handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent) - Method in class apollo.gui.Controller: A NamedFeatureSelectionEvent nominates only the name of the feature to be selected - the panel responds by (1) finding the feature of interest and rebouncing the event as a feature selection event.
handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent) - Method in interface apollo.gui.event.NamedFeatureSelectionListener
handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel: If we are handed a feature selected only by name, then - as long as we are not the source of the event, we will try to find the features in our result set which correspond to the named features.
handleOpenApplication(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handleOpenFile(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handleOrientationEvent(OrientationEvent) - Method in class apollo.gui.Controller
handleOrientationEvent(OrientationEvent) - Method in interface apollo.gui.event.OrientationListener
handleOrientationEvent(OrientationEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handlePreferences(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handlePrintFile(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in interface apollo.config.PropSchemeChangeListener
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in class apollo.gui.Controller
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in class apollo.gui.ControllerDebugListener
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in class apollo.gui.genomemap.FeatureTierManager
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel
handlePropSchemeChangeEvent(PropSchemeChangeEvent) - Method in class apollo.gui.TypePanel
handleQuit(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handleReopenApplication(ApplicationEvent) - Method in class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport
handleResultChangeEvent(ResultChangeEvent) - Method in interface apollo.editor.ResultChangeListener
handleResultChangeEvent(ResultChangeEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleResultChangeEvent(ResultChangeEvent) - Method in class apollo.gui.Controller
handleResultChangeEvent(ResultChangeEvent) - Method in class apollo.gui.ControllerDebugListener
handleResultChangeEvent(ResultChangeEvent) - Method in class apollo.gui.genomemap.ResultView
handleReverseComplementEvent(ReverseComplementEvent) - Method in class apollo.gui.Controller
handleReverseComplementEvent(ReverseComplementEvent) - Method in interface apollo.gui.event.ReverseComplementListener
handleReverseComplementEvent(ReverseComplementEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleReverseComplementEvent(ReverseComplementEvent) - Method in class apollo.gui.synteny.SyntenyPanel
handleRubberbandEvent(RubberbandEvent) - Method in interface apollo.gui.event.RubberbandListener
handleRubberbandEvent(RubberbandEvent) - Method in class apollo.gui.genomemap.ApolloPanel
handleRubberbandEvent(RubberbandEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleRubberbandEvent(RubberbandEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel: Rubberbanding a link centers on the link (no selection)
handleScrollEvent(ScrollEvent) - Method in class apollo.gui.Controller
handleScrollEvent(ScrollEvent) - Method in interface apollo.gui.event.ScrollListener
handleScrollEvent(ScrollEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleScrollEvent(ScrollEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel
handleSequenceSelectionEvent(SequenceSelectionEvent) - Method in class apollo.gui.ApolloJalviewEventBridge
handleSetActiveCurStateEvent(SetActiveCurStateEvent) - Method in class apollo.gui.Controller
handleSetActiveCurStateEvent(SetActiveCurStateEvent) - Method in interface apollo.gui.event.SetActiveCurStateListener
handleSetActiveCurStateEvent(SetActiveCurStateEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleSetSelected() - Method in class apollo.dataadapter.synteny.builder.Controller
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.EvidenceTagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.ExonTagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.LocusTagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.SequenceFragmentTagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.SequenceSetTagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.TagHandler
handleStartElement(OtterContentHandler, String, String, String, Attributes) - Method in class apollo.dataadapter.otter.parser.TranscriptTagHandler
handleTierManagerEvent(TierManagerEvent) - Method in interface apollo.gui.event.TierManagerListener
handleTierManagerEvent(TierManagerEvent) - Method in class apollo.gui.genomemap.AnnotationView
handleTierManagerEvent(TierManagerEvent) - Method in class apollo.gui.genomemap.SiteView
handleTierManagerEvent(TierManagerEvent) - Method in class apollo.gui.genomemap.TierView
handleUpdateNode() - Method in class apollo.dataadapter.synteny.builder.Controller
handleViewEvent(ViewEvent) - Method in interface apollo.gui.event.ViewListener
handleViewEvent(ViewEvent) - Method in class apollo.gui.genomemap.ApolloPanel
handleZoomEvent(ZoomEvent) - Method in class apollo.gui.Controller
handleZoomEvent(ZoomEvent) - Method in interface apollo.gui.event.ZoomListener
handleZoomEvent(ZoomEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
handleZoomEvent(ZoomEvent) - Method in class apollo.gui.synteny.SyntenyLinkPanel: Zoom events are delivered by one of the two controllers I listen to.
hasAlignable() - Method in class apollo.datamodel.FeaturePair: Returns true if has a real alignment or if theres a "trivial" alignment from SeqFeature.getTrivialAlignable
hasAlignable() - Method in class apollo.datamodel.SeqFeature: A sequence feature is always alignable if it has sequence
hasAlignable() - Method in interface apollo.datamodel.SeqFeatureI: Returns true if feat has an alignable (may be an ISA but thats inconsequetial here)
hasAnalogousOppositeStrandFeature() - Method in class apollo.datamodel.SeqFeature: Returns false if analog opp strand fs not set
hasAnalogousOppositeStrandFeature() - Method in interface apollo.datamodel.SeqFeatureI: Returns false if analog opp strand fs not set
hasAnnotatedFeature() - Method in class apollo.datamodel.AnnotatedFeature
hasAnnotatedFeature() - Method in class apollo.datamodel.SeqFeature: Whether the SeqFeature is an annotation - return false by default - AnnotatedFeature overrides
hasAnnotatedFeature() - Method in interface apollo.datamodel.SeqFeatureI: Whether the SeqFeature is an annotation - annotation here meaning gene, transcript or exon - not just top level annot - i fear the term "annotation" has 2 meanings - strictly the top level annotation, and loosely any level of the annotation.
hasBothSpecies() - Method in class apollo.datamodel.SpeciesComparison
hasChromosomes() - Static method in class apollo.config.Config
hasCigar() - Method in class apollo.datamodel.FeaturePair
hasCigar() - Method in class apollo.datamodel.SeqFeature
hasCompoundType() - Method in class apollo.editor.CompoundTransaction
hasCompoundType() - Method in class apollo.editor.UpdateParentTransaction
hasDescendents() - Method in class apollo.datamodel.FeatureSet
hasDescendents() - Method in interface apollo.datamodel.FeatureSetI: returns true if the count of the number of leaf features (those that can't have child features themselves) is > 0.
hasFeatureType() - Method in class apollo.datamodel.Range
hasFeatureType() - Method in interface apollo.datamodel.RangeI: convenience method returns !getType()==NO_TYPE
hashCode() - Method in class apollo.util.interval.Interval
hashCode() - Method in class apollo.util.Pair: Overload Object.hashCode to return the sum of the the values hashCode
HashDB - Class in apollo.analysis
HashDB(DataInputStream) - Constructor for class apollo.analysis.HashDB
hasHitFeature() - Method in class apollo.datamodel.FeaturePair: from SeqFeatureI
hasHitFeature() - Method in class apollo.datamodel.SeqFeature: Whether SeqFeatureI has a hit feature.
hasHitFeature() - Method in interface apollo.datamodel.SeqFeatureI: Whether SeqFeatureI has a hit feature.
HashMatch - Class in apollo.analysis
HashMatch(SequenceI, HashDB) - Constructor for class apollo.analysis.HashMatch
hasId() - Method in class apollo.datamodel.SeqFeature
hasId() - Method in interface apollo.datamodel.SeqFeatureI: returns false if getId() == null
hasInput() - Method in class apollo.dataadapter.DataInput
hasKids() - Method in class apollo.datamodel.SeqFeature: Return true if getFeatures().size() > 0, we actually have a kid
hasKids() - Method in interface apollo.datamodel.SeqFeatureI: Returns false if getFeatures().size() == 0
hasKids() - Method in class apollo.editor.Transaction: returns true for comp trans if actually has kid trans
hasLinkData() - Method in class apollo.dataadapter.AbstractApolloAdapter: Whether data adapter contains link data used for synteny, returns false by default override if otherwise
hasLinkData() - Method in interface apollo.dataadapter.ApolloDataAdapterI: Whether data adapter contains link data used for synteny (e.g.
hasLinkData() - Method in class apollo.dataadapter.chado.ChadoAdapter: Return true - this means that the features potentially have synteny data associated with them and then can be used in the synteny viewer this follows the game model of embedding links in the features
hasLinkData() - Method in class apollo.dataadapter.gamexml.GAMEAdapter: Returns true as game data contains link data that can be used by synteny
hasLinkSet() - Method in class apollo.datamodel.SpeciesComparison: Returns true if there is a link set, even if its empty
hasListener(EventListener) - Method in class apollo.gui.Controller
hasModel() - Method in class apollo.gui.ScoreCalculator: Whether getModel() is non null
hasModel() - Method in class apollo.gui.WindowScoreCalculator
hasName() - Method in class apollo.datamodel.AbstractSequence: Return true if name is NO_NAME.
hasName() - Method in class apollo.datamodel.Range
hasName() - Method in interface apollo.datamodel.RangeI: return true if name !equal NO_NAME
hasName() - Method in interface apollo.datamodel.SequenceI
hasNameBeenSet() - Method in class apollo.datamodel.FeatureSet
hasNameBeenSet() - Method in interface apollo.datamodel.FeatureSetI
hasNames() - Method in class apollo.datamodel.Link: Returns true if query and hit have names
hasNext() - Method in class apollo.util.FeatureIterator
hasNextFeature() - Method in class apollo.util.FeatureIterator
hasNonDefaultNameAdapter() - Method in class apollo.config.FeatureProperty: Has nameadapter if this is an annotation tier
hasNonEmptyLinkSet() - Method in class apollo.datamodel.CompositeDataHolder
hasOpenTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
hasOverlapper() - Method in class apollo.config.FeatureProperty: Has overlapper if this is an annotation tier
hasOwner() - Method in class apollo.datamodel.Synonym
hasParentTransaction() - Method in class apollo.editor.Transaction
hasPeptideSequence() - Method in class apollo.datamodel.SeqFeature: Whether feature has a peptide sequence - default is false - override if otherwise (Transcript returns true)
hasPeptideSequence() - Method in interface apollo.datamodel.SeqFeatureI: Whether feature has a peptide sequence
hasPeptideSequence() - Method in class apollo.datamodel.Transcript: If we have a translation start(nonzero) we have a peptide seq do i have this right? translate may still return null if we have start but no transcript sequence(if theres no sequence for the entry).
hasPercentIdentity() - Method in class apollo.datamodel.Link: Return false if species feat has no score or if its score is no perc id
hasPrevious() - Method in class apollo.util.FeatureIterator
hasProteinFeat() - Method in class apollo.datamodel.Transcript
hasRange() - Method in class apollo.datamodel.AbstractSequence: Convenience for getRange null check
hasReadThroughStop() - Method in class apollo.datamodel.FeatureSet
hasReadThroughStop() - Method in interface apollo.datamodel.FeatureSetI
hasRefSequence() - Method in class apollo.datamodel.Range
hasRefSequence() - Method in interface apollo.datamodel.RangeI: return false if no ref seq, ranges should generally have ref seq, only during initialization might it not
hasResidues() - Method in class apollo.datamodel.AbstractSequence: This will return false if getResidues() is null or "", clearResidues() will set residues to "" causing this to be false.
hasResidues() - Method in interface apollo.datamodel.SequenceI: This will return false if there are no residues (null || "", cleared).
hasResidueType() - Method in class apollo.datamodel.AbstractSequence
hasResidueType() - Method in interface apollo.datamodel.SequenceI: Calculates residue type by comparing seq length to feat length.
hasResults() - Method in class apollo.analysis.SeqAnalysisBase
hasResults() - Method in interface apollo.analysis.SeqAnalysisI: does the analysis have any results to read yet? note: an analysis implementation may choose to give results incrementally, so it need not be finished before returning results
hasSecondSpecies() - Method in class apollo.datamodel.SpeciesComparison
hasSequence() - Method in class apollo.datamodel.seq.GAMESequence
hasSequenceFilename() - Method in class apollo.dataadapter.DataInput
hasSpeciesFeatures() - Method in class apollo.datamodel.Link
hasStartAndEnd() - Method in class apollo.dataadapter.chado.SeqType
hasStyleForSpecies(String) - Static method in class apollo.config.Config
hasSubpart() - Method in class apollo.editor.FeatureChangeEvent
hasSynonym(String) - Method in class apollo.datamodel.AnnotatedFeature
hasSynonym(String) - Method in interface apollo.datamodel.AnnotatedFeatureI
hasSyntenyLinkInfo() - Method in class apollo.datamodel.SeqFeature
hasSyntenyLinkInfo() - Method in interface apollo.datamodel.SeqFeatureI
hasTermWithId(String) - Method in class apollo.util.OBOParser: Check to see if a term with the given ID exists
hasTermWithName(String) - Method in class apollo.util.OBOParser: Check to see if a term with the given name exists
hasTransactionManager() - Method in class apollo.datamodel.CurationSet
hasTransactions() - Method in class apollo.datamodel.CurationSet
hasTransactions() - Method in class apollo.editor.AnnotationChangeLog
hasTransactions() - Method in class apollo.editor.TransactionManager
hasTranslation() - Method in class apollo.datamodel.FeatureSet: FeatureSets have translations.
hasTranslation() - Method in class apollo.datamodel.SeqFeature: Return false by default - FeatureSet overrides - if this is the same as isProteinCodingGene then we should delete it
hasTranslation() - Method in interface apollo.datamodel.SeqFeatureI: im thinking maybe there should be a separate interface for translation methods (yes i know there is - its called a feature set) and seqfeatureI would have this - not be implemented in a subclass (or if it is not have that be noticaeable at the api/interface level) in other words a HASA not a ISA! i think that would be cleaner
hasTranslationEnd() - Method in class apollo.datamodel.FeatureSet: Returns true if there is end of translation for the transcript, ie getTranslationEnd()!=0.
hasTranslationEnd() - Method in class apollo.datamodel.Protein: well this is actually controversial - translation end is just beyond the protien - this should either be refactored or just be in transcript - need to think about this...
hasTranslationEnd() - Method in interface apollo.datamodel.TranslationI
hasTranslationStart() - Method in class apollo.datamodel.FeatureSet: Returns true if transcript has a translation start (!=0)
hasTranslationStart() - Method in class apollo.datamodel.Protein: should this just be hasStart? translation is implicit now isnt it?
hasTranslationStart() - Method in interface apollo.datamodel.TranslationI
haveAnnots() - Method in class apollo.dataadapter.CurationState: Returns true if curSet have >0 annotations
haveAnnots() - Method in class apollo.gui.synteny.GuiCurationState: Returns true if curSet have >0 annotations
haveExplicitAlignment() - Method in class apollo.datamodel.SeqFeature
haveExplicitAlignment() - Method in interface apollo.datamodel.SeqFeatureI
haveRealAlignment() - Method in class apollo.datamodel.SeqFeature
haveRealAlignment() - Method in interface apollo.datamodel.SeqFeatureI
haveSequence() - Method in class apollo.dataadapter.CurationState: Whether curationSet has ref sequence (formerly in ApolloFrame)
haveSequence() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
haveSequence() - Method in class apollo.gui.synteny.GuiCurationState: Whether curationSet has ref sequence (formerly in ApolloFrame)
haveWholeSequence() - Method in class apollo.datamodel.Transcript: Returns true if transcript is hanging off the bounds of the entry Does this belong in FeatureSet? Or even SeqFeature? Delete this - replaced by isContainedByRefSeq
header - Variable in class apollo.datamodel.seq.GenbankSequence
heading - Variable in class apollo.config.ColumnProperty
height - Variable in class apollo.gui.genomemap.SiteView
HelpMenu - Class in apollo.gui.menus
HelpMenu(ApolloFrame) - Constructor for class apollo.gui.menus.HelpMenu
hi - Variable in class apollo.gui.Transformer.PixelRange
HIDE_OR_SHOW_ANNOTATIONS - Static variable in class apollo.dataadapter.ensj.controller.Controller
HIDE_OR_SHOW_DATABASE - Static variable in class apollo.dataadapter.ensj.controller.Controller
HIDE_OR_SHOW_LOCATION - Static variable in class apollo.dataadapter.ensj.controller.Controller
HIDE_OR_SHOW_OPTIONS - Static variable in class apollo.dataadapter.ensj.controller.Controller
HIDE_OR_SHOW_TYPES - Static variable in class apollo.dataadapter.ensj.controller.Controller
hideLabelTier(String) - Method in class apollo.gui.genomemap.FeatureTierManager
hideLabelTier(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager
HideShowAnnotationsHandler - Class in apollo.dataadapter.ensj.controller: Declare the types panel (as represented by the model) to be either showing or not, and refresh!
HideShowAnnotationsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.HideShowAnnotationsHandler
HideShowDatabasesHandler - Class in apollo.dataadapter.ensj.controller: Declare the types panel (as represented by the model) to be either showing or not, and refresh!
HideShowDatabasesHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.HideShowDatabasesHandler
HideShowLocationsHandler - Class in apollo.dataadapter.ensj.controller: Declare the types panel (as represented by the model) to be either showing or not, and refresh!
HideShowLocationsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.HideShowLocationsHandler
HideShowOptionsHandler - Class in apollo.dataadapter.ensj.controller: Declare the options panel (as represented by the model) to be either showing or not, and refresh!
HideShowOptionsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.HideShowOptionsHandler
HideShowTypesHandler - Class in apollo.dataadapter.ensj.controller: Declare the types panel (as represented by the model) to be either showing or not, and refresh!
HideShowTypesHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.HideShowTypesHandler
hideTier(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager
high - Variable in class apollo.datamodel.Range
HIGH - Static variable in class apollo.gui.DetailInfo
HIGH_AFFINITY - Static variable in class apollo.seq.ResidueProperties
highestBase - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
highestBase - Variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: The base pair the panel ends at in outside world(chromosomal)
HIGHLIGHTED - Static variable in class apollo.gui.drawable.DrawableSeqFeature
highlightEdges(Selection, boolean) - Method in class apollo.gui.genomemap.ApolloPanel: I believe this highlights edges in other views that line up with the edges in the selection
His - Static variable in class apollo.seq.ResidueProperties
history_listener - Variable in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI
history_listener - Variable in class apollo.dataadapter.das2.DAS2AdapterGUI
hitClip(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics
hitSequence - Variable in class apollo.datamodel.FeatureSet
hitZones - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
hitZones - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
hitZones - Variable in class apollo.gui.detailviewers.sequencealigner.FindDialog
holdsType(String) - Method in class apollo.config.TierProperty
homeInOnSelectedLink() - Method in class apollo.gui.synteny.SyntenyLinkPanel: Zoom to features of link and hide strands not linked
HomogeneousPanel - Class in apollo.gui.detailviewers.sequencealigner.DNAPanel
HomogeneousPanel(PanelFactory) - Constructor for class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel
HomogeneousPanel(PanelFactory, FeaturePlaceFinder.Type) - Constructor for class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel
HORIZONTAL - Static variable in class apollo.gui.genomemap.ApolloLayoutManager
HORIZONTAL - Static variable in interface apollo.gui.Orientations
horizontalMode - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
horizontalMode - Variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel: Related to the scroll policy.
HorizontalScrollBarAdjustmentListener - Class in apollo.gui.detailviewers.sequencealigner
HorizontalScrollBarAdjustmentListener(JViewport) - Constructor for class apollo.gui.detailviewers.sequencealigner.HorizontalScrollBarAdjustmentListener
host - Variable in class apollo.dataadapter.GbrowseAdapter
host - Variable in class apollo.dataadapter.mysql.Database
HOST - Static variable in class apollo.dataadapter.StateInformation
HTMLUtil - Class in apollo.util
HTTP_PROXY_HOST - Static variable in class apollo.dataadapter.StateInformation
HTTP_PROXY_PORT - Static variable in class apollo.dataadapter.StateInformation
HTTP_PROXY_SET - Static variable in class apollo.dataadapter.StateInformation
httpServerIsEnabled() - Static method in class apollo.config.Config
HuffNode - Class in apollo.analysis.filter
HuffNode(String) - Constructor for class apollo.analysis.filter.HuffNode
HuffNode(HuffNode, HuffNode) - Constructor for class apollo.analysis.filter.HuffNode

I

id - Variable in class apollo.dataadapter.das.simple.SimpleDASFeature
ID - Static variable in class apollo.dataadapter.ensj.EnsJAdapter
ID - Static variable in class apollo.dataadapter.otter.parser.TagHandler
id - Variable in class apollo.datamodel.SeqFeature
ID - Static variable in class apollo.editor.TransactionOperation
ID - Static variable in class apollo.editor.TransactionSubpart
ID - Static variable in class apollo.gui.DetailInfo
ID_PATTERN - Static variable in class apollo.dataadapter.ensj.EnsJAdapter
idAndNameHaveSameFormat(SeqFeatureI, String, String) - Method in interface apollo.config.ApolloNameAdapterI: Return true if id and name have same format
idAndNameHaveSameFormat(SeqFeatureI, String, String) - Method in class apollo.config.ChadoJdbcNameAdapter: Return true if id and name have same format
idAndNameHaveSameFormat(SeqFeatureI, String, String) - Method in class apollo.config.DefaultNameAdapter: Returns true if name and id of feat are in the same format.
idAndNameHaveSameFormat(SeqFeatureI, String, String) - Method in class apollo.config.ParameciumNameAdapter: Return true if id and name have same format
idAndNameHaveSameFormat(SeqFeatureI, String, String) - Method in class apollo.config.TigrAnnotNameAdapter
Identifier - Class in apollo.datamodel
Identifier(String) - Constructor for class apollo.datamodel.Identifier
identity(SeqFeatureI) - Method in class apollo.analysis.filter.AnalysisFilter
IgbBridge - Class in apollo.external: Gets selection events from apollo - via controller, set up by CuiCurationState, configured in style - sends selection to igb via http
IgbBridge(GenomicRange) - Constructor for class apollo.external.IgbBridge
igbHttpConnectionEnabled() - Method in class apollo.config.Style
igbLinksEnabled() - Static method in class apollo.gui.menus.LinksMenu
ignorableWhitespace(char[], int, int) - Method in class apollo.dataadapter.gamexml.XMLParser
ignoreEvents() - Method in class apollo.dataadapter.synteny.builder.Controller
ignoreScoreThresholds() - Method in class apollo.gui.TierManager
Ile - Static variable in class apollo.seq.ResidueProperties
importData(JComponent, Transferable) - Method in class apollo.gui.ArrayListTransferHandler
in - Variable in class apollo.dataadapter.CGI
inBatchMode - Static variable in class apollo.config.Config
INCLUDE_CONTIG_FEATURE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_CONTIG_FEATURE_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DITAG_FEATURE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DITAG_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DNA_DNA_ALIGNMENT - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DNA_DNA_ALIGNMENT_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DNA_PROTEIN_ALIGNMENT - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_DNA_PROTEIN_ALIGNMENT_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_FEATURE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_FEATURE_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_GENE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_GENE_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_PREDICTION_TRANSCRIPT - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_PREDICTION_TRANSCRIPT_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_REPEAT_FEATURE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_REPEAT_FEATURE_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_SIMPLE_PEPTIDE_FEATURE - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_SIMPLE_PEPTIDE_FEATURE_TYPES - Static variable in class apollo.dataadapter.StateInformation
INCLUDE_VARIATION - Static variable in class apollo.dataadapter.StateInformation
includeAbInitioPredictions() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeContigs() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeDitagFeatures() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeDnaDnaAlignments() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeDnaProteinAlignments() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeGenes() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeProteinAnnotations() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeRepeats() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeSimpleFeatures() - Method in class apollo.dataadapter.ensj.model.TypesModel
includeVariations() - Method in class apollo.dataadapter.ensj.model.TypesModel
incrementGeneTranscriptRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
incrementTierHeight() - Method in class apollo.gui.genomemap.TierView
incrementTierHeight() - Method in interface apollo.gui.genomemap.TierViewI
incrementTierHeight() - Method in class apollo.gui.TierManager
incrementTierHeight() - Method in interface apollo.gui.TierManagerI
incrementTranscriptExonRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
INDENT - Static variable in class apollo.dataadapter.otter.parser.TagHandler
indexOf(Object) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
inDrag - Variable in class apollo.gui.genomemap.ApolloPanel
inFile - Variable in class apollo.io.FileParse
informationDialog(String) - Static method in class apollo.util.IOUtil: Display an information dialog box (if not running in headless mode or command line mode and outputs information to logger).
inheritWarnOnEdit(boolean) - Method in class apollo.config.FeatureProperty: Initially, the value of warnonedit is inherited from the parent tier--may later be overridden.
init() - Method in class apollo.analysis.SeqAnalysisBase
init() - Method in class apollo.analysis.SeqAnalysisLocal
init() - Method in class apollo.dataadapter.AbstractApolloAdapter: From org.bdgp.io.DataAdapter interface.
init() - Method in class apollo.dataadapter.analysis.AnalysisAdapter
init() - Method in class apollo.dataadapter.BaseGFFAdapter
init() - Method in class apollo.dataadapter.chado.ChadoAdapter
init(String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: This method must be called before calling any of the other methods of this class (or those of its subclasses.) This will typically be done by an instance of apollo.dataadapter.chado.ChadoAdaptor.
init() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapterGUI
init() - Method in class apollo.dataadapter.ChromosomeAdapter
init() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter
init() - Method in class apollo.dataadapter.das2.DAS2Adapter
init() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI
init() - Method in class apollo.dataadapter.DummySequenceAdapter
init() - Method in class apollo.dataadapter.EfetchSequenceAdapter
init() - Method in class apollo.dataadapter.EnsCGIAdapter
init() - Method in class apollo.dataadapter.ensj.EnsJAdapter: From org.bdgp.DataAdapter interface.
init() - Method in class apollo.dataadapter.ensj19.DriverDialog
init() - Method in class apollo.dataadapter.ensj19.EnsJAdapter
init() - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapter
init() - Method in class apollo.dataadapter.gamexml.GAMEAdapter
init() - Method in class apollo.dataadapter.gamexml.GAMEAdapterGUI
init() - Method in class apollo.dataadapter.GbrowseAdapter
init() - Method in class apollo.dataadapter.genbank.GenbankAdapter
init() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Initialize the adapter
init() - Method in class apollo.dataadapter.otter.OtterAdapter
init() - Method in class apollo.dataadapter.otter.OtterXMLAdapter
init() - Method in class apollo.dataadapter.sample.SampleAdapter: From org.bdgp.DataAdapter interface.
init() - Method in class apollo.dataadapter.SerialDiskAdapter
init() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter
init() - Method in class apollo.dataadapter.synteny.ChromosomePanel
init() - Method in class apollo.dataadapter.synteny.FullEnsJDBCSyntenyPanel
init() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
init() - Method in class apollo.dataadapter.SyntenyGFFAdapter
init(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
init() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
init(char, int, int, SequenceI) - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
init() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
init() - Method in class apollo.gui.detailviewers.sequencealigner.FindDialog
init() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame
init() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel: Creates all of the components and lays everything out
init(char) - Method in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
init() - Method in class apollo.gui.evidencepanel.SetDetailPanel
init() - Method in class apollo.gui.FullSyntenyPanel
init(JComponent, String, boolean) - Method in class apollo.gui.genomemap.LinearView
init() - Method in class apollo.gui.ProxyDialog
initAlignment(SequenceI, int) - Method in class apollo.dataadapter.analysis.AlignmentParser
initAlignPair() - Method in class apollo.dataadapter.analysis.AlignmentParser
initAnalysis(StrandedFeatureSetI, int, String) - Method in class apollo.dataadapter.analysis.AbstractParser
initCuration(CurationSet, SequenceI) - Method in class apollo.dataadapter.analysis.AbstractParser
initFeature() - Method in class apollo.dataadapter.analysis.AbstractParser
initGUI() - Method in class apollo.gui.GenericFileAdapterGUI
initialiseChromosomeDropdown() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
initialiseDatabaseDriver(Properties) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
initialiseGUI() - Method in class apollo.dataadapter.ensj.view.LocationPanel
initialiseGUI() - Method in class apollo.dataadapter.ensj.view.OptionsPanel
initialiseGUI() - Method in class apollo.dataadapter.ensj.view.TypesPanel
initialiseGUI() - Method in class apollo.dataadapter.synteny.builder.View
initialiseView() - Method in class apollo.dataadapter.ensj.view.View
initializeConfiguration() - Static method in class apollo.config.Config
initialLockedScrolling() - Method in class apollo.config.Style: Whether synteny's initial state is to lock scrolling.
initialShiftForLockedZooming() - Method in class apollo.config.Style: Whether synteny should lock zooming with a shift or vice versa, initially.
initLabel(String) - Method in class apollo.gui.annotinfo.FeatureEditPanel
initLoad(CurationSet, boolean, InputStream, AnalysisInput) - Method in class apollo.dataadapter.analysis.AbstractParser
initLocations() - Method in class apollo.dataadapter.genbank.PublicDbFeature
initSeqAnalysis() - Method in class apollo.analysis.SeqAnalysisBase
initSeqAnalysisBDGP() - Method in class apollo.analysis.SeqAnalysisBDGP
initSeqAnalysisLocal() - Method in class apollo.analysis.SeqAnalysisLocal
initSeqAnalysisNCBI() - Method in class apollo.analysis.SeqAnalysisNCBI
initSeqAnalysisRemote() - Method in class apollo.analysis.SeqAnalysisRemote
initSequence(CurationSet, String, int) - Method in class apollo.dataadapter.analysis.AbstractParser
initSet(String, int) - Method in class apollo.dataadapter.analysis.AbstractParser
initSet() - Method in class apollo.gui.drawable.DrawableFeatureSet: feature holds a reference to the real feature.
initStatus(String) - Method in class apollo.config.PeptideStatus
initSynonyms() - Method in class apollo.dataadapter.genbank.PublicDbFeature
initTier(TierProperty, String, boolean) - Method in class apollo.config.TiersIO
initTier(TierProperty, String) - Method in class apollo.config.TiersIO: Used for updating existing tier--no need to set isFirstTier
initTiersList(String) - Method in class apollo.dataadapter.analysis.AnalysisPanel
initTypesList(String) - Method in class apollo.dataadapter.analysis.AnalysisPanel
initWithException(String, String, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: This method must be called before calling any of the other methods of this class (or those of its subclasses.) This will typically be done by an instance of apollo.dataadapter.chado.ChadoAdaptor.
initWithSeqFeat(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature
INPUT_DATA_SET - Static variable in class apollo.dataadapter.StateInformation
INPUT_FILE_NAME - Static variable in class apollo.dataadapter.StateInformation
INPUT_ID - Static variable in class apollo.dataadapter.StateInformation
INPUT_SERVER_NAME - Static variable in class apollo.dataadapter.StateInformation
INPUT_STRING - Static variable in class apollo.dataadapter.StateInformation
INPUT_TYPE - Static variable in class apollo.dataadapter.StateInformation
INSERT - Static variable in class apollo.dataadapter.chado.ChadoTransaction
insert(Interval) - Method in class apollo.util.interval.IntervalTree
insert(RbNode) - Method in class apollo.util.interval.RbTree
insertDbRowIfNeeded(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertDbXrefRowIfNeeded(long, String, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeatureAt(SeqFeatureI, int) - Method in class apollo.datamodel.FeatureSet: Add feature(kid) to features list at position position.
insertFeatureDbXrefRow(long, long, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeaturelocRow(Long, Long, Integer, Integer, boolean, boolean, Integer, Integer, String, int, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeaturepropPubRow(Long, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeaturepropRow(Long, Long, String, long, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeaturepropRow(Long, Long, String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeatureRelationshipRow(Long, Long, Long, String, Long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeatureRow(Long, long, String, String, String, Long, Long, Integer, Date) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertFeatureSynonymRow(Long, Long, Integer, boolean, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertIntoTabbedPane(JTabbedPane, int) - Method in class apollo.dataadapter.GuiTabPanel: Inserts panel into tabbed pane with name and tooltip at index
INSERTION - Static variable in interface apollo.datamodel.SequenceI: These are SO terms (under general family of sequence_variation) changed insertion to nucleotide_insertion as its more specific and i believe thats what we are doing here, same with deletion eventually should come from SO (should this be in tiers file?)
InsertionDialog - Class in apollo.gui.detailviewers.sequencealigner.menus
InsertionDialog(String) - Constructor for class apollo.gui.detailviewers.sequencealigner.menus.InsertionDialog
insertionMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel
insertionMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
insertionMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
insertionsBefore(int, String) - Method in class apollo.datamodel.FeaturePair
insertPubRowIfNeeded(String, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
insertRow(String, Map, Map) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter: Generic method to insert a single row into a named table.
insertSynonymRowIfNeeded(String, Long, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
installListeners() - Method in class apollo.gui.detailviewers.sequencealigner.FindDialog
installListeners() - Method in class apollo.gui.ProgressFrame
integersTheSame(Integer, Integer) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
interactionListener - Variable in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
internalMode() - Static method in class apollo.config.Config
internalMode() - Method in class apollo.config.Style
interpretDrop(DragViewI, MouseEvent) - Method in class apollo.gui.genomemap.AnnotationView
interpretDrop(DragViewI, MouseEvent, boolean, StringBuffer) - Method in class apollo.gui.genomemap.AnnotationView: Returns true if drop is sucessful (?) If editing is disabled does nothing, returns false.
interpretDrop(DragViewI, MouseEvent) - Method in interface apollo.gui.genomemap.DropTargetViewI
interpretDrop(DragViewI, MouseEvent, boolean, StringBuffer) - Method in interface apollo.gui.genomemap.DropTargetViewI
interpretDrop(DragViewI, MouseEvent) - Method in class apollo.gui.genomemap.TierView
interpretDrop(DragViewI, MouseEvent, boolean, StringBuffer) - Method in class apollo.gui.genomemap.TierView
interrupt() - Method in class apollo.gui.SwingWorker: A new method that interrupts the worker thread.
intersects(Rectangle, Transformer, TierManagerI) - Method in interface apollo.gui.drawable.Drawable
intersects(Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature
Interval - Class in apollo.util.interval
Interval(int, int) - Constructor for class apollo.util.interval.Interval
IntervalComponent - Class in apollo.gui.detailviewers.sequencealigner.overview: This is the class which draws intervals.
IntervalComponent() - Constructor for class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent: Empty Constructor
IntervalComponent.Valignment - Enum in apollo.gui.detailviewers.sequencealigner.overview
IntervalTree - Class in apollo.util.interval
IntervalTree() - Constructor for class apollo.util.interval.IntervalTree
inTierDrag - Variable in class apollo.gui.genomemap.ApolloPanel
INTRON - Static variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel
INTRON - Static variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
intSort(int[], int, int, Object[]) - Static method in class apollo.util.QuickSort
invalid - Variable in class apollo.gui.genomemap.ApolloPanel
invalidateLayout(Container) - Method in class apollo.gui.genomemap.ApolloLayoutManager
invertViews() - Method in class apollo.gui.genomemap.LaidoutViewContainer
invertViews() - Method in class apollo.gui.genomemap.SplitterView
IOUtil - Class in apollo.util: I can't believe these basic IO utilities didn't already exist somewhere, but I didn't see them.
IOUtil() - Constructor for class apollo.util.IOUtil
IS_DICISTRONIC - Static variable in class apollo.editor.TransactionSubpart
is_drawn - Variable in class apollo.gui.drawable.DrawableSeqFeature
IS_PROBLEMATIC - Static variable in class apollo.editor.TransactionSubpart
isAA() - Method in class apollo.datamodel.AbstractSequence: convenience
isAA() - Method in interface apollo.datamodel.SequenceI: Return true if getResidueType() == AA
isAbInitioTypeCountInitialised() - Method in class apollo.dataadapter.ensj.model.TypesModel
isActive() - Method in class apollo.gui.genomemap.Rubberband
isActiveCurName(String) - Method in class apollo.gui.synteny.CurationManager
isAdd() - Method in class apollo.editor.AddTransaction
isAdd() - Method in class apollo.editor.AnnotationAddEvent
isAdd() - Method in class apollo.editor.FeatureChangeEvent
isAdd() - Method in class apollo.editor.Transaction
isAddPeptide() - Method in class apollo.editor.AddTransaction
isAddPeptide() - Method in class apollo.editor.Transaction
isAllowed(String) - Method in class apollo.config.TiersIO
isAllowed(String, String) - Method in class apollo.config.TiersIO
isAminoAcidAlignment(String) - Static method in class apollo.util.SeqFeatureUtil
isAminoAcidAlignment(SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil
isAncestorOf(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature: Returns true if this == sf.
isAncestorOf(SeqFeatureI) - Method in interface apollo.datamodel.SeqFeatureI: Whether this is the ancestor of sf.
isAnnot() - Method in class apollo.datamodel.SeqFeature: If we have an AnnotatedFeature then we are an annot and vice versa
isAnnot() - Method in interface apollo.datamodel.SeqFeatureI
isAnnotation() - Method in class apollo.dataadapter.gff3.GFF3Entry: Check whether this feature is annotation (evidence otherwise)
isAnnotationChanged() - Method in class apollo.gui.Controller
isAnnotationsPanelVisible() - Method in class apollo.dataadapter.ensj.model.Model
isAnnotationTier(String) - Method in class apollo.config.PropertyScheme: Returns true if this tiername contains annotations rather than results.
isAnnotationType() - Method in class apollo.config.FeatureProperty
isAnnotId(SeqFeatureI) - Method in class apollo.config.GmodNameAdapter
isAnnotTop() - Method in class apollo.datamodel.AnnotatedFeature
isAnnotTop() - Method in class apollo.datamodel.SeqFeature
isAnnotTop() - Method in interface apollo.datamodel.SeqFeatureI: true for top level annots (e.g.
isAsynchronous() - Method in class apollo.analysis.SeqAnalysisBase: is the analysis asynchronous? (ie will launching the analysis cause the program to block?)
isAsynchronous() - Method in interface apollo.analysis.SeqAnalysisI: is the analysis asynchronous (ie will launching the analysis cause the program to block?) hmmm, this should probably be a property...
isAvoidingTextOverlaps() - Method in class apollo.gui.genomemap.FeatureTierManager
isAvoidingTextOverlaps() - Method in interface apollo.gui.genomemap.FeatureTierManagerI
isBoolean() - Method in class apollo.editor.TransactionSubpart
isBooleanUpdate() - Method in class apollo.editor.AnnotationUpdateEvent
isBottomForwardVisible() - Method in class apollo.gui.synteny.SyntenyLinkPanel
isBottomReverseVisible() - Method in class apollo.gui.synteny.SyntenyLinkPanel
isCellEditable(EventObject) - Method in class apollo.gui.DisabledEditor
isChadoTnOutputNeeded() - Static method in class apollo.config.Config: To see if chado transaction output is needed.
isChanged() - Method in interface apollo.gui.EditWindowI
isChromosomeArmUsed() - Method in class apollo.datamodel.CurationSet: A rather strange implemenation.
isChromosomeListInitialised() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI
isClone() - Method in class apollo.datamodel.SeqFeature
isClone() - Method in interface apollo.datamodel.SeqFeatureI: Check to see if this feature is a cloned feature
isCoalescedDone() - Method in class apollo.editor.TransactionManager: Check if coalescing is done.
isCodon() - Method in class apollo.datamodel.SeqFeature: Returns true if feature is start or stop codon currently does with feature type - perhaps should have a setIsCodon(bool) method?
isCodon() - Method in interface apollo.datamodel.SeqFeatureI: Returns true if feature is start or stop codon
isComment(String) - Method in class apollo.config.TiersIO
isComment() - Method in class apollo.editor.TransactionSubpart
isCommentary() - Method in class apollo.dataadapter.analysis.FgeneshGFFParser
isCommentary() - Method in class apollo.dataadapter.analysis.FgeneshParser
isCommentary() - Method in class apollo.dataadapter.analysis.GeneFinderParser
isCommentary() - Method in class apollo.dataadapter.analysis.GenieParser
isCommentary() - Method in class apollo.dataadapter.analysis.GenscanParser
isCommentChange() - Method in class apollo.editor.AnnotationChangeEvent
isCommentUpdate() - Method in class apollo.editor.AnnotationUpdateEvent
isCommentUpdate() - Method in interface apollo.editor.UpdateDetailsI
isCompletelyObscured(int, int, int) - Method in class apollo.gui.genomemap.PixelMask: start and stop are for x coords, yindex corresponds to vertical level Returns true if the range of xcoords in the yindex level is completely masked out
isCompletelyObscured(int, int, int) - Method in interface apollo.gui.genomemap.PixelMaskI
isComposite() - Method in class apollo.dataadapter.AbstractApolloAdapter: By default return false - data adapter is not composite.
isComposite() - Method in interface apollo.dataadapter.ApolloDataAdapterI: returns true if the data adapter holds species adapters.
isComposite() - Method in class apollo.dataadapter.synteny.SyntenyAdapter
isCompositeDataHolder() - Method in interface apollo.datamodel.ApolloDataI
isCompositeDataHolder() - Method in class apollo.datamodel.CompositeDataHolder
isCompositeDataHolder() - Method in class apollo.datamodel.CurationSet
isCompound() - Method in class apollo.editor.AnnotationCompoundEvent
isCompound() - Method in class apollo.editor.CompoundTransaction
isCompound() - Method in class apollo.editor.FeatureChangeEvent: whether event is a compound event - ie contains child transactions/events.
isCompound() - Method in class apollo.editor.Transaction: default false.
isContainedByRefSeq() - Method in class apollo.datamodel.Range
isContainedByRefSeq() - Method in interface apollo.datamodel.RangeI: Return true if ref seq contains this range
isControlPanelVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
isCoordSystemInitialised() - Method in class apollo.dataadapter.ensj.model.LocationModel
isCurated() - Method in class apollo.config.TierProperty
isCurationSet() - Method in interface apollo.datamodel.ApolloDataI
isCurationSet() - Method in class apollo.datamodel.CompositeDataHolder: ApolloDataI - we are not a curation set so returning false.
isCurationSet() - Method in class apollo.datamodel.CurationSet: ApolloDataI
isCurationSetLoaded() - Method in class apollo.gui.Controller
isDatabaseListFound() - Method in class apollo.dataadapter.ensj.model.DatabaseModel
isDatabasePanelVisible() - Method in class apollo.dataadapter.ensj.model.Model
isDataFlavorSupported(DataFlavor) - Method in class apollo.gui.ArrayListTransferHandler.ArrayListTransferable
isDbXref() - Method in class apollo.editor.TransactionSubpart
isDecorated() - Method in interface apollo.gui.drawable.Drawable
isDecorated() - Method in class apollo.gui.drawable.DrawableSeqFeature
isDelete() - Method in class apollo.editor.AnnotationDeleteEvent
isDelete() - Method in class apollo.editor.DeleteTransaction
isDelete() - Method in class apollo.editor.FeatureChangeEvent
isDelete() - Method in class apollo.editor.Transaction
isDeletion() - Method in class apollo.datamodel.SequenceEdit
isDescription() - Method in class apollo.editor.TransactionSubpart
isDitagFeatureTypeCountInitialised() - Method in class apollo.dataadapter.ensj.model.TypesModel
isDnaDnaAlignmentTypeCountInitialised() - Method in class apollo.dataadapter.ensj.model.TypesModel
isDnaProteinAlignmentTypeCountInitialised() - Method in class apollo.dataadapter.ensj.model.TypesModel
isDownOrientation() - Method in class apollo.gui.genomemap.TierView: Down Orientation happens with reverse strand normal and forward strand in reverse comp (below axis)
isDrawn() - Method in interface apollo.gui.drawable.Drawable: returns true if FeatureSetI is really just a holder.
isDrawn() - Method in class apollo.gui.drawable.DrawableSeqFeature
isEditingEnabled() - Static method in class apollo.config.Config
isEditingEnabled(String) - Static method in class apollo.config.Config
isEditingEnabled() - Method in class apollo.config.Style
isEditingEnabled() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
isEditingEnabled() - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser
isEditingEnabled() - Method in class apollo.gui.genomemap.AnnotationView
isEmpty() - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel
isEmpty() - Method in class apollo.util.CaseInsensitiveStringHash
isEndOfEditSession() - Method in class apollo.editor.AnnotationCompoundEvent: Returns true.
isEndOfEditSession() - Method in class apollo.editor.AnnotSessionDoneEvent
isEndOfEditSession() - Method in class apollo.editor.FeatureChangeEvent: once compound transactions are fully in place i think this can be phased out essentially this can be seen as a hack around a lack of compound transactions.
isExactOverlap(RangeI) - Method in class apollo.datamodel.Range
isExactOverlap(RangeI) - Method in interface apollo.datamodel.RangeI
isExon() - Method in class apollo.dataadapter.chado.ChadoTransaction
isExon() - Method in class apollo.datamodel.Exon
isExon() - Method in class apollo.datamodel.SeqFeature
isExon() - Method in interface apollo.datamodel.SeqFeatureI
isExonChange() - Method in class apollo.editor.FeatureChangeEvent: Replaces Object Class EXON
isExpanded() - Method in class apollo.config.TierProperty
isExpanded(String) - Method in class apollo.gui.genomemap.FeatureTierManager
isExtensionListInDescription() - Method in class apollo.util.ExampleFileFilter: Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFastaFromGff() - Method in class apollo.dataadapter.gff3.GFF3Adapter: Checks whether to parse FASTA from GFF or external FASTA file
isFile() - Method in class apollo.dataadapter.DataInput
isFileChooserOpen() - Method in class apollo.dataadapter.ensj.model.AnnotationsModel
isFinished() - Method in class apollo.analysis.SeqAnalysisBase
isFinished() - Method in interface apollo.analysis.SeqAnalysisI: has the analysis finished?
isFinished() - Method in class apollo.datamodel.AnnotatedFeature
isFinished() - Method in interface apollo.datamodel.AnnotatedFeatureI
isFinished() - Method in class apollo.editor.TransactionSubpart
isFirstTier - Variable in class apollo.config.TierProperty
isFirstTier() - Method in class apollo.config.TierProperty
isFirstTierAnnot(FeatureSetI) - Method in class apollo.editor.AnnotationEditor: Returns true if this is a first-tier annotation
isFlagSet(int) - Method in class apollo.datamodel.FeatureSet: return the current state of the bit for this flag
isFlagSet(int) - Method in interface apollo.datamodel.FeatureSetI: some useful flags, hopefully using minimal space, to pass information about handling through from the parser to the filter when running bop.
isForward() - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent: true if the component will be rendered forwards false otherwise
isForwardStrand() - Method in class apollo.datamodel.Range: Convenience method for getStrand() == 1
isForwardStrand() - Method in interface apollo.datamodel.RangeI
isForwardStrand() - Method in class apollo.gui.drawable.DrawableSeqFeature
isForwardStrand1() - Method in class apollo.datamodel.Link
isForwardStrand2() - Method in class apollo.datamodel.Link
isForwardStrandVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel
isGeneTypeCountInitialised() - Method in class apollo.dataadapter.ensj.model.TypesModel
isGoodUser() - Method in class apollo.gui.annotinfo.FeatureEditPanel
isHeadlessApplication() - Static method in class apollo.config.Config: Checks whether the system is running in headless mode.
isHighlighted() - Method in class apollo.gui.drawable.DrawableSeqFeature
isId() - Method in class apollo.editor.TransactionSubpart
isIdentical(RangeI) - Method in class apollo.datamodel.Range: Returns true if same start,end,type and name.
isIdentical(RangeI) - Method in interface apollo.datamodel.RangeI: Returns true if same start,end,type and name.
isInCommandLineMode() - Static method in class apollo.main.CommandLine: If input & output (or batch) is fully specified, then we are in command line mode; no need for GUI.
isInsertion() - Method in class apollo.datamodel.SequenceEdit
isInt() - Method in class apollo.editor.TransactionSubpart
isInternal() - Method in class apollo.datamodel.Comment
isIntUpdate() - Method in class apollo.editor.AnnotationUpdateEvent
isIntUpdate() - Method in interface apollo.editor.UpdateDetailsI
isInvalid() - Method in class apollo.gui.genomemap.LinearView
isInvalid() - Method in interface apollo.gui.genomemap.ViewI: Get a flag indicating whether the view is invalid
isJavaWebStartApplication() - Static method in class apollo.config.Config: Checks to see if this application is a Java Web Start application
isLabeled() - Method in class apollo.config.TierProperty
isLabeled(boolean) - Method in class apollo.config.TierProperty
isLabeled() - Method in class apollo.gui.drawable.DrawableSeqFeature
isLabeled() - Method in class apollo.gui.genomemap.FeatureTier
isLabeled() - Method in class apollo.gui.genomemap.SiteTier
isLabeled() - Method in class apollo.gui.Tier
isLazy() - Method in class apollo.datamodel.AbstractSequence
isLazy() - Method in class apollo.datamodel.seq.AbstractLazySequence
isLazy() - Method in class apollo.datamodel.seq.GAMESequence: Change this to return true when GAMESequence actually becomes lazy
isLazy() - Method in interface apollo.datamodel.SequenceI: Cleanup dangling references when SequenceI not needed anymore.
isLeftEdge() - Method in class apollo.gui.drawable.DrawableSeqFeature
isLeftMouseClick(MouseEvent) - Static method in class apollo.gui.event.MouseButtonEvent
isLimits() - Method in class apollo.editor.TransactionSubpart
isLinkById() - Method in class apollo.config.LinkType
isLocation() - Method in class apollo.dataadapter.DataInputType
isLocationsPanelVisible() - Method in class apollo.dataadapter.ensj.model.Model
isMac() - Static method in class apollo.util.IOUtil
isManagingSZAP(StrandedZoomableApolloPanel) - Method in class apollo.gui.synteny.SyntenyLinkPanel
isMerge() - Method in class apollo.editor.CompoundTransaction
isMerge() - Method in class apollo.editor.FeatureChangeEvent
isMerge() - Method in class apollo.editor.Transaction
isMiddleMouseClick(MouseEvent) - Static method in class apollo.gui.event.MouseButtonEvent
isMiddleMouseClickNoShift(MouseEvent) - Static method in class apollo.gui.event.MouseButtonEvent
isMissing3prime() - Method in class apollo.datamodel.FeatureSet
isMissing3prime() - Method in interface apollo.datamodel.TranslationI
isMissing5prime() - Method in class apollo.datamodel.FeatureSet
isMissing5prime() - Method in interface apollo.datamodel.TranslationI: If true this means there is no real start codon - its missing, rename this isMissing5PrimeStart? or isMissingTranslationStart? hasTranslationStart() can be true while isMissing5prime is true - this means that theres a "contrived" start at the beginning of the transcript
isMousePressShifted() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel.ShiftAwareButton
isMove() - Method in class apollo.editor.AnnotationCompoundEvent
isMove() - Method in class apollo.editor.AnnotationUpdateEvent: A "move" is when a parent is updated
isMove() - Method in class apollo.editor.FeatureChangeEvent: Move is a special case of UPDATE - updating parent subpart AnnotationUpdateEvent overrides this
isMove() - Method in interface apollo.editor.UpdateDetailsI: isMove means parent is updated, ie isParent
isMultiCuration() - Method in class apollo.gui.synteny.CurationManager: Whether we have more than one curationState or not
isMultiSpecies() - Method in interface apollo.datamodel.ApolloDataI: Temporary method until all synteny stuff uses CompositeDataHolder
isMultiSpecies() - Method in class apollo.datamodel.CompositeDataHolder: If we have more than one species, it answers 'true', otherwise not.
isMultiSpecies() - Method in class apollo.datamodel.CurationSet: Temporary method until all synteny stuff uses CompositeDataHolder rename isComposite?
isName() - Method in class apollo.editor.TransactionSubpart
isNameSet() - Method in class apollo.dataadapter.gff3.GFF3Entry: Check if the feature name is set
isNavigationManagerEnabled() - Static method in class apollo.config.Config
isNewCuration() - Method in class apollo.dataadapter.analysis.AnalysisPanel