apollo.gui.detailviewers.sequencealigner
Class MultiSequenceAlignerPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

All Implemented Interfaces:

AnnotationChangeListener, BaseScrollable, ControlledObjectI, FeatureSelectionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

Direct Known Subclasses:

AAMultiSequenceAlignerPanel, DNAMultiSequenceAlignerPanel

public abstract class MultiSequenceAlignerPanel
extends javax.swing.JPanel
implements FeatureSelectionListener, ControlledObjectI, AnnotationChangeListener, java.beans.PropertyChangeListener, BaseScrollable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected static int	colorIndex
protected static java.awt.Color[]	colorList

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

MultiSequenceAlignerPanel(GuiCurationState curationState)

Method Summary

int	addAnnotations(java.util.Collection<SeqFeatureI> features) Adds a collection of annotations to the list of annotations (but not the annotation panel)
void	addEditRegion() puts up vertical lines in szap(main window) indicating what region that is currently displayed
protected AbstractTierPanel	addFeatureToPanel(SeqFeatureI feature, MultiTierPanel panel)
int	addResults(java.util.Collection<SeqFeatureI> features) Adds a collection of results to the list of results (but not to the result panel)
abstract boolean	annotationFilter(SeqFeatureI f) I don't think this is used in any way...
boolean	canHandleSelection(FeatureSelectionEvent evt, java.lang.Object self) Does all the handle selection checks
void	cleanUp() cleanup extra components when closing down
abstract void	clearAnnotations() removes all the annotations from the annotation list and the annotation panel
abstract void	clearResults() removes all of the results from the results list and the result panel
static java.util.Set<SeqFeatureI>	filter(java.util.Collection<SeqFeatureI> collection, Filter f) Passes a collection of features through a filter
void	flipOrientation() Flipping the orientation will not work, more work is needed to implement...
abstract AbstractScrollablePanel	getAddressComponent() Gets the address bar (shows the base numbers you are looking at)
abstract MultiComparator	getAnnotationComparator() Gets the comparator used to order annotations
abstract MultiFilter<SeqFeatureI>	getAnnotationFilter() Gets the filter used to decide which annotations to display
abstract MultiTierPanelHeaderTable	getAnnotationHeader() Gets the header for the annotation panel
abstract javax.swing.JScrollPane	getAnnotationPane() Gets the JScrollPane which holds the Annotation Panel
abstract MultiTierPanel	getAnnotationPanel() Gets the Annotation Panel
abstract java.util.List<SeqFeatureI>	getAnnotations() Gets the list of annotations.
static java.util.Set<SeqFeatureI>	getAnnotations(SeqFeatureI featureSet) Gets all the annotations in a particular feature set
java.awt.Color[][]	getColorArray() The inner array is an array of 2 colors, for alternating exon colors.
GuiCurationState	getCurationState()
abstract ReadingFrame	getFrame() Gets the frame that is currently being viewed
java.awt.Color	getIndicatorColor()
abstract javax.swing.JMenu	getMenu() Gets the Menu object
javax.swing.JMenuBar	getMenuBar() Method for easy access to MenuBar
abstract Overview	getOverview() Gets the overview object for the panel
abstract MultiTierPanel	getReferencePanel() Gets the reference panel (the one in between the annotation and result)
abstract SequenceI	getReferenceSequence(Strand s, ReadingFrame rf) Creates a Sequence object which can be used as a reference for the given strand/frame pair
abstract MultiComparator	getResultComparator() Gets the comparator used to order results
abstract MultiFilter<SeqFeatureI>	getResultFilter() Gets the filter used to decide which results to display
abstract MultiTierPanelHeaderTable	getResultHeader() Gets the header for the result panel
abstract MultiTierPanel	getResultPanel() Gets the Result Panel
abstract java.util.List<SeqFeatureI>	getResults() Gets the list of results.
static java.util.Set<SeqFeatureI>	getResults(SeqFeatureI featureSet, Filter f) Gets all the results from a particular feature set that pass the filter
static java.util.Set<SeqFeatureI>	getResults(java.lang.String type, SeqFeatureI featureSet) Gets all the results from a particular feature set Don't think this is used...
abstract javax.swing.JScrollBar	getScrollBar() Gets the main horizontal scrollbar for the window
AnnotatedFeatureI	getSelection() Gets the currently sellected annotation
abstract Strand	getStrand() Gets the strand of the annotations currently being viewed
MultiSequenceAlignerPanel	getThis()
AnnotatedFeatureI	getTransOrOneLevelAnn(AnnotatedFeatureI af) AssemblyFeature is the only GAI at the moment that has no relation to // a transcript.
abstract java.lang.String	getType() Gets the type
boolean	handleAnnotationChangeEvent(AnnotationChangeEvent evt)
abstract void	init() Creates all of the components and lays everything out
static MultiSequenceAlignerPanel	makeAligner(java.lang.String type, GuiCurationState curationState, int strand, ReadingFrame frame) Factory method to create the correct display panel based on the type
javax.swing.JMenu	makeMenu() Creates a drop down menu for this component
void	nextAnnotation() Scrolls the window to the start/end of the next annotation to the right.
boolean	noExternalSelection() true if no external selection is allowed false otherwise
void	prevAnnotation() Scrolls the window to the start/end of the next annotation to the left
void	reformatAnnotationPanel() clears and repopulates the annotation panel based on current state
abstract void	reformatReferenceHeader() updates the header for the reference panel
void	reformatReferencePanel(Orientation orientation) updates and paints the reference panel based on current state
void	reformatResultPanel() clears and repopulates the result panel based on the current state
abstract boolean	resultFilter(SeqFeatureI f) I don't think this is used in any way...
abstract void	setAnnotations(java.util.List<SeqFeatureI> annotations) Sets the annotations (no side effects)
void	setCurationState(GuiCurationState cs)
void	setIndicatorColor(java.awt.Color c)
void	setNoExternalSelection(boolean noExternalselection)
abstract void	setResults(java.util.List<SeqFeatureI> results) Sets the results (no side effects)
void	setSelection(AnnotatedFeatureI gai) Sets the selection the the feature given
abstract void	setStrand(Strand s) Sets the currently selected strand (no side effects)
java.util.List<SeqFeatureI>	sort(java.util.Collection<SeqFeatureI> collection, java.util.Comparator comparator) Sorts a collection of features using the given comparator
void	sortAnnotations(java.util.Comparator comparator) Sorts the annotation list using the given comparator I dont' think this is used anymore...
void	sortResults(java.util.Comparator comparator) Sorts the result list using the given comparator I dont think this is used anymore...
void	switchAnnotations() Changes the view to look at the annotations on the opposite strand
void	switchResults() Switches the strand for the result panel.
protected void	updateEditRegion() Something to do with the box that shows what part is being displayed in the main apollo window
void	updateTitle() Sets the title for the window

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface apollo.gui.event.FeatureSelectionListener

handleFeatureSelectionEvent

Methods inherited from interface apollo.gui.ControlledObjectI

getController, getControllerWindow, needsAutoRemoval, setController

Methods inherited from interface java.beans.PropertyChangeListener

propertyChange

Methods inherited from interface apollo.gui.BaseScrollable

getVisibleBase, getVisibleBaseCount, scrollToBase

Field Detail

colorIndex

protected static int colorIndex

colorList

protected static final java.awt.Color[] colorList

Constructor Detail

MultiSequenceAlignerPanel

public MultiSequenceAlignerPanel(GuiCurationState curationState)

Method Detail

getColorArray

public java.awt.Color[][] getColorArray()

The inner array is an array of 2 colors, for alternating exon colors. The "outer" array represents transcript coloring. Transcripts can have different exon coloring pairs(see SelectableDNARenderer's exonColorIndex and transcriptColorIndex). This now takes in 2 colors from Config edeFeatureColor. It no longer is setting up 4 colors for alternating transcripts as well as exons. Easy enough to reinstate if desired.

getIndicatorColor

public java.awt.Color getIndicatorColor()

setIndicatorColor

public void setIndicatorColor(java.awt.Color c)

getCurationState

public GuiCurationState getCurationState()

setCurationState

public void setCurationState(GuiCurationState cs)

getMenuBar

public javax.swing.JMenuBar getMenuBar()

Method for easy access to MenuBar

Returns:

getThis

public MultiSequenceAlignerPanel getThis()

makeMenu

public javax.swing.JMenu makeMenu()

Creates a drop down menu for this component

Returns:

a menu

flipOrientation

public void flipOrientation()

Flipping the orientation will not work, more work is needed to implement...

getReferenceSequence

public abstract SequenceI getReferenceSequence(Strand s,
                                               ReadingFrame rf)

Creates a Sequence object which can be used as a reference for the given strand/frame pair

Parameters:

s - the strand

rf - the frame

Returns:

a reference sequence

getScrollBar

public abstract javax.swing.JScrollBar getScrollBar()

Gets the main horizontal scrollbar for the window

Returns:

getOverview

public abstract Overview getOverview()

Gets the overview object for the panel

Returns:

switchResults

public void switchResults()

Switches the strand for the result panel.
side effects: repaint result panel, repaint reference panel

setSelection

public void setSelection(AnnotatedFeatureI gai)

Sets the selection the the feature given

Parameters:

gai - the new selection
side effects: update the overview, and update the title

getSelection

public AnnotatedFeatureI getSelection()

Gets the currently sellected annotation

Returns:

updateTitle

public void updateTitle()

Sets the title for the window

getAnnotationPanel

public abstract MultiTierPanel getAnnotationPanel()

Gets the Annotation Panel

getAnnotationPane

public abstract javax.swing.JScrollPane getAnnotationPane()

Gets the JScrollPane which holds the Annotation Panel

getAnnotationHeader

public abstract MultiTierPanelHeaderTable getAnnotationHeader()

Gets the header for the annotation panel

getResultPanel

public abstract MultiTierPanel getResultPanel()

Gets the Result Panel

getResultHeader

public abstract MultiTierPanelHeaderTable getResultHeader()

Gets the header for the result panel

getReferencePanel

public abstract MultiTierPanel getReferencePanel()

Gets the reference panel (the one in between the annotation and result)

getAddressComponent

public abstract AbstractScrollablePanel getAddressComponent()

Gets the address bar (shows the base numbers you are looking at)

Returns:

getType

public abstract java.lang.String getType()

Gets the type

getStrand

public abstract Strand getStrand()

Gets the strand of the annotations currently being viewed

setStrand

public abstract void setStrand(Strand s)

Sets the currently selected strand (no side effects)

getFrame

public abstract ReadingFrame getFrame()

Gets the frame that is currently being viewed

getMenu

public abstract javax.swing.JMenu getMenu()

Gets the Menu object

init

public abstract void init()

Creates all of the components and lays everything out

cleanUp

public void cleanUp()

cleanup extra components when closing down

getAnnotations

public abstract java.util.List<SeqFeatureI> getAnnotations()

Gets the list of annotations. This list is used to determine if an annotation is already added to the panel. TODO redesign use of annotations, probably a better way to do this.

setAnnotations

public abstract void setAnnotations(java.util.List<SeqFeatureI> annotations)

Sets the annotations (no side effects)

getResults

public abstract java.util.List<SeqFeatureI> getResults()

Gets the list of results. This list is used to determine if a result is already added to the panel. TODO redesign use of results, probably a better way to do this.

setResults

public abstract void setResults(java.util.List<SeqFeatureI> results)

Sets the results (no side effects)

clearAnnotations

public abstract void clearAnnotations()

removes all the annotations from the annotation list and the annotation panel

clearResults

public abstract void clearResults()

removes all of the results from the results list and the result panel

reformatResultPanel

public void reformatResultPanel()

clears and repopulates the result panel based on the current state

reformatAnnotationPanel

public void reformatAnnotationPanel()

clears and repopulates the annotation panel based on current state

reformatReferencePanel

public void reformatReferencePanel(Orientation orientation)

updates and paints the reference panel based on current state

reformatReferenceHeader

public abstract void reformatReferenceHeader()

updates the header for the reference panel

switchAnnotations

public void switchAnnotations()

Changes the view to look at the annotations on the opposite strand

annotationFilter

public abstract boolean annotationFilter(SeqFeatureI f)

I don't think this is used in any way... should probably remove

resultFilter

public abstract boolean resultFilter(SeqFeatureI f)

I don't think this is used in any way... should probably remove

addAnnotations

public int addAnnotations(java.util.Collection<SeqFeatureI> features)

Adds a collection of annotations to the list of annotations (but not the annotation panel)

Parameters:

features - a list of annotations

Returns:

the number of annotations added

addResults

public int addResults(java.util.Collection<SeqFeatureI> features)

Adds a collection of results to the list of results (but not to the result panel)

Parameters:

features - a list of results

Returns:

the number of results added

getResultComparator

public abstract MultiComparator getResultComparator()

Gets the comparator used to order results

getAnnotationComparator

public abstract MultiComparator getAnnotationComparator()

Gets the comparator used to order annotations

getResultFilter

public abstract MultiFilter<SeqFeatureI> getResultFilter()

Gets the filter used to decide which results to display

getAnnotationFilter

public abstract MultiFilter<SeqFeatureI> getAnnotationFilter()

Gets the filter used to decide which annotations to display

sortResults

public void sortResults(java.util.Comparator comparator)

Sorts the result list using the given comparator I dont think this is used anymore...

Parameters:

comparator -

sortAnnotations

public void sortAnnotations(java.util.Comparator comparator)

Sorts the annotation list using the given comparator I dont' think this is used anymore...

Parameters:

comparator -

sort

public java.util.List<SeqFeatureI> sort(java.util.Collection<SeqFeatureI> collection,
                                        java.util.Comparator comparator)

Sorts a collection of features using the given comparator

Parameters:

collection -

comparator -

Returns:

the sorted set

handleAnnotationChangeEvent

public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt)

Specified by:

handleAnnotationChangeEvent in interface AnnotationChangeListener

makeAligner

public static MultiSequenceAlignerPanel makeAligner(java.lang.String type,
                                                    GuiCurationState curationState,
                                                    int strand,
                                                    ReadingFrame frame)

Factory method to create the correct display panel based on the type

getAnnotations

public static java.util.Set<SeqFeatureI> getAnnotations(SeqFeatureI featureSet)

Gets all the annotations in a particular feature set

Parameters:

featureSet -

Returns:

getResults

public static java.util.Set<SeqFeatureI> getResults(java.lang.String type,
                                                    SeqFeatureI featureSet)

Gets all the results from a particular feature set Don't think this is used...

Parameters:

type - the type of results wanted, ether AA or DNA

featureSet -

Returns:

getResults

public static java.util.Set<SeqFeatureI> getResults(SeqFeatureI featureSet,
                                                    Filter f)

Gets all the results from a particular feature set that pass the filter

Parameters:

featureSet -

f - the filter used to decide which results to get

Returns:

filter

public static java.util.Set<SeqFeatureI> filter(java.util.Collection<SeqFeatureI> collection,
                                                Filter f)

Passes a collection of features through a filter

Parameters:

collection -

f -

Returns:

the features in the given collection that pass the filter

addEditRegion

public void addEditRegion()

puts up vertical lines in szap(main window) indicating what region that is currently displayed

updateEditRegion

protected void updateEditRegion()

Something to do with the box that shows what part is being displayed in the main apollo window

nextAnnotation

public void nextAnnotation()

Scrolls the window to the start/end of the next annotation to the right.

prevAnnotation

public void prevAnnotation()

Scrolls the window to the start/end of the next annotation to the left

noExternalSelection

public boolean noExternalSelection()

true if no external selection is allowed false otherwise

Returns:

setNoExternalSelection

public void setNoExternalSelection(boolean noExternalselection)

canHandleSelection

public boolean canHandleSelection(FeatureSelectionEvent evt,
                                  java.lang.Object self)

Does all the handle selection checks

getTransOrOneLevelAnn

public AnnotatedFeatureI getTransOrOneLevelAnn(AnnotatedFeatureI af)

AssemblyFeature is the only GAI at the moment that has no relation to // a transcript. Dont think they can end up in ede (??). // Would be nice to have an interface that was solely for the exon // trans gene heirarchy? Should we actively make sure AssemblyFeatures dont // get into ede? (filter in AnnotationMenu?) returns null if no transcript can be found.

addFeatureToPanel

protected AbstractTierPanel addFeatureToPanel(SeqFeatureI feature,
                                              MultiTierPanel panel)