apollo.config.Config
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java.lang.Object
public class Config
A class with static data members and static methods for setting and retrieving configuration information for the apollo gui. from apollo.ebi email: createStyle(...) is used to create a new style that is coming in from the apollo.cfg DataAdapterInstall line as you've probably seen: DataAdapterInstall "apollo.dataadapter.EnsCGIAdapter" "ensembl.style" Config sees this line and installs a new Style whose settings are in ensembl.style and will get associated with the EnsCGIAdapter. This will NOT then become the present style. apollo.cfg can specify many DataAdapters with styles, and styles can be shared. At initialization time createStyle() creates these styles and puts them in a hash to be called up later. When the user selects a data adapter (with the DataAdapterChooser gui) then newDataAdapter is called with the new DataAdapter Class (which calls setDataAdapterType with the class string). At this point Config sets its style class variable because we now know which style the user wants. NameAdapters are specific to a an annotation type now; NameAdapterInstall has been moved to TiersIO
| Field Summary | |
|---|---|
static boolean |
DEBUG
Debug mode for Apollo developers; references to this variable are scattered throughout the Apollo code. |
static boolean |
DO_ONE_LEVEL_ANNOTS
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static boolean |
inBatchMode
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static java.lang.String |
javaws
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static java.lang.String |
jvm
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static java.lang.String |
osarch
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static java.lang.String |
osname
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| Constructor Summary | |
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Config()
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| Method Summary | |
|---|---|
static boolean |
commandLineXmlFileFormatIsConfigged()
Returns true if commandLineXmlFileFormat is nonnull and is "game" or "chado" |
static Style |
createStyle(java.lang.String styleFilename)
If already have style for styleFilename, return that. |
static boolean |
dataAdapterIsAvailable(org.bdgp.io.IOOperation io)
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static java.lang.String |
digForConfigFile(java.lang.String styleFilename)
Look around for style file, pulling out of the jar if necessary (needed for webstart) |
static boolean |
doUserTranscriptColouring()
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static void |
ensureExists(java.io.File thing,
java.lang.String resource)
Default is not to recreate. |
static void |
ensureExists(java.io.File thing,
java.lang.String resource,
boolean recreate)
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static java.lang.String |
getAdapterHistoryFile()
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static org.bdgp.io.DataAdapterRegistry |
getAdapterRegistry()
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static java.awt.Color |
getAnnotationBackground()
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static java.awt.Color |
getAnnotationColor(AnnotatedFeatureI annot)
New method take an AnnotatedFeatureI (an annot or transcript) |
static java.awt.Color |
getAnnotationColor(java.lang.String username,
FeatureProperty fp)
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static java.util.Vector |
getAnnotationComments()
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static java.awt.Color |
getAnnotationLabelColor()
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static java.lang.String |
getApolloOboFilename()
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static java.lang.String |
getAutosaveFile()
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static int |
getAutosaveInterval()
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static java.lang.String |
getBandUrl()
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static java.lang.String |
getBlixemLocation()
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static java.lang.String |
getBrowserProgram()
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static java.lang.String |
getCGIHost()
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static int |
getCGIPort()
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static java.lang.String |
getCGIScript()
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static java.lang.String |
getChadoJdbcAdapterConfigFile()
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static java.lang.String |
getChadoTemplateName()
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static boolean |
getCheckOwnership()
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static java.util.Vector |
getChromosomes()
Returns a vector of chromosome names as strings, null if none given |
static java.lang.String |
getCommandLineXmlFileFormat()
Indicates adapter to use for command line xml file, "game" or "chado". |
static boolean |
getConfirmDeleteSelection()
Return true if configged to true AND NOT in command-line/batch mode |
static boolean |
getConfirmOverwrite()
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 |
static Controller |
getController()
This should be taken out of here and made a singleton method in controller Config has nothing to do with the controller |
static java.awt.Color |
getCoordBackground()
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static java.awt.Color |
getCoordForeground()
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static java.awt.Color |
getCoordRevcompColor()
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static boolean |
getDashSets()
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static java.lang.String |
getDASServer()
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static java.lang.String |
getDataDir()
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static java.awt.Color |
getDataLoaderBackgroundColor()
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static java.awt.Color |
getDataLoaderLabelColor()
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static java.awt.Color |
getDataLoaderTitleColor()
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static java.lang.String |
getDBHost()
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static java.lang.String |
getDBName()
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static boolean |
getDebug()
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static java.awt.Color |
getDefaultAnnotationColor()
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static java.awt.Font |
getDefaultFeatureLabelFont()
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 |
static java.awt.Font |
getDefaultFont()
Should there be an apollo wide font as well as style level font? |
static java.lang.String |
getDefaultSingleSpeciesName()
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 |
static DisplayPrefsI |
getDisplayPrefs()
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static boolean |
getDraw3D()
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static boolean |
getDrawOutline()
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static java.awt.Color |
getEdgematchColor()
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static int |
getEdgematchWidth()
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static java.awt.Color |
getExonDetailEditorBackgroundColor1()
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static java.awt.Color |
getExonDetailEditorBackgroundColor2()
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static java.awt.Color |
getExonDetailEditorFeatureColor1()
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static java.awt.Color |
getExonDetailEditorFeatureColor2()
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static java.awt.Font |
getExonDetailEditorSequenceFont()
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static java.lang.String |
getExonSyntenyDir()
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static java.lang.String |
getExternalRefURL()
previously fban url - attempting to make more general |
static float |
getFastDrawLimit()
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static java.awt.Color |
getFeatureBackground()
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static java.awt.Color |
getFeatureLabelColor()
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static java.lang.String |
getFileName()
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static java.lang.String |
getFrameOrientation()
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static java.lang.String |
getFullNameForUser(java.lang.String user)
Returns full name of user - if dont have full name just returns user |
static java.lang.String |
getGeneUrl()
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static int |
getGeneWindow()
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static java.lang.String |
getGPName()
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static java.awt.Color |
getHighlightColor()
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static java.lang.String |
getJavaWebStartVersion()
Get the Java Web Start version. |
static java.lang.String |
getJVM()
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static java.lang.String |
getKaryotypeFile()
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static java.lang.String |
getLayoutIniFile()
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static int |
getMainWindowWidth()
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static int |
getMaxHistoryLength()
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static long |
getMemoryAllocation()
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static boolean |
getNoStripes()
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static java.awt.Color |
getOutlineColor()
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static OverlapI |
getOverlapper(SeqFeatureI sf)
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static java.io.File |
getParentFile(java.io.File thing)
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static java.util.Hashtable |
getPeptideStates()
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static PeptideStatus |
getPeptideStatus(java.lang.String pep_status)
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static java.lang.String |
getPFetchServer()
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static java.lang.String |
getProjectName(java.lang.String username)
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static PropertyScheme |
getPropertyScheme()
When multi-curations have multi-propSchemes this method will become pase. |
static java.util.Hashtable |
getPublicDbList()
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static java.lang.String |
getRangeUrl()
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static boolean |
getRefreshPeptides()
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static java.lang.String |
getRootDir()
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static boolean |
getSaveClonedFeaturesInTransactions()
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static java.lang.String |
getScaffoldUrl()
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static java.awt.Color |
getSelectionColor()
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static java.awt.Color |
getSeqGapColor()
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static java.awt.Color |
getSequenceColor()
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static java.lang.String |
getSeqUrl()
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static boolean |
getShowAnnotations()
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static boolean |
getShowResults()
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static boolean |
getShowSaveAsOptionInFileMenu()
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static boolean |
getShowSaveOptionInFileMenu()
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static boolean |
getShowSyntenyEvidencePanels()
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static int |
getSiteShowLimit()
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static java.lang.String |
getSoOboFilename()
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static java.lang.String |
getSRSServer()
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static Style |
getStyle()
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static Style |
getStyle(java.lang.String adapterType)
Returns Style for adapter class string, null if non existent |
static java.lang.String |
getSyntenyDatabaseForSpecies(java.lang.String species)
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static java.lang.String |
getSyntenyDir()
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static int |
getSyntenyPanelRelativeSize()
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static int |
getTextAvoidLimit()
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static java.lang.String |
getTiersFile()
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static java.lang.String |
getTigrAnnotNameAdapterNewNameCommand()
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static java.lang.String |
getTimestamp()
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static java.util.Vector |
getTranscriptComments()
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static int |
getTranslationShowLimit()
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static java.lang.String |
getUsersFullName()
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static boolean |
hasChromosomes()
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static boolean |
hasStyleForSpecies(java.lang.String species)
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static boolean |
httpServerIsEnabled()
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static void |
initializeConfiguration()
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static boolean |
internalMode()
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static boolean |
isChadoTnOutputNeeded()
To see if chado transaction output is needed. |
static boolean |
isEditingEnabled()
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static boolean |
isEditingEnabled(java.lang.String adapterClassName)
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static boolean |
isHeadlessApplication()
Checks whether the system is running in headless mode. |
static boolean |
isJavaWebStartApplication()
Checks to see if this application is a Java Web Start application |
static boolean |
isNavigationManagerEnabled()
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static void |
main(java.lang.String[] args)
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static void |
newDataAdapter(org.bdgp.io.DataAdapter da)
Data adapter has changed - fetch the matching style - i think the purpose of this was to change the style - but AbstractApolloAdapter seems to do this explicitly now through setStyle(s) because if a dataadapter is a child to the synteny adapter, the synteny style will be used in lieu of the data adapters normal style - though im not sure what i think about that AnalysisAdapterGUI still uses this but it probably shouldnt because of synteny |
static boolean |
outputTransactionXML()
Whether to write a .tnxml file |
static void |
reset()
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static void |
setBrowserProgram(java.lang.String browser)
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static void |
setConfirmDeleteSelection(boolean state)
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static void |
setConfirmOverwrite(boolean state)
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static void |
setController(Controller newValue)
controller should be taken out of config at some point - controller now set by default to master controller - take out setController? not used |
static void |
setDBHost(java.lang.String host)
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static void |
setDBName(java.lang.String name)
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static void |
setGPName(java.lang.String name)
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static void |
setRefreshPeptides(boolean value)
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static void |
setSaveClonedFeaturesInTransactions(boolean state)
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static void |
setShowSaveAsOptionInFileMenu(boolean state)
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static void |
setShowSaveOptionInFileMenu(boolean state)
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static void |
setStyle(Style s)
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static void |
setStyle(Style s,
boolean updateStyleHash)
if updateStyleHash is true add key style filename to value style to filenameToStyle hash |
static void |
setStyleForSpecies(java.lang.String species)
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static void |
setTigrAnnotNameAdapterNewNameCommand(java.lang.String command)
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static boolean |
supressMacJvmPopupMessage()
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static boolean |
useFastClipGraphics()
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static boolean |
verticallyMovePopups()
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| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
|---|
public static java.lang.String osarch
public static java.lang.String osname
public static java.lang.String jvm
public static java.lang.String javaws
public static boolean DO_ONE_LEVEL_ANNOTS
public static boolean inBatchMode
public static boolean DEBUG
| Constructor Detail |
|---|
public Config()
| Method Detail |
|---|
public static boolean getDebug()
public static void setStyle(Style s)
public static void setStyle(Style s,
boolean updateStyleHash)
public static void newDataAdapter(org.bdgp.io.DataAdapter da)
public static Style getStyle(java.lang.String adapterType)
public static Style getStyle()
public static boolean hasStyleForSpecies(java.lang.String species)
public static void setStyleForSpecies(java.lang.String species)
public static java.awt.Color getAnnotationBackground()
public static java.awt.Color getFeatureBackground()
public static int getEdgematchWidth()
public static boolean verticallyMovePopups()
public static java.awt.Color getCoordBackground()
public static java.awt.Color getCoordForeground()
public static java.awt.Color getCoordRevcompColor()
public static java.awt.Color getSequenceColor()
public static java.awt.Color getEdgematchColor()
public static java.awt.Color getHighlightColor()
public static java.awt.Color getSelectionColor()
public static java.awt.Color getSeqGapColor()
public static java.awt.Color getFeatureLabelColor()
public static java.awt.Color getAnnotationLabelColor()
public static java.awt.Color getDataLoaderBackgroundColor()
public static java.awt.Color getDataLoaderLabelColor()
public static java.awt.Color getDataLoaderTitleColor()
public static java.awt.Color getExonDetailEditorBackgroundColor1()
public static java.awt.Color getExonDetailEditorBackgroundColor2()
public static java.awt.Color getExonDetailEditorFeatureColor1()
public static java.awt.Color getExonDetailEditorFeatureColor2()
public static java.util.Vector getAnnotationComments()
public static java.util.Vector getTranscriptComments()
public static java.util.Hashtable getPeptideStates()
public static PeptideStatus getPeptideStatus(java.lang.String pep_status)
public static org.bdgp.io.DataAdapterRegistry getAdapterRegistry()
public static boolean dataAdapterIsAvailable(org.bdgp.io.IOOperation io)
public static DisplayPrefsI getDisplayPrefs()
public static OverlapI getOverlapper(SeqFeatureI sf)
public static java.lang.String getTiersFile()
public static java.lang.String getKaryotypeFile()
public static java.lang.String getSyntenyDir()
public static java.lang.String getExonSyntenyDir()
public static boolean getShowAnnotations()
public static java.lang.String getLayoutIniFile()
public static boolean getShowResults()
public static boolean getShowSyntenyEvidencePanels()
public static boolean isEditingEnabled()
public static boolean isEditingEnabled(java.lang.String adapterClassName)
public static boolean isNavigationManagerEnabled()
public static int getAutosaveInterval()
public static int getCGIPort()
public static java.lang.String getCGIScript()
public static java.lang.String getCGIHost()
public static java.lang.String getDBHost()
public static java.lang.String getDBName()
public static java.lang.String getGPName()
public static java.lang.String getSRSServer()
public static java.lang.String getPFetchServer()
public static java.lang.String getDASServer()
public static java.lang.String getAutosaveFile()
public static Controller getController()
public static void setController(Controller newValue)
public static int getSiteShowLimit()
public static int getSyntenyPanelRelativeSize()
public static int getTranslationShowLimit()
public static int getTextAvoidLimit()
public static java.awt.Font getDefaultFont()
public static java.awt.Font getDefaultFeatureLabelFont()
public static float getFastDrawLimit()
public static boolean getDrawOutline()
public static java.awt.Color getOutlineColor()
public static java.lang.String getFrameOrientation()
public static int getMainWindowWidth()
public static java.lang.String getGeneUrl()
public static java.lang.String getBandUrl()
public static java.lang.String getScaffoldUrl()
public static java.lang.String getSeqUrl()
public static java.lang.String getRangeUrl()
public static boolean hasChromosomes()
public static java.util.Vector getChromosomes()
public static java.lang.String getExternalRefURL()
public static boolean internalMode()
public static java.lang.String getProjectName(java.lang.String username)
public static java.lang.String getFileName()
public static Style createStyle(java.lang.String styleFilename)
public static java.lang.String digForConfigFile(java.lang.String styleFilename)
public static java.lang.String getRootDir()
public static java.lang.String getDataDir()
public static int getMaxHistoryLength()
public static java.lang.String getAdapterHistoryFile()
public static boolean getConfirmOverwrite()
public static void setConfirmOverwrite(boolean state)
public static boolean getShowSaveOptionInFileMenu()
public static void setShowSaveOptionInFileMenu(boolean state)
public static boolean getShowSaveAsOptionInFileMenu()
public static void setShowSaveAsOptionInFileMenu(boolean state)
public static boolean getConfirmDeleteSelection()
public static void setConfirmDeleteSelection(boolean state)
public static boolean getCheckOwnership()
public static boolean getSaveClonedFeaturesInTransactions()
public static void setSaveClonedFeaturesInTransactions(boolean state)
public static java.lang.String getTigrAnnotNameAdapterNewNameCommand()
public static void setTigrAnnotNameAdapterNewNameCommand(java.lang.String command)
public static boolean httpServerIsEnabled()
public static boolean getDashSets()
public static boolean useFastClipGraphics()
public static boolean doUserTranscriptColouring()
public static boolean getDraw3D()
public static boolean getNoStripes()
public static PropertyScheme getPropertyScheme()
public static java.awt.Color getAnnotationColor(AnnotatedFeatureI annot)
public static java.awt.Color getAnnotationColor(java.lang.String username,
FeatureProperty fp)
public static java.awt.Color getDefaultAnnotationColor()
public static java.lang.String getBlixemLocation()
public static java.lang.String getBrowserProgram()
public static void setBrowserProgram(java.lang.String browser)
public static java.awt.Font getExonDetailEditorSequenceFont()
public static long getMemoryAllocation()
public static void main(java.lang.String[] args)
public static void initializeConfiguration()
public static boolean isJavaWebStartApplication()
public static java.lang.String getJavaWebStartVersion()
public static boolean isHeadlessApplication()
public static void setDBName(java.lang.String name)
public static void setDBHost(java.lang.String host)
public static void setGPName(java.lang.String name)
public static int getGeneWindow()
public static java.lang.String getJVM()
public static void setRefreshPeptides(boolean value)
public static boolean getRefreshPeptides()
public static void ensureExists(java.io.File thing,
java.lang.String resource,
boolean recreate)
public static void ensureExists(java.io.File thing,
java.lang.String resource)
public static java.io.File getParentFile(java.io.File thing)
public static void reset()
public static java.lang.String getTimestamp()
public static java.lang.String getUsersFullName()
public static java.lang.String getFullNameForUser(java.lang.String user)
public static java.util.Hashtable getPublicDbList()
public static java.lang.String getSyntenyDatabaseForSpecies(java.lang.String species)
public static java.lang.String getDefaultSingleSpeciesName()
public static java.lang.String getChadoTemplateName()
public static java.lang.String getChadoJdbcAdapterConfigFile()
public static boolean isChadoTnOutputNeeded()
public static boolean outputTransactionXML()
public static java.lang.String getCommandLineXmlFileFormat()
public static boolean commandLineXmlFileFormatIsConfigged()
public static boolean supressMacJvmPopupMessage()
public static java.lang.String getSoOboFilename()
public static java.lang.String getApolloOboFilename()
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| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | ||||||||