Index

_ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | Z

_

__dict__ (functions.Pool attribute)
(functions.RandomColor attribute)
(session.annotation.AnnotationFactory attribute)
(session.dataTypes.DataType attribute)
(session.numeric.NumericFactory attribute)
(session.reads.NucleotideCache attribute)
(session.reads.NucleotideCacheBlock attribute)
(session.reads.Read attribute)
__init__() (additionalUI.about.About method)
(additionalUI.globalSettings.GlobalSettings method)
(additionalUI.globalSettings.SettingsPage method)
(additionalUI.printOut.PrintOut method)
(additionalUI.search.SearchUI method)
(additionalUI.trackHeight.trackHeightUI method)
(additionalUI.trackSettings.ColorPushButton method)
(additionalUI.trackSettings.DatasetListModel method)
(additionalUI.trackSettings.TrackSettings method)
(mainUI.dataTree.DataTreeDock method)
(mainUI.dataTree.DataTreeMenu method)
(mainUI.dataTree.DataTreeModel method)
(mainUI.dataTree.DataTreeView method)
(mainUI.infoDock.InfoDock method)
(mainUI.legendDock.LegendDock method)
(mainUI.mainWindow.MainWindow method)
(mainUI.toolBar.ToolBar method)
(mainUI.trackSplitter.SplitterSpacer method)
(mainUI.trackSplitter.TrackSplitter method)
(session.annotation.Annotation method)
(session.annotation.AnnotationLine method)
(session.annotation.GtfAnnotation method)
(session.annotation.GtfGzAnnotation method)
(session.annotation.InvalidAnnotation method)
(session.annotation.RefFlatAnnotation method)
(session.dataTypes.DataType method)
(session.dataset.Dataset method)
(session.junctions.Junctions method)
(session.numeric.FixedStepNumeric method)
(session.numeric.InvalidNumeric method)
(session.numeric.Numeric method)
(session.numeric.VariableStepNumeric method)
(session.reads.NucleotideCache method)
(session.reads.NucleotideCacheBlock method)
(session.reads.Read method)
(session.reads.Reads method)
(session.regions.Region method)
(session.regions.Regions method)
(session.sequence.Sequence method)
(session.session.Session method)
(session.transcripts.Transcript method)
(session.transcripts.Transcripts method)
(tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.HeatmapBar method)
(tracks.graphicsItem.HistogramColumn method)
(tracks.graphicsItem.InsertionNucleotide method)
(tracks.graphicsItem.Nucleotide method)
(tracks.graphicsItem.ReadItem method)
(tracks.junctionGraph.JunctionBarItem method)
(tracks.junctionGraph.JunctionLineItem method)
(tracks.readsGraph.CoverageColumn method)
(tracks.readsGraph.CoverageColumnPart method)
(tracks.readsGraph.ReadsGraph method)
(tracks.regionGraph.RegionGraph method)
(tracks.regionGraph.RegionItem method)
(tracks.regionGraph.RegionLabel method)
(tracks.scene.GraphicsScene method)
(tracks.sequenceGraph.SequenceGraph method)
(tracks.track.Track method)
(tracks.track.TrackHandle method)
(tracks.trackManager.TrackManager method)
(tracks.transcriptGraph.TranscriptGraph method)
(tracks.transcriptGraph.TranscriptItem method)
(tracks.views.GraphicsView method)
__len__() (tracks.readsGraph.ReadsGraph method)
(tracks.track.Track method)
__new__() (session.annotation.AnnotationFactory static method)
(session.numeric.NumericFactory static method)
__weakref__ (functions.Pool attribute)
(functions.RandomColor attribute)
(session.annotation.AnnotationFactory attribute)
(session.dataTypes.DataType attribute)
(session.dataset.DatasetNotValid attribute)
(session.numeric.NumericFactory attribute)
(session.reads.NucleotideCache attribute)
(session.reads.NucleotideCacheBlock attribute)
(session.reads.Read attribute)

A

About (class in additionalUI.about)
abscissa() (tracks.trackManager.TrackManager method)
accept() (additionalUI.dialog.Dialog static method)
activatedFlags() (session.reads.Read method)
activatedRole (mainUI.dataTree.DataTreeModel attribute)
addActions() (mainUI.mainWindow.MainWindow method)
addAnnotations() (session.session.Session method)
addChromosome() (session.dataset.Dataset method)
addData() (mainUI.mainWindow.MainWindow method)
addDataset() (session.session.Session method)
addHeatmapTypeLine() (additionalUI.globalSettings.SettingsPage method)
additionalUI (module)
additionalUI.about (module)
additionalUI.dialog (module)
additionalUI.globalSettings (module)
additionalUI.printOut (module)
additionalUI.search (module)
additionalUI.trackHeight (module)
additionalUI.trackSettings (module)
addLine() (additionalUI.globalSettings.SettingsPage method)
(mainUI.dataTree.DataTreeModel method)
addNucleotideContent() (tracks.graphicsItem.ReadItem method)
addSequence() (session.session.Session method)
addStretch() (mainUI.dataTree.DataTreeMenu method)
(mainUI.toolBar.ToolBar method)
addTrack() (session.dataset.Dataset method)
(tracks.trackManager.TrackManager method)
addViewTypeLine() (additionalUI.globalSettings.SettingsPage method)
addWidget() (mainUI.trackSplitter.TrackSplitter method)
adjustColumnsWidth() (mainUI.dataTree.DataTreeView method)
Annotation (class in session.annotation)
AnnotationFactory (class in session.annotation)
AnnotationGraph (class in tracks.annotationGraph)
AnnotationItem (class in tracks.annotationGraph)
AnnotationLine (class in session.annotation)
annotationsAdded (session.session.Session attribute)
apply() (functions.Pool static method)
applySettings() (additionalUI.globalSettings.GlobalSettings method)
averageTrackHeight() (tracks.trackManager.TrackManager method)

B

BlankReadItem (class in tracks.graphicsItem)
boundingRect() (tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.HeatmapBar method)
(tracks.graphicsItem.HistogramColumn method)
(tracks.graphicsItem.Nucleotide method)
(tracks.junctionGraph.JunctionLineItem method)
(tracks.readsGraph.CoverageColumn method)
(tracks.readsGraph.CoverageColumnPart method)
(tracks.regionGraph.RegionItem method)
(tracks.regionGraph.RegionLabel method)
boxHeight (tracks.regionGraph.RegionItem attribute)
brush (tracks.graphicsItem.BlankReadItem attribute)
brushHover (tracks.graphicsItem.BlankReadItem attribute)
buttonClicked() (additionalUI.globalSettings.GlobalSettings method)

C

callSamtools() (in module functions)
callTabix() (in module functions)
categoryContentChanged (mainUI.dataTree.DataTreeModel attribute)
categoryFromIndex() (mainUI.dataTree.DataTreeModel method)
categoryRole (mainUI.dataTree.DataTreeModel attribute)
checkAnnotations() (tracks.readsGraph.ReadsGraph method)
chromID() (session.dataset.Dataset method)
chromName() (in module functions)
chromosomeList() (session.session.Session method)
classParameters (additionalUI.dialog.Dialog attribute)
clear() (tracks.numericGraph.NumericGraph method)
(tracks.readsGraph.ReadsGraph method)
(tracks.regionGraph.RegionGraph method)
(tracks.scene.GraphicsScene method)
(tracks.sequenceGraph.SequenceGraph method)
(tracks.track.Track method)
clearOldCaches() (session.reads.NucleotideCache method)
closeEvent() (mainUI.mainWindow.MainWindow method)
closeSession() (mainUI.mainWindow.MainWindow method)
color() (tracks.junctionGraph.JunctionBarItem method)
(tracks.junctionGraph.JunctionItem method)
(tracks.regionGraph.RegionItem method)
(tracks.transcriptGraph.TranscriptItem method)
colorChanged (additionalUI.trackSettings.ColorPushButton attribute)
colorPalette (functions.RandomColor attribute)
colorPalettes (in module tracks.graphicsItem)
colorPreview() (in module functions)
ColorPushButton (class in additionalUI.trackSettings)
columnCount() (mainUI.dataTree.DataTreeModel method)
computeFileInfo() (session.sequence.Sequence method)
computeLength() (tracks.regionGraph.RegionGraph method)
computeMinMax() (tracks.transcriptGraph.TranscriptGraph method)
contextMenuEvent() (tracks.track.Track method)
CoverageColumn (class in tracks.readsGraph)
CoverageColumnPart (class in tracks.readsGraph)
createAction() (mainUI.mainWindow.MainWindow method)
currentIndex (functions.RandomColor attribute)

D

data() (additionalUI.trackSettings.DatasetListModel method)
(mainUI.dataTree.DataTreeModel method)
dataChanged (session.session.Session attribute)
Dataset (class in session.dataset)
datasetAdded (session.session.Session attribute)
DatasetListModel (class in additionalUI.trackSettings)
DatasetNotValid (class in session.dataset)
datasetRemoved (session.session.Session attribute)
datasetRole (additionalUI.trackSettings.DatasetListModel attribute)
DataTreeDelegate (class in mainUI.dataTree)
DataTreeDock (class in mainUI.dataTree)
DataTreeMenu (class in mainUI.dataTree)
DataTreeModel (class in mainUI.dataTree)
DataTreeView (class in mainUI.dataTree)
DataType (class in session.dataTypes)
dataTypes (in module session.dataTypes)
defaultBrush (in module tracks.graphicsItem)
defaultColor (in module tracks.graphicsItem)
defaultHeatmapType() (tracks.track.Track class method)
defaultPen (in module tracks.graphicsItem)
defaultViewType() (tracks.track.Track class method)
(tracks.transcriptGraph.TranscriptGraph class method)
deleteTrack() (mainUI.dataTree.DataTreeMenu method)
Dialog (class in additionalUI.dialog)
disableHighlight() (tracks.views.GraphicsView method)
docPath (in module generateDoc)
download() (session.save.SessionSaving method)
dragEnterEvent() (mainUI.trackSplitter.SplitterSpacer method)
(tracks.track.Track method)
(tracks.views.GraphicsView method)
dragLeaveEvent() (tracks.views.GraphicsView method)
dragMoveEvent() (tracks.views.GraphicsView method)
draw() (tracks.junctionGraph.JunctionGraph method)
(tracks.numericGraph.NumericGraph method)
(tracks.readsGraph.ReadsGraph method)
(tracks.regionGraph.RegionGraph method)
(tracks.sequenceGraph.SequenceGraph method)
(tracks.track.Track method)
drawAll() (tracks.trackManager.TrackManager method)
drawBars() (tracks.junctionGraph.JunctionGraph method)
drawCollapseRegions() (tracks.regionGraph.RegionGraph method)
(tracks.transcriptGraph.TranscriptGraph method)
drawExpandedRegions() (tracks.regionGraph.RegionGraph method)
(tracks.transcriptGraph.TranscriptGraph method)
drawHeatRegions() (tracks.readsGraph.ReadsGraph method)
drawIntronLimits() (tracks.track.Track method)
drawLines() (tracks.junctionGraph.JunctionGraph method)
drawReadCoverage() (tracks.readsGraph.ReadsGraph method)
drawReads() (tracks.readsGraph.ReadsGraph method)
drawRegion() (tracks.annotationGraph.AnnotationGraph method)
(tracks.junctionGraph.JunctionGraph method)
(tracks.regionGraph.RegionGraph method)
(tracks.transcriptGraph.TranscriptGraph method)
drawSequence() (tracks.sequenceGraph.SequenceGraph method)
dropEvent() (mainUI.trackSplitter.SplitterSpacer method)
(tracks.track.Track method)
(tracks.views.GraphicsView method)
duplicateTrack() (mainUI.dataTree.DataTreeMenu method)

E

editorEvent() (mainUI.dataTree.DataTreeDelegate method)
emitDataChanged() (mainUI.dataTree.DataTreeModel method)
enterEvent() (tracks.track.Track method)
error() (additionalUI.dialog.Dialog static method)
event() (tracks.scene.GraphicsScene method)
exonLimits() (session.reads.Read method)

F

fitWidth() (tracks.views.GraphicsView method)
FixedStepNumeric (class in session.numeric)
focusInEvent() (additionalUI.search.SearchInput method)
formatPosition() (in module functions)
formatToolTip() (tracks.graphicsItem.GraphicsItem static method)
ForwardStrand (session.annotation.AnnotationLine attribute)
(session.regions.Region attribute)
freeze (module)
functions (module)

G

generate() (functions.RandomColor static method)
generateClass() (in module generateDoc)
generateDoc (module)
generateModule() (in module generateDoc)
generatePackage() (in module generateDoc)
getAnnotationDataset() (session.session.Session method)
getAnnotations() (tracks.readsGraph.ReadsGraph static method)
getBlockLimits() (session.regions.Region method)
getCacheBlock() (session.reads.NucleotideCache method)
getCategories() (session.session.Session method)
getChromosomes() (session.dataset.Dataset method)
(session.reads.Reads method)
(session.regions.Regions method)
getData() (session.session.Session method)
getFileName() (session.dataset.Dataset method)
getFormat() (session.dataset.Dataset method)
getFullPath() (session.dataset.Dataset method)
getLines() (session.annotation.Annotation method)
(session.annotation.GtfAnnotation method)
(session.annotation.GtfGzAnnotation method)
(session.annotation.RefFlatAnnotation method)
(session.regions.Regions method)
(session.transcripts.Transcripts method)
getOpenFileName() (additionalUI.dialog.Dialog static method)
getReadCoverage() (in module session.reads)
getReads() (session.reads.Reads method)
getSaveDir() (additionalUI.dialog.Dialog static method)
getSavePath() (additionalUI.dialog.Dialog static method)
getSeq() (session.sequence.Sequence method)
getSequence() (session.session.Session method)
getTypeByClass() (in module session.dataTypes)
getTypeByName() (in module session.dataTypes)
getTypeByTrack() (in module session.dataTypes)
getTypeInfo() (in module session.dataTypes)
getValues() (session.numeric.FixedStepNumeric method)
(session.numeric.Numeric method)
(session.numeric.VariableStepNumeric method)
(session.reads.NucleotideCache method)
(session.reads.NucleotideCacheBlock method)
GlobalSettings (class in additionalUI.globalSettings)
GraphicsItem (class in tracks.graphicsItem)
GraphicsScene (class in tracks.scene)
GraphicsView (class in tracks.views)
GtfAnnotation (class in session.annotation)
GtfGzAnnotation (class in session.annotation)

H

hasViewType() (tracks.track.Track method)
hcl2rgb() (in module functions)
heatColors() (in module tracks.graphicsItem)
HeatmapBar (class in tracks.graphicsItem)
heatmapType() (tracks.readsGraph.ReadsGraph class method)
(tracks.transcriptGraph.TranscriptGraph method)
heatmapTypes (tracks.readsGraph.ReadsGraph attribute)
(tracks.transcriptGraph.TranscriptGraph attribute)
hide() (tracks.trackManager.TrackManager method)
hideAll() (tracks.trackManager.TrackManager method)
hideAllRequested (mainUI.dataTree.DataTreeDelegate attribute)
hideLegend() (mainUI.legendDock.LegendDock method)
hideRequested (mainUI.dataTree.DataTreeDelegate attribute)
highlight() (tracks.sequenceGraph.SequenceGraph method)
(tracks.track.Track method)
highlightAll() (tracks.trackManager.TrackManager method)
HistogramColumn (class in tracks.graphicsItem)
hoverEnterEvent() (tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.HeatmapBar method)
(tracks.graphicsItem.InsertionNucleotide method)
(tracks.regionGraph.RegionItem method)
(tracks.regionGraph.RegionLabel method)
hoverLeaveEvent() (tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.HeatmapBar method)
(tracks.graphicsItem.InsertionNucleotide method)
(tracks.regionGraph.RegionItem method)
(tracks.regionGraph.RegionLabel method)

I

importClass() (in module functions)
index() (mainUI.dataTree.DataTreeModel method)
indexFile() (session.annotation.GtfAnnotation method)
indexOfCategory() (mainUI.dataTree.DataTreeModel method)
InfoDock (class in mainUI.infoDock)
initializeClass() (tracks.graphicsItem.Nucleotide static method)
initializeScene() (tracks.numericGraph.NumericGraph method)
(tracks.readsGraph.ReadsGraph method)
(tracks.regionGraph.RegionGraph method)
(tracks.track.Track method)
initializeView() (tracks.numericGraph.NumericGraph method)
(tracks.readsGraph.ReadsGraph method)
(tracks.track.Track method)
InsertionNucleotide (class in tracks.graphicsItem)
insertWidget() (mainUI.trackSplitter.TrackSplitter method)
instance() (functions.Pool static method)
instances (tracks.readsGraph.ReadsGraph attribute)
intronList() (session.session.Session method)
invalid (session.dataset.Dataset attribute)
InvalidAnnotation (class in session.annotation)
InvalidNumeric (class in session.numeric)
isInfoDockVisible() (tracks.trackManager.TrackManager method)
isSorted() (session.reads.Reads method)

J

JunctionBarItem (class in tracks.junctionGraph)
JunctionGraph (class in tracks.junctionGraph)
JunctionItem (class in tracks.junctionGraph)
JunctionLineItem (class in tracks.junctionGraph)
Junctions (class in session.junctions)

L

lang (module)
lang.generateTs (module)
launchAbout() (mainUI.mainWindow.MainWindow method)
launchHelp() (mainUI.mainWindow.MainWindow method)
launchSearch() (mainUI.mainWindow.MainWindow method)
launchSettings() (mainUI.mainWindow.MainWindow method)
launchTrackHeight() (mainUI.mainWindow.MainWindow method)
leaveEvent() (tracks.track.Track method)
(tracks.views.GraphicsView method)
left() (tracks.graphicsItem.ReadItem method)
LegendDock (class in mainUI.legendDock)
legendInfo() (tracks.junctionGraph.JunctionGraph method)
(tracks.readsGraph.ReadsGraph method)
(tracks.track.Track method)
(tracks.transcriptGraph.TranscriptGraph method)
length() (session.sequence.Sequence method)
levelOfDetailsChanged (tracks.trackManager.TrackManager attribute)
limits() (session.reads.Read method)
(session.regions.Region method)
logRequest() (additionalUI.search.SearchUI method)

M

main() (in module RNAseqViewer)
mainUI (module)
mainUI.dataTree (module)
mainUI.infoDock (module)
mainUI.legendDock (module)
mainUI.mainWindow (module)
mainUI.toolBar (module)
mainUI.trackSplitter (module)
MainWindow (class in mainUI.mainWindow)
maxReadCount() (session.reads.Reads method)
messageHandler() (in module additionalUI.dialog)
minimumSizeHint() (mainUI.trackSplitter.SplitterSpacer method)
mouseDoubleClickEvent() (tracks.views.GraphicsView method)
mouseMoveEvent() (tracks.track.TrackHandle method)
(tracks.views.GraphicsView method)
mousePressEvent() (tracks.track.TrackHandle method)
mouseReleaseEvent() (tracks.views.GraphicsView method)
move() (tracks.trackManager.TrackManager method)
moveRequested (mainUI.toolBar.ToolBar attribute)
my_excepthook() (in module RNAseqViewer)

N

nbDatasets() (session.session.Session method)
nbTracks() (session.dataset.Dataset method)
newAction() (mainUI.dataTree.DataTreeMenu method)
newSession() (mainUI.mainWindow.MainWindow method)
nodeType() (mainUI.dataTree.DataTreeModel method)
nodeTypeRole (mainUI.dataTree.DataTreeModel attribute)
notify() (additionalUI.dialog.Dialog static method)
Nucleotide (class in tracks.graphicsItem)
NucleotideCache (class in session.reads)
NucleotideCacheBlock (class in session.reads)
nucleotideInfo() (tracks.trackManager.TrackManager method)
nucleotideWidth() (tracks.trackManager.TrackManager method)
Numeric (class in session.numeric)
NumericFactory (class in session.numeric)
NumericGraph (class in tracks.numericGraph)

O

okToQuit() (mainUI.mainWindow.MainWindow method)
openColorPicker() (additionalUI.trackSettings.ColorPushButton method)
openSession() (mainUI.mainWindow.MainWindow method)
(session.save.SessionSaving method)

P

p (tracks.graphicsItem.Nucleotide attribute)
paint() (tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.HeatmapBar method)
(tracks.graphicsItem.HistogramColumn method)
(tracks.graphicsItem.Nucleotide method)
(tracks.junctionGraph.JunctionLineItem method)
(tracks.readsGraph.CoverageColumn method)
(tracks.readsGraph.CoverageColumnPart method)
(tracks.regionGraph.RegionItem method)
(tracks.regionGraph.RegionLabel method)
paintEvent() (tracks.track.TrackHandle method)
paintTracks() (additionalUI.printOut.PrintOut method)
parameters (tracks.readsGraph.ReadsGraph attribute)
parent() (mainUI.dataTree.DataTreeModel method)
pen (tracks.graphicsItem.BlankReadItem attribute)
penHover (tracks.graphicsItem.BlankReadItem attribute)
pixelToCoordinate() (tracks.trackManager.TrackManager method)
Pool (class in functions)
populateInfoDock() (tracks.trackManager.TrackManager method)
pos() (tracks.graphicsItem.ReadItem method)
previewPrint() (additionalUI.printOut.PrintOut method)
PrintOut (class in additionalUI.printOut)
printTracks() (additionalUI.printOut.PrintOut method)

Q

qCleanupResources() (in module qrc_resources)
qInitResources() (in module qrc_resources)
qrc_resources (module)
quality() (session.reads.Read method)

R

RandomColor (class in functions)
Read (class in session.reads)
readCSV() (session.dataset.Dataset method)
readGtfAttributes() (in module functions)
ReadItem (class in tracks.graphicsItem)
Reads (class in session.reads)
readsCount() (session.reads.Reads method)
ReadsGraph (class in tracks.readsGraph)
redraw() (mainUI.legendDock.LegendDock method)
redrawAfterResize() (tracks.trackManager.TrackManager method)
redrawNucleotides() (tracks.readsGraph.ReadsGraph method)
RefFlatAnnotation (class in session.annotation)
refresh() (mainUI.dataTree.DataTreeView method)
refreshData() (tracks.track.TrackHandle method)
Region (class in session.regions)
RegionGraph (class in tracks.regionGraph)
RegionItem (class in tracks.regionGraph)
RegionLabel (class in tracks.regionGraph)
Regions (class in session.regions)
removeDataset() (session.session.Session method)
removeFromScene() (tracks.graphicsItem.ReadItem method)
removeNucleotideContent() (tracks.graphicsItem.ReadItem method)
removeTrack() (session.dataset.Dataset method)
(tracks.trackManager.TrackManager method)
reportProgress() (session.save.SessionSaving static method)
resetAll() (mainUI.dataTree.DataTreeView method)
resetCache() (session.reads.Reads method)
resizeEvent() (mainUI.dataTree.DataTreeView method)
(tracks.track.TrackHandle method)
(tracks.views.GraphicsView method)
resizeTracks() (additionalUI.trackHeight.trackHeightUI method)
restoreDefaults() (additionalUI.globalSettings.GlobalSettings method)
restoreWindowSate() (mainUI.mainWindow.MainWindow method)
ReverseStrand (session.annotation.AnnotationLine attribute)
(session.regions.Region attribute)
right() (tracks.graphicsItem.ReadItem method)
RNAseqViewer (module)
rowCount() (additionalUI.trackSettings.DatasetListModel method)
(mainUI.dataTree.DataTreeModel method)
rowOfCategory() (mainUI.dataTree.DataTreeModel method)
rowOfTrack() (mainUI.dataTree.DataTreeModel method)

S

saveAsCollapsed() (mainUI.dataTree.DataTreeView method)
saveAsExpanded() (mainUI.dataTree.DataTreeView method)
saveAsImage() (additionalUI.printOut.PrintOut method)
(tracks.track.Track method)
saveSamtoolsResult() (session.reads.NucleotideCacheBlock method)
saveSession() (mainUI.mainWindow.MainWindow method)
(session.save.SessionSaving method)
saveWindowState() (mainUI.mainWindow.MainWindow method)
scaleChanged (tracks.track.Track attribute)
sceneWidth() (tracks.trackManager.TrackManager method)
search() (additionalUI.search.SearchUI method)
(session.annotation.Annotation method)
(session.annotation.GtfAnnotation method)
(session.annotation.GtfGzAnnotation method)
(session.annotation.RefFlatAnnotation method)
(session.session.Session method)
SearchInput (class in additionalUI.search)
SearchUI (class in additionalUI.search)
seeGene() (additionalUI.search.SearchUI method)
Sequence (class in session.sequence)
SequenceGraph (class in tracks.sequenceGraph)
sequencesChanged (session.session.Session attribute)
Session (class in session.session)
session (module)
session.annotation (module)
session.dataset (module)
session.dataTypes (module)
session.junctions (module)
session.numeric (module)
session.reads (module)
session.regions (module)
session.save (module)
session.sequence (module)
session.session (module)
session.transcripts (module)
SessionSaving (class in session.save)
setAllViewType() (tracks.trackManager.TrackManager method)
setAnnotations() (tracks.readsGraph.ReadsGraph method)
setChromList() (mainUI.toolBar.ToolBar method)
setChromosome() (mainUI.toolBar.ToolBar method)
setCurrentTrack() (mainUI.dataTree.DataTreeMenu method)
setData() (tracks.track.Track method)
setDefaultHeatmapType() (tracks.track.Track class method)
setDefaultSettings() (additionalUI.globalSettings.GlobalSettings static method)
setDefaultViewType() (tracks.track.Track class method)
setDictToolTip() (tracks.graphicsItem.GraphicsItem method)
setHandleWidth() (tracks.trackManager.TrackManager method)
setHeatmapType() (tracks.readsGraph.ReadsGraph method)
(tracks.transcriptGraph.TranscriptGraph method)
setHideIntronButtonState() (mainUI.toolBar.ToolBar method)
setHideIntronsMode() (tracks.trackManager.TrackManager method)
setPos() (tracks.graphicsItem.ReadItem method)
setPositionFormEnabled() (mainUI.toolBar.ToolBar method)
setProgress() (additionalUI.dialog.Dialog static method)
setSceneRect() (tracks.readsGraph.ReadsGraph method)
(tracks.views.GraphicsView method)
setSceneWidth() (tracks.trackManager.TrackManager method)
setStatus() (additionalUI.dialog.Dialog static method)
SettingsPage (class in additionalUI.globalSettings)
setTrack() (mainUI.legendDock.LegendDock method)
setTrackHeight() (tracks.trackManager.TrackManager method)
setup (module)
setViewType() (tracks.readsGraph.ReadsGraph method)
(tracks.track.Track method)
(tracks.trackManager.TrackManager method)
setWindow() (additionalUI.dialog.Dialog static method)
shape() (tracks.junctionGraph.JunctionBarItem method)
showError() (mainUI.toolBar.ToolBar method)
showInfo() (mainUI.infoDock.InfoDock method)
sizeHint() (tracks.track.TrackHandle method)
(tracks.views.GraphicsView method)
sortedNicely() (in module functions)
SplitterSpacer (class in mainUI.trackSplitter)
switchArea() (tracks.trackManager.TrackManager method)

T

testColors() (in module functions)
ToolBar (class in mainUI.toolBar)
toolTip() (tracks.annotationGraph.AnnotationItem method)
(tracks.graphicsItem.BlankReadItem method)
(tracks.graphicsItem.Nucleotide method)
(tracks.junctionGraph.JunctionBarItem method)
(tracks.junctionGraph.JunctionItem method)
(tracks.readsGraph.CoverageColumn method)
(tracks.readsGraph.CoverageColumnPart method)
(tracks.regionGraph.RegionItem method)
(tracks.transcriptGraph.TranscriptItem method)
tr() (in module functions)
Track (class in tracks.track)
trackAdded (tracks.trackManager.TrackManager attribute)
trackFromIndex() (mainUI.dataTree.DataTreeModel method)
TrackHandle (class in tracks.track)
trackHeightUI (class in additionalUI.trackHeight)
TrackManager (class in tracks.trackManager)
trackRemoved (tracks.trackManager.TrackManager attribute)
trackRole (mainUI.dataTree.DataTreeModel attribute)
tracks (module)
tracks.annotationGraph (module)
tracks.graphicsItem (module)
tracks.junctionGraph (module)
tracks.numericGraph (module)
tracks.readsGraph (module)
tracks.regionGraph (module)
tracks.scene (module)
tracks.sequenceGraph (module)
tracks.track (module)
tracks.trackManager (module)
tracks.transcriptGraph (module)
tracks.views (module)
TrackSettings (class in additionalUI.trackSettings)
TrackSplitter (class in mainUI.trackSplitter)
Transcript (class in session.transcripts)
TranscriptGraph (class in tracks.transcriptGraph)
TranscriptItem (class in tracks.transcriptGraph)
Transcripts (class in session.transcripts)
transformAll() (tracks.trackManager.TrackManager method)
transformLike() (tracks.trackManager.TrackManager method)
treeRefreshed (mainUI.dataTree.DataTreeView attribute)

U

update() (tracks.track.Track method)
updateAll() (tracks.trackManager.TrackManager method)
updateButtonsAvailability() (mainUI.toolBar.ToolBar method)
updateChromList() (mainUI.mainWindow.MainWindow method)
updateChromosome() (tracks.regionGraph.RegionGraph method)
(tracks.sequenceGraph.SequenceGraph method)
updateColor() (additionalUI.trackSettings.ColorPushButton method)
updateColumns() (tracks.readsGraph.ReadsGraph static method)
updateLevelOfDetail() (tracks.trackManager.TrackManager method)
updatePosition() (mainUI.toolBar.ToolBar method)
updatePositionStatus() (tracks.trackManager.TrackManager method)
updateTotalReadCount() (session.reads.Reads method)
updateValues() (tracks.readsGraph.ReadsGraph method)
updateVisibleArea() (tracks.trackManager.TrackManager method)

V

validateAreaLabel() (mainUI.toolBar.ToolBar method)
validateSearch() (mainUI.toolBar.ToolBar method)
validateSettings() (additionalUI.trackSettings.TrackSettings method)
VariableStepNumeric (class in session.numeric)
viewChangeAllRequested (mainUI.dataTree.DataTreeDelegate attribute)
viewChangeRequested (mainUI.dataTree.DataTreeDelegate attribute)
viewTypeChanged (tracks.trackManager.TrackManager attribute)
viewTypeRole (mainUI.dataTree.DataTreeModel attribute)
viewTypes (tracks.junctionGraph.JunctionGraph attribute)
(tracks.numericGraph.NumericGraph attribute)
(tracks.readsGraph.ReadsGraph attribute)
(tracks.regionGraph.RegionGraph attribute)
(tracks.sequenceGraph.SequenceGraph attribute)
(tracks.track.Track attribute)
viewTypes() (session.dataTypes.DataType method)
visibleAreaChanged (tracks.trackManager.TrackManager attribute)
visibleChromArea() (tracks.trackManager.TrackManager method)

W

wheelEvent() (tracks.views.GraphicsView method)

Z

zoom() (tracks.trackManager.TrackManager method)
zoomRequested (mainUI.toolBar.ToolBar attribute)

Table Of Contents