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

A

AbsoluteFocusPanel - Class in org.utgenome.gwt.utgb.client.ui
Absolute panel with Focus panel
AbsoluteFocusPanel() - Constructor for class org.utgenome.gwt.utgb.client.ui.AbsoluteFocusPanel
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.BEDGene
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.Gap
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
accept(GenomeRangeVisitor) - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.ReadCoverage
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.ReadList
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.ReferenceSequence
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPair
 
accept(GenomeRangeVisitor) - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
 
accept(String) - Method in class org.utgenome.shell.Create.CreateAllScaffoldFileFilter
 
accept(String) - Method in interface org.utgenome.shell.Create.ScaffoldFileFilter
 
AcceptSpecies - Class in org.utgenome.format.legacy
 
AcceptSpecies() - Constructor for class org.utgenome.format.legacy.AcceptSpecies
 
acceptSpeciesEntries - Variable in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
ACGT - Class in org.utgenome.gwt.utgb.server.app
Web action: ACGT
ACGT() - Constructor for class org.utgenome.gwt.utgb.server.app.ACGT
 
ACGTEncoder - Class in org.utgenome.gwt.utgb.client.bio
Nucleotide ACGT <-> 2bit code conversion utility
ACGTEncoder() - Constructor for class org.utgenome.gwt.utgb.client.bio.ACGTEncoder
 
ActionInfo - Class in org.utgenome.config
action tag in track-config.xml
ActionInfo() - Constructor for class org.utgenome.config.ActionInfo
 
ActionPackage - Interface in org.utgenome.gwt.utgb.server
ActionPackageAlias - Annotation Type in org.utgenome.gwt.utgb.server
 
activeImageURL - Variable in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
activeReads() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
adaptor - Variable in class org.utgenome.format.bed.BEDParser
 
adaptor - Variable in class org.utgenome.format.wig.WIGParser
 
add(ReadStat.ReadAlignmentStat) - Method in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
add(GenomeKeywordEntry) - Method in class org.utgenome.format.keyword.KeywordDB
 
add(GenomeKeywordEntry.KeywordAlias) - Method in class org.utgenome.format.keyword.KeywordDB
 
add(T) - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
add(String, T) - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
add(int, CIGAR.Type) - Method in class org.utgenome.gwt.utgb.client.bio.CIGAR
 
add(T) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
Add an entry [start, end)
add(DataType) - Method in class org.utgenome.gwt.utgb.client.db.Relation
 
add(AbsolutePanel, OperationArea) - Static method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
add(Widget) - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
Widget must implements SourcesMouseEvents
add(Widget, Widget) - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
Add the widget with the specified drag hanel
add(String, String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
add(String, int) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
add(String, long) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
add(String, float) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
add(String, boolean) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
add(String, String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
add(String, int) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
add(String, long) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
add(String, float) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
add(String, boolean) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
add(Node) - Method in class org.utgenome.gwt.utgb.client.util.xml.NodeListImpl
 
add(String, String) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLAttribute
 
add(String, int) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLAttribute
 
add(String, long) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLAttribute
 
add(String, boolean) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLAttribute
 
add(String, Class<RequestHandler>) - Method in class org.utgenome.gwt.utgb.server.RequestHandlerTable
 
add(Widget) - Method in interface org.utgenome.gwt.widget.client.TrackPanel
 
add(Widget) - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
Do not make the widget draggable
add(Widget, Widget) - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
Add the widget with the specified drag hanel
add(E) - Method in class org.utgenome.util.repeat.DisjointSet
 
addAction(ActionInfo) - Method in class org.utgenome.config.TrackConfiguration
 
AddAction - Class in org.utgenome.shell
A UTGBShell sub-command for adding new action class
AddAction() - Constructor for class org.utgenome.shell.AddAction
 
addAlignment(Alignment) - Method in class org.utgenome.gwt.utgb.client.bio.AlignmentResult
 
addAttribute(BED2Silk.BEDHeaderAttribute) - Method in class org.utgenome.format.bed.BED2Silk.BEDHeaderDescription
 
addAttribute(WIG2Silk.WIGHeaderAttribute) - Method in class org.utgenome.format.wig.WIG2Silk.WIGHeaderDescription
 
addAttribute(WIGDatabaseGenerator.WIGHeaderAttribute) - Method in class org.utgenome.format.wig.WIGDatabaseGenerator.WIGHeaderDescription
 
addAuthor(String) - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
addBlockSizes(int) - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
addCDS(CDS) - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType.BooleanTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType.DoubleTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType.FloatTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.InputForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeListBox
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType.PasswordTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeForm
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeListBox
 
addChangeHandler(ChangeHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType.TextTypeForm
 
addChangeListener(TrackInfoChangeListener) - Method in class org.utgenome.gwt.utgb.client.track.TrackInfo
add a change listener
addChild(Widget) - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
addChild(TreePanel) - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
addClickHanlder(ClickHandler) - Method in class org.utgenome.gwt.widget.client.Icon
 
addCommand(FrameCommand) - Method in class org.utgenome.gwt.utgb.client.track.operation.FrameOperation
 
addConfig(DataType, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConfig(String, DataType, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConfigBoolean(String, String, boolean) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConfigDouble(String, String, double) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConfigInteger(String, String, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConfigString(String, String, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addConnection(ConnectionInfo) - Method in class org.utgenome.config.DatabaseInfo
 
addContext(String, String) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
addDatabase(DatabaseInfo) - Method in class org.utgenome.config.TrackConfiguration
 
addEntry(SpeciesEntry) - Method in class org.utgenome.format.legacy.AcceptSpecies
 
addEventHandler(EventHandler) - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
addExon(Exon) - Method in class org.utgenome.format.egt.Gene
 
addExon(Exon) - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
addGene(BEDEntry) - Method in class org.utgenome.format.bed.BEDDatabase.BEDRangeQuery
 
addGene(BEDEntry) - Method in class org.utgenome.format.bed.BEDDatabase.DBBuilder
 
addGene(BEDEntry) - Method in interface org.utgenome.format.bed.BEDQuery
 
addGene(Gene) - Method in class org.utgenome.format.egt.EGTXMLReader
 
addHidden(HiddenParameter) - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
addHidden(HiddenParameter) - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
addHiddenConfig(String, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
addIcon(int, IconImage) - Static method in class org.utgenome.gwt.utgb.client.track.Design
 
addImport(ImportStmt) - Method in class org.utgenome.config.TrackConfiguration
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType.BooleanTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType.DoubleTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType.FloatTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.InputForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeListBox
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType.PasswordTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeForm
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeListBox
 
addKeyPressHandler(KeyPressHandler) - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType.TextTypeForm
 
addKeyword(String) - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
addLayer(Layer) - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
addLine(String) - Method in class org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
 
addMenuItem(MenuOperationItem) - Method in class org.utgenome.gwt.utgb.client.track.operation.MenuOperation
 
addMouseDownHandler(MouseDownHandler) - Method in class org.utgenome.gwt.utgb.client.ui.AbsoluteFocusPanel
 
addMouseDownHandler(MouseDownHandler) - Method in class org.utgenome.gwt.widget.client.Tab
 
addMouseMoveHandler(MouseMoveHandler) - Method in class org.utgenome.gwt.utgb.client.ui.AbsoluteFocusPanel
 
addName(String) - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
addOperation(Operation) - Method in class org.utgenome.gwt.utgb.client.track.operation.EventImpl
 
addOption(Option) - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
addParam(Parameter) - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
addParam(Parameter) - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
addParameter(String) - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
addParameter(String, String) - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
addPrettyAlignment(String) - Method in class org.utgenome.gwt.utgb.client.bio.AlignmentResult
 
addQueryStarts(int) - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
addRead(Read) - Method in class org.utgenome.format.silk.read.ReadDBBuilder.ReferenceReader
 
addRead(Read) - Method in class org.utgenome.format.silk.read.Reference
 
addRead(GenomeRange) - Method in class org.utgenome.gwt.utgb.client.bio.ReadList
 
addReference(ReadDBBuilder.ReferenceReader) - Method in class org.utgenome.format.silk.read.ReadDBBuilder
 
addRequestMap(RequestMap) - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
address - Variable in class org.utgenome.config.UTGBConfig.Database
 
ADDRESS_PREFIX - Static variable in class org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess
 
addResult(Result) - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
addRevision(String) - Method in class org.utgenome.gwt.utgb.client.track.bean.SequenceInfo
 
addRow(String) - Method in class org.utgenome.gwt.utgb.client.db.DatabaseTable
 
addRow(JSONValue) - Method in class org.utgenome.gwt.utgb.client.db.DatabaseTable
 
addRow(Object[]) - Method in class org.utgenome.gwt.utgb.client.ui.EditableTable
 
addRow(Object[]) - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
addServerListener(ServerListener) - Method in class org.utgenome.shell.UTGBPortable
 
addSiblign(Widget) - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
addSibling(TreePanel) - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
addSpecies(Species) - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
addTab(TrackPanel, Tab) - Method in class org.utgenome.gwt.widget.client.TabbedTrackFrame
 
addTabEntry(TabEntry.TabEntryFactory) - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabViewer
 
addTableChangeListener(TableChangeListener) - Method in class org.utgenome.gwt.utgb.client.ui.EditableTable
 
addTargetStarts(int) - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
addTouchCancelHandler(TouchCancelHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableComposite
 
addTouchCancelHandler(TouchCancelHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableFocusPanel
 
addTouchCancelHandler(TouchCancelHandler) - Method in interface org.utgenome.gwt.ipad.event.HasTouchHandlers
 
addTouchEndHandler(TouchEndHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableComposite
 
addTouchEndHandler(TouchEndHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableFocusPanel
 
addTouchEndHandler(TouchEndHandler) - Method in interface org.utgenome.gwt.ipad.event.HasTouchHandlers
 
addTouchMoveHandler(TouchMoveHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableComposite
 
addTouchMoveHandler(TouchMoveHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableFocusPanel
 
addTouchMoveHandler(TouchMoveHandler) - Method in interface org.utgenome.gwt.ipad.event.HasTouchHandlers
 
addTouchStartHandler(TouchStartHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableComposite
 
addTouchStartHandler(TouchStartHandler) - Method in class org.utgenome.gwt.ipad.client.TouchableFocusPanel
 
addTouchStartHandler(TouchStartHandler) - Method in interface org.utgenome.gwt.ipad.event.HasTouchHandlers
 
addTrack(BEDTrack) - Method in class org.utgenome.format.bed.BEDDatabase.BEDRangeQuery
 
addTrack(BEDTrack) - Method in class org.utgenome.format.bed.BEDDatabase.DBBuilder
 
addTrack(BEDTrack) - Method in interface org.utgenome.format.bed.BEDQuery
 
addTrack(TrackBean) - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
addTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Add a new track to this group.
addTrackButtonListener(TrackButtonListener) - Method in class org.utgenome.gwt.widget.client.impl.IconSetPanel
 
addTrackButtonListener(TrackButtonListener) - Method in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
addTrackButtonListener(TrackButtonListener) - Method in class org.utgenome.gwt.widget.client.TrackFrame
 
addTrackButtonListener(TrackButtonListener) - Method in class org.utgenome.gwt.widget.client.TrackWindowPanel
 
addTrackFactory(String, Track.TrackFactory) - Method in class org.utgenome.gwt.utgb.client.track.lib.ToolBoxTrack
 
addTrackFactory(String, Track.TrackFactory) - Static method in class org.utgenome.gwt.utgb.client.track.TrackFactoryHolder
 
addTrackGroup(TrackGroupBean) - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
addTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Add a track group as a child of this track group.
addTrackGroupFactory(String, HasFactory.TrackGroupFactory) - Static method in class org.utgenome.gwt.utgb.client.track.TrackFactoryHolder
 
addTrackGroupPropertyChangeListener(TrackGroupPropertyChangeListener) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
addTrackGroupPropertyChangeListener(TrackGroupPropertyChangeListener) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Add a TrackGroupPropertyChangeListener
addTrackUpdateListener(TrackUpdateListener) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Add a TrackUpdateListener
addValue(String) - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
addValueList(Value) - Method in class org.utgenome.gwt.utgb.client.db.ValueDomain
 
addWidget(Widget) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ConfigInputForm
 
addWidgetSizeChangeListener(WidgetSizeChangeListener) - Method in interface org.utgenome.gwt.utgb.client.ui.SourcesWidgetSizeChanges
 
addWindowListener(WindowListener) - Method in interface org.utgenome.gwt.utgb.client.ui.SourcesWindowEvents
 
addWindowListener(WindowListener) - Method in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
addWorker(Worker) - Method in class org.utgenome.gwt.utgb.client.util.WorkQueue
 
adjustFrameHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
adjustHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
adjustToOneOrigin() - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
adjustToOneOrigin() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
afterStart() - Method in interface org.utgenome.shell.ServerListener
 
afterStart() - Method in class org.utgenome.shell.UTGBPortableWidget
 
afterStop() - Method in interface org.utgenome.shell.ServerListener
 
afterStop() - Method in class org.utgenome.shell.UTGBPortableWidget
 
AGPPullParser - Class in org.utgenome.format.agp
 
AGPPullParser(Reader) - Constructor for class org.utgenome.format.agp.AGPPullParser
 
alias - Variable in class org.utgenome.config.UTGBConfig.WebAction
 
alias - Variable in class org.utgenome.format.keyword.GenomeKeywordEntry.KeywordAlias
 
aligningAssembly - Variable in class org.utgenome.format.axt.AXTAlignment
 
alignment - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult
 
Alignment - Class in org.utgenome.gwt.utgb.client.bio
Alignment result
Alignment() - Constructor for class org.utgenome.gwt.utgb.client.bio.Alignment
 
alignment - Variable in class org.utgenome.gwt.utgb.client.bio.BSSRead
 
alignment - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment
 
alignmentLength - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult.BlastAlignment
 
AlignmentResult - Class in org.utgenome.gwt.utgb.client.bio
 
AlignmentResult() - Constructor for class org.utgenome.gwt.utgb.client.bio.AlignmentResult
 
allowPEOverlap - Variable in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
altAA - Variable in class org.utgenome.util.sv.EnhancedGeneticVariation
 
altCodon - Variable in class org.utgenome.util.sv.EnhancedGeneticVariation
 
AminoAcid - Enum in org.utgenome.gwt.utgb.client.bio
AminoAcid table
Animation - Class in org.utgenome.gwt.utgb.client.ui
A modified version of the animation support class included in GWT.
Animation() - Constructor for class org.utgenome.gwt.utgb.client.ui.Animation
 
Animation(int) - Constructor for class org.utgenome.gwt.utgb.client.ui.Animation
 
answerYes - Variable in class org.utgenome.shell.Create
 
APP_FOLDER - Static variable in class org.utgenome.shell.UTGBShellCommand
 
append(String) - Method in class org.utgenome.format.fasta.CompactACGTWriter
 
append(char) - Method in class org.utgenome.format.fasta.CompactACGTWriter
 
append(String) - Method in class org.utgenome.format.fasta.Kmer
 
append(T, String, U) - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
appendSequence(String) - Method in class org.utgenome.format.silk.read.ReadDBBuilder.ReferenceReader
 
appendSequence(String) - Method in class org.utgenome.format.silk.read.Reference
 
apply(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
apply(TrackGroupPropertyChange) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyWriter
Apply the property changes to this writer
ARC - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
Assembly - Class in org.utgenome.format.agp
File Format: One feature of the AGP file is that column definitions change depending on whether the line is a component line or a gap line.
Assembly() - Constructor for class org.utgenome.format.agp.Assembly
 
atomicSetStartAndEnd(int, int) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
Attribute - Static variable in class org.utgenome.format.bed.BEDLexer
 
Attribute - Static variable in class org.utgenome.format.bed.BEDParser
 
attribute() - Method in class org.utgenome.format.bed.BEDParser
 
Attribute - Static variable in class org.utgenome.format.wig.WIGLexer
 
Attribute - Static variable in class org.utgenome.format.wig.WIGParser
 
attribute() - Method in class org.utgenome.format.wig.WIGParser
 
attributes - Variable in class org.utgenome.format.gff3.GFF3Entry
 
attributeValue() - Method in class org.utgenome.format.bed.BEDParser
 
attributeValue() - Method in class org.utgenome.format.wig.WIGParser
 
autoScale - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
autoScaledMax - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
autoScaledMin - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
availaableFreeMemory() - Static method in class org.utgenome.util.OSInfo
 
available() - Method in class org.utgenome.util.ReaderInputStream
 
availableProcessors() - Static method in class org.utgenome.util.OSInfo
 
AXTAlignment - Class in org.utgenome.format.axt
Record in AXT format
AXTAlignment() - Constructor for class org.utgenome.format.axt.AXTAlignment
 
AXTLens - Class in org.utgenome.format.axt
Lens for AXT format
AXTLens(BufferedReader) - Constructor for class org.utgenome.format.axt.AXTLens
 
AXTLens(URL) - Constructor for class org.utgenome.format.axt.AXTLens
 

B

backgroundColor(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundImage(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundNoRepeat(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundPosition(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundRepeat(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundRepeatX(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
backgroundRepeatY(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
bamFile - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
bamFileName - Variable in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
BarGraphCanvas - Class in org.utgenome.gwt.utgb.client.canvas
Canvas for drawing CompactWIGData
BarGraphCanvas(TrackWindow, int) - Constructor for class org.utgenome.gwt.utgb.client.canvas.BarGraphCanvas
 
baseLine - Variable in class org.utgenome.gwt.utgb.server.app.FontPanel.FontInfo
 
baseURL - Variable in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
BED2Silk - Class in org.utgenome.format.bed
Converting BED into Silk format.
BED2Silk(File) - Constructor for class org.utgenome.format.bed.BED2Silk
 
BED2Silk(Reader) - Constructor for class org.utgenome.format.bed.BED2Silk
 
BED2Silk.BEDHeaderAttribute - Class in org.utgenome.format.bed
 
BED2Silk.BEDHeaderAttribute() - Constructor for class org.utgenome.format.bed.BED2Silk.BEDHeaderAttribute
 
BED2Silk.BEDHeaderDescription - Class in org.utgenome.format.bed
 
BED2Silk.BEDHeaderDescription() - Constructor for class org.utgenome.format.bed.BED2Silk.BEDHeaderDescription
 
BED2SilkReader - Class in org.utgenome.format.bed
BED2SilkReader read the input BED data, and the user can read it as if it were a Silk format.
BED2SilkReader(Reader) - Constructor for class org.utgenome.format.bed.BED2SilkReader
 
BEDDatabase - Class in org.utgenome.format.bed
Query/Update interface for BED database stored in SQLite
BEDDatabase() - Constructor for class org.utgenome.format.bed.BEDDatabase
 
BEDDatabase.BEDRangeQuery - Class in org.utgenome.format.bed
 
BEDDatabase.BEDRangeQuery(List<GenomeRange>, String, int, int) - Constructor for class org.utgenome.format.bed.BEDDatabase.BEDRangeQuery
 
BEDDatabase.DBBuilder - Class in org.utgenome.format.bed
 
BEDDatabase.DBBuilder(Connection) - Constructor for class org.utgenome.format.bed.BEDDatabase.DBBuilder
 
BEDEntry - Class in org.utgenome.format.bed
Representing each gene line of BED format
BEDEntry() - Constructor for class org.utgenome.format.bed.BEDEntry
 
BEDGene - Class in org.utgenome.gwt.utgb.client.bio
Representing each gene line of BED format
BEDGene() - Constructor for class org.utgenome.gwt.utgb.client.bio.BEDGene
 
BEDGene(BEDGene) - Constructor for class org.utgenome.gwt.utgb.client.bio.BEDGene
 
BEDLexer - Class in org.utgenome.format.bed
 
BEDLexer() - Constructor for class org.utgenome.format.bed.BEDLexer
 
BEDLexer(CharStream) - Constructor for class org.utgenome.format.bed.BEDLexer
 
BEDLexer(CharStream, RecognizerSharedState) - Constructor for class org.utgenome.format.bed.BEDLexer
 
BEDParser - Class in org.utgenome.format.bed
 
BEDParser(TokenStream) - Constructor for class org.utgenome.format.bed.BEDParser
 
BEDParser(TokenStream, RecognizerSharedState) - Constructor for class org.utgenome.format.bed.BEDParser
 
BEDParser.attribute_return - Class in org.utgenome.format.bed
 
BEDParser.attribute_return() - Constructor for class org.utgenome.format.bed.BEDParser.attribute_return
 
BEDParser.attributeValue_return - Class in org.utgenome.format.bed
 
BEDParser.attributeValue_return() - Constructor for class org.utgenome.format.bed.BEDParser.attributeValue_return
 
BEDParser.description_return - Class in org.utgenome.format.bed
 
BEDParser.description_return() - Constructor for class org.utgenome.format.bed.BEDParser.description_return
 
BEDParser.descriptionName_return - Class in org.utgenome.format.bed
 
BEDParser.descriptionName_return() - Constructor for class org.utgenome.format.bed.BEDParser.descriptionName_return
 
BEDQuery - Interface in org.utgenome.format.bed
An interface for extracting BED entries using BED2SilkReader.
BEDTrack - Class in org.utgenome.format.bed
BEDTrack represents a track line in BED files.
BEDTrack() - Constructor for class org.utgenome.format.bed.BEDTrack
 
BEDTrack - Class in org.utgenome.gwt.utgb.client.track.lib
Deprecated. Use ReadTrack instead
BEDTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.BEDTrack
Deprecated.  
BEDViewer - Class in org.utgenome.gwt.utgb.server.app
BED viewer
BEDViewer() - Constructor for class org.utgenome.gwt.utgb.server.app.BEDViewer
 
beforeChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
beforeChangeTrackWindow(TrackWindow) - Method in interface org.utgenome.gwt.utgb.client.track.Track
An event handler that will be invoked before the track window location change
beforeChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
beforeStart() - Method in interface org.utgenome.shell.ServerListener
 
beforeStart() - Method in class org.utgenome.shell.UTGBPortableWidget
 
beforeStop() - Method in interface org.utgenome.shell.ServerListener
 
beforeStop() - Method in class org.utgenome.shell.UTGBPortableWidget
 
bitFlag - Variable in enum org.utgenome.gwt.utgb.client.bio.IUPAC
 
bitScore - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult.BlastAlignment
 
bitScore - Variable in class org.utgenome.gwt.utgb.client.bio.BlastResult
 
bitScore - Variable in class org.utgenome.gwt.utgb.client.bio.BSSRead
 
bitScore - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment
 
Blast2Silk - Class in org.utgenome.format.blast
Converting blast (default) format into Silk
Blast2Silk(Reader) - Constructor for class org.utgenome.format.blast.Blast2Silk
 
Blast2Silk.Blast2SilkConverter - Class in org.utgenome.format.blast
 
Blast2Silk.Blast2SilkConverter() - Constructor for class org.utgenome.format.blast.Blast2Silk.Blast2SilkConverter
 
Blast2Silk.BlastResult - Class in org.utgenome.format.blast
 
Blast2Silk.BlastResult() - Constructor for class org.utgenome.format.blast.Blast2Silk.BlastResult
 
Blast2Silk.BlastResult.BlastAlignment - Class in org.utgenome.format.blast
 
Blast2Silk.BlastResult.BlastAlignment() - Constructor for class org.utgenome.format.blast.Blast2Silk.BlastResult.BlastAlignment
 
Blast2Silk.BlastResult.BlastAlignment.Strand - Enum in org.utgenome.format.blast
 
Blast2Silk.PeekableReader - Class in org.utgenome.format.blast
 
Blast2Silk.PeekableReader(BufferedReader) - Constructor for class org.utgenome.format.blast.Blast2Silk.PeekableReader
 
BlastResult - Class in org.utgenome.gwt.utgb.client.bio
Read with cigar and sequence information
BlastResult() - Constructor for class org.utgenome.gwt.utgb.client.bio.BlastResult
 
block - Variable in class org.utgenome.gwt.utgb.client.bio.GenomeRangeDataSet
 
BlockReader - Class in org.utgenome.format
 
BlockReader() - Constructor for class org.utgenome.format.BlockReader
 
BlockwiseFileReader - Class in org.utgenome.format
Reading files in block-wise manner
BlockwiseFileReader(File, int) - Constructor for class org.utgenome.format.BlockwiseFileReader
 
bold(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
BooleanType - Class in org.utgenome.gwt.utgb.client.db.datatype
 
BooleanType(String) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.BooleanType
 
BooleanType.BooleanTypeForm - Class in org.utgenome.gwt.utgb.client.db.datatype
 
BooleanType.BooleanTypeForm() - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.BooleanType.BooleanTypeForm
 
Border - Class in org.utgenome.gwt.utgb.client.ui
 
Border(int, int, int, String) - Constructor for class org.utgenome.gwt.utgb.client.ui.Border
 
Border(int, int, int, String, float) - Constructor for class org.utgenome.gwt.utgb.client.ui.Border
 
border(Widget, int, String, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
border(Widget, int, int, String, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
BORDER_DASHED - Static variable in class org.utgenome.gwt.widget.client.Style
 
BORDER_FULL - Static variable in class org.utgenome.gwt.utgb.client.ui.RoundCornerFrame
 
BORDER_FULL - Static variable in class org.utgenome.gwt.widget.client.FrameBorder
 
BORDER_INSET - Static variable in class org.utgenome.gwt.widget.client.Style
 
BORDER_OUTSET - Static variable in class org.utgenome.gwt.widget.client.Style
 
BORDER_SOLID - Static variable in class org.utgenome.gwt.widget.client.Style
 
borderCollapse(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
BOTTOM - Static variable in class org.utgenome.gwt.widget.client.Style
 
broadcastChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Broadcast the property change to all of the tracks in this track group.
broadCastScrollTrackWindow(double) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
broadCastWindowSizeChange(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
BrowserInfo - Class in org.utgenome.gwt.utgb.client.util
URL query string reader.
BrowserInfo() - Constructor for class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
BrowserInfo.Agent - Enum in org.utgenome.gwt.utgb.client.util
 
BrowserService - Interface in org.utgenome.gwt.utgb.client
 
BrowserServiceAsync - Interface in org.utgenome.gwt.utgb.client
 
BrowserServiceImpl - Class in org.utgenome.gwt.utgb.server
{"species":{"type":0, "target":"human"}, "genome":{"type":0}, "chromosome":{"type":0}}
BrowserServiceImpl() - Constructor for class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
bssQuery - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView
 
bssQuery - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
BSSRead - Class in org.utgenome.gwt.utgb.client.bio
BSS read data object
BSSRead() - Constructor for class org.utgenome.gwt.utgb.client.bio.BSSRead
 
BSSReadView - Class in org.utgenome.gwt.utgb.server.app
BSS Read Viewer
BSSReadView() - Constructor for class org.utgenome.gwt.utgb.server.app.BSSReadView
 
BSSReadView.BSSAlignment - Class in org.utgenome.gwt.utgb.server.app
 
BSSReadView.BSSAlignment() - Constructor for class org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment
 
BUFFER_SIZE - Variable in class org.utgenome.format.fasta.CompactFASTAGenerator
 
build(Reader) - Method in class org.utgenome.format.silk.read.ReadDBBuilder
 
build(URL) - Method in class org.utgenome.format.silk.read.ReadDBBuilder
 
buildGUI() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
buildGUI() - Method in class org.utgenome.shell.UTGBPortableWidget
 
BUTTON_ADJUST - Static variable in interface org.utgenome.gwt.utgb.client.ui.Frame
 
BUTTON_ADJUSTHEIGHT - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 
BUTTON_ALL - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 
BUTTON_CLOSE - Static variable in interface org.utgenome.gwt.utgb.client.ui.Frame
 
BUTTON_CLOSE - Static variable in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
BUTTON_CLOSE - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 
BUTTON_CONFIG - Static variable in interface org.utgenome.gwt.utgb.client.ui.Frame
 
BUTTON_CONFIG - Static variable in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
BUTTON_CONFIG - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 
BUTTON_MINIMIZE - Static variable in interface org.utgenome.gwt.utgb.client.ui.Frame
 
BUTTON_MINIMIZE - Static variable in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
BUTTON_MINIMIZE - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 
BUTTON_PACK - Static variable in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
BUTTON_RELOAD - Static variable in class org.utgenome.gwt.widget.client.TrackFrame
 

C

calcGenomePosition(int, int) - Method in class org.utgenome.graphics.GenomeWindow
 
calcLighterValue(int) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
calcXPositionOnWindow(long, long, long, int) - Static method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
call() - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
cancel() - Method in class org.utgenome.gwt.utgb.client.ui.Animation
Immediately cancel this animation.
CanonicalProperties - Class in org.utgenome.gwt.utgb.client.util
Using canonical parameter keys for providing case and space insensitive property map.
CanonicalProperties() - Constructor for class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
canvas - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
canvas - Variable in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
caption - Variable in class org.utgenome.gwt.utgb.client.track.operation.MenuOperationItem
 
category - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.FeatureType
 
CDS - Class in org.utgenome.gwt.utgb.client.bio
Coding Sequence (CDS)
CDS() - Constructor for class org.utgenome.gwt.utgb.client.bio.CDS
 
CDS(int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.CDS
 
cdsRange() - Method in class org.utgenome.gwt.utgb.client.bio.BEDGene
 
center() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
changedKeySet() - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChange
Get the key set of the changed property keys
changedTouches() - Method in class org.utgenome.gwt.ipad.event.TouchEvent
 
charAt(int) - Method in class org.utgenome.format.fasta.CompactACGT
 
charAt(int) - Method in class org.utgenome.format.fasta.FASTA.RawStringWrapper
 
charAt(int) - Method in interface org.utgenome.format.fasta.GenomeSequence
 
charAt(int) - Method in class org.utgenome.format.fasta.Kmer
 
chr - Variable in class org.utgenome.format.keyword.GenomeKeywordEntry
 
chr - Variable in class org.utgenome.gwt.ribbon.client.model.GenomeCoordinate
chromosome/contig/scaffold name.
chr - Variable in class org.utgenome.gwt.utgb.client.bio.BEDGene
 
chr - Variable in class org.utgenome.gwt.utgb.client.bio.ChrInterval
 
chr - Variable in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
chr - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
chr - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.Coordinate
name of chromosome, contig, scaffold, etc.
chr - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
chr - Variable in class org.utgenome.gwt.utgb.server.app.ReadView
 
chr - Variable in class org.utgenome.util.sv.GeneticVariation
 
ChrInterval - Class in org.utgenome.gwt.utgb.client.bio
Interval in a chromosome
ChrInterval() - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrInterval
 
ChrInterval(String, Interval) - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrInterval
 
ChrInterval(String, int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrInterval
 
ChrLoc - Class in org.utgenome.gwt.utgb.client.bio
 
ChrLoc() - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
ChrLoc(String, int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
chrNameWidth - Variable in class org.utgenome.gwt.utgb.client.bio.ChrRange
 
ChromosomeMap - Class in org.utgenome.gwt.utgb.server.app
draw chromosome map
ChromosomeMap() - Constructor for class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
ChromosomeMap.Comparator4ChrName - Class in org.utgenome.gwt.utgb.server.app
 
ChromosomeMap.Comparator4ChrName() - Constructor for class org.utgenome.gwt.utgb.server.app.ChromosomeMap.Comparator4ChrName
 
ChromosomeMap.CytoBandComprator - Class in org.utgenome.gwt.utgb.server.app
 
ChromosomeMap.CytoBandComprator() - Constructor for class org.utgenome.gwt.utgb.server.app.ChromosomeMap.CytoBandComprator
 
ChromosomeMap.ReadLocus - Class in org.utgenome.gwt.utgb.server.app
 
ChromosomeMap.ReadLocus() - Constructor for class org.utgenome.gwt.utgb.server.app.ChromosomeMap.ReadLocus
 
ChromosomeMapCanvas - Class in org.utgenome.graphics
drawing chromosome map
ChromosomeMapCanvas(int, int, HashMap<String, ChromosomeWindow>) - Constructor for class org.utgenome.graphics.ChromosomeMapCanvas
 
ChromosomeMapTrack - Class in org.utgenome.gwt.utgb.client.track.lib
ChromosomeMapTrack is for visualizing Chromosome Map.
ChromosomeMapTrack(String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
ChromosomeMapTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
ChromosomeWindow - Class in org.utgenome.graphics
 
ChromosomeWindow(long, long, int) - Constructor for class org.utgenome.graphics.ChromosomeWindow
 
ChromosomeWindow(long, long) - Constructor for class org.utgenome.graphics.ChromosomeWindow
 
ChrRange - Class in org.utgenome.gwt.utgb.client.bio
 
ChrRange() - Constructor for class org.utgenome.gwt.utgb.client.bio.ChrRange
 
chrRange - Variable in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
chrSeq - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
cigar - Variable in class org.utgenome.gwt.utgb.client.bio.BlastResult
 
CIGAR - Class in org.utgenome.gwt.utgb.client.bio
CIGAR string (in SAM format) management utility
CIGAR() - Constructor for class org.utgenome.gwt.utgb.client.bio.CIGAR
Creates an empty CIGAR
CIGAR(String) - Constructor for class org.utgenome.gwt.utgb.client.bio.CIGAR
 
cigar - Variable in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
CIGAR.Element - Class in org.utgenome.gwt.utgb.client.bio
 
CIGAR.Element() - Constructor for class org.utgenome.gwt.utgb.client.bio.CIGAR.Element
 
CIGAR.Element(CIGAR.Type, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.CIGAR.Element
 
CIGAR.Type - Enum in org.utgenome.gwt.utgb.client.bio
 
class_ - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.Track
Java class name of this track.
class_ - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.TrackGroup
Java class name of this track group.
className - Variable in class org.utgenome.config.OldViewXML.Track
 
className - Variable in class org.utgenome.config.OldViewXML.TrackGroup
 
Clean - Class in org.utgenome.shell
UTGB Shell Sub Command for cleaning target directory
Clean() - Constructor for class org.utgenome.shell.Clean
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.BarGraphCanvas
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.GraphScale
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
clear() - Method in class org.utgenome.gwt.utgb.client.canvas.TrackWindowChain
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.Track.TrackFactory
 
clear() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
clear() - Method in class org.utgenome.gwt.utgb.client.ui.AbsoluteFocusPanel
 
clear() - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
 
clear() - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
clear() - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
 
clearCanvas() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
clearKeyword() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
clearOutSideOf(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
clearScale() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
clearScaleBar() - Method in class org.utgenome.gwt.utgb.client.canvas.GraphScale
 
clearScaleLabel() - Method in class org.utgenome.gwt.utgb.client.canvas.GraphScale
 
clearStatus() - Method in class org.utgenome.shell.UTGBPortableWidget
 
clearValues() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
clearWidgets() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
clippedRegionAlpha - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
clippedRegionAlpha - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
close() - Method in class org.utgenome.format.bed.BED2Silk
 
close() - Method in class org.utgenome.format.fasta.CompactACGTWriter
 
close() - Method in class org.utgenome.format.fasta.CompactFASTA
 
close() - Method in class org.utgenome.format.fasta.CompactFASTA.OnDiskAccess
 
close() - Method in class org.utgenome.format.fasta.CompactFASTA.OnMemoryBuffer
 
close() - Method in interface org.utgenome.format.fasta.CompactFASTA.PacFileAccess
 
close() - Method in class org.utgenome.format.fasta.FASTAPullParser
 
close() - Method in class org.utgenome.format.fastq.FastqReader
 
close() - Method in class org.utgenome.format.FormatConversionReader
 
close() - Method in class org.utgenome.format.keyword.KeywordDB
 
close() - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
close() - Method in class org.utgenome.format.sam.Sam2WigConverter.SAMRecordCursor
 
close() - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
CLOSE - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
close() - Method in class org.utgenome.util.ReaderInputStream
Closes the Stringreader.
close() - Method in class org.utgenome.util.StandardInputStream
 
close() - Method in class org.utgenome.util.StandardOutputStream
 
CodonTable - Class in org.utgenome.gwt.utgb.client.bio
Codon table
CodonTable() - Constructor for class org.utgenome.gwt.utgb.client.bio.CodonTable
 
color - Variable in class org.utgenome.format.bed.BEDTrack
 
color - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
color - Variable in class org.utgenome.gwt.utgb.server.app.FontPanel
 
color - Variable in class org.utgenome.gwt.utgb.server.app.RoundCircle
 
color - Variable in class org.utgenome.gwt.utgb.server.app.Transparent
 
COLOR_BLACK - Static variable in class org.utgenome.gwt.widget.client.Style
 
COLOR_FORWARD_STRAND - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_GAP - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_GRAY - Static variable in class org.utgenome.gwt.widget.client.Style
 
COLOR_ORPHAN_READ_F - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_ORPHAN_READ_R - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_PADDING - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_READ_DEFAULT - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_RED - Static variable in class org.utgenome.gwt.widget.client.Style
 
COLOR_REVERSE_STRAND - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_SHADOW - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_SKYBLUE - Static variable in class org.utgenome.gwt.widget.client.Style
 
COLOR_WHITE - Static variable in class org.utgenome.gwt.widget.client.Style
 
COLOR_WIRED_READ_F - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
COLOR_WIRED_READ_R - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
colorA - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorA - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
colorC - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorC - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
colorG - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorG - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
colorLighter(Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
colorMode - Variable in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
colorMode - Variable in class org.utgenome.gwt.utgb.client.track.lib.SAMTrack
 
colorN - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
colorN - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorN - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
colorO - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
coloro - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorOffset(int, float) - Method in class org.utgenome.graphics.GeneCanvas
 
colors - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
colorT - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
colorT - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
ColorType - Class in org.utgenome.gwt.utgb.client.track.lib.old.datatype
 
ColorType(String, String[], String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ColorType
 
ColorUtil - Class in org.utgenome.gwt.utgb.client.canvas
Color code generator
ColorUtil() - Constructor for class org.utgenome.gwt.utgb.client.canvas.ColorUtil
 
com.google.gwt.user.client.impl - package com.google.gwt.user.client.impl
 
commands - Variable in class org.utgenome.gwt.utgb.client.track.operation.FrameOperation
 
commit() - Method in class org.utgenome.format.silk.read.ReadDBBuilder
 
CompactACGT - Class in org.utgenome.format.fasta
Compact array for ACGT (and N) sequences
CompactACGTWriter - Class in org.utgenome.format.fasta
ACGT sequence compressor
CompactACGTWriter(OutputStream, OutputStream) - Constructor for class org.utgenome.format.fasta.CompactACGTWriter
 
CompactFASTA - Class in org.utgenome.format.fasta
CompactFASTA is a packed FASTA file, supporting random accesses to sub sequences of a specified chromosome.
CompactFASTA(String) - Constructor for class org.utgenome.format.fasta.CompactFASTA
 
CompactFASTA.OnDiskAccess - Class in org.utgenome.format.fasta
 
CompactFASTA.OnDiskAccess(File, File) - Constructor for class org.utgenome.format.fasta.CompactFASTA.OnDiskAccess
 
CompactFASTA.OnMemoryBuffer - Class in org.utgenome.format.fasta
 
CompactFASTA.OnMemoryBuffer(File, File) - Constructor for class org.utgenome.format.fasta.CompactFASTA.OnMemoryBuffer
 
CompactFASTA.PacFileAccess - Interface in org.utgenome.format.fasta
 
CompactFASTAGenerator - Class in org.utgenome.format.fasta
 
CompactFASTAGenerator() - Constructor for class org.utgenome.format.fasta.CompactFASTAGenerator
 
CompactFASTAIndex - Class in org.utgenome.format.fasta
A sequence index to packed FASTA files
CompactFASTAIndex() - Constructor for class org.utgenome.format.fasta.CompactFASTAIndex
 
CompactWIGData - Class in org.utgenome.gwt.utgb.client.bio
 
CompactWIGData() - Constructor for class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
compare(TrackEntry, TrackEntry) - Method in class org.utgenome.gwt.utgb.client.track.TrackComparator
 
compare(String, String) - Method in class org.utgenome.gwt.utgb.server.app.ChromosomeMap.Comparator4ChrName
 
compare(CytoBand, CytoBand) - Method in class org.utgenome.gwt.utgb.server.app.ChromosomeMap.CytoBandComprator
 
compareChrName(String, String) - Static method in class org.utgenome.gwt.utgb.server.app.ChromosomeMap.Comparator4ChrName
 
compareTo(Interval) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
compareTo(TrackBean) - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
compareTo(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
compareTo(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
compareTo(Command) - Method in class org.utgenome.shell.UTGBShellCommand
 
compareTo(RepeatChainFinder.Interval2D) - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
compareTo(RepeatChainFinder.IntervalCluster) - Method in class org.utgenome.util.repeat.RepeatChainFinder.IntervalCluster
 
Compile - Class in org.utgenome.shell
A UTGBShell sub command for compiling java source codes with Maven
Compile() - Constructor for class org.utgenome.shell.Compile
 
complement() - Method in enum org.utgenome.gwt.utgb.client.bio.IUPAC
 
component - Variable in class org.utgenome.util.repeat.RepeatChainFinder.IntervalCluster
 
compute(String, Iterator<GenomeRange>, ReadDepth.DepthOutput) - Static method in class org.utgenome.util.ReadDepth
Compute the read depth of the input read set.
computeCoverage(List<GenomeRange>, int, int, int) - Static method in class org.utgenome.gwt.utgb.server.app.ReadView
 
computeDepth(String, Iterator<GenomeRange>) - Method in class org.utgenome.util.ReadDepth
 
computeTrackWidth() - Static method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
config - Variable in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
CONFIG_COVERAGE_STYLE - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_DRAW_SHADOW - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_FILENAME - Variable in class org.utgenome.gwt.utgb.client.track.lib.BEDTrack
Deprecated.  
CONFIG_GRAPH_WINDOW - Static variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
CONFIG_HIDE_MATCHED_BASE - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_LAYOUT - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_MIN_READ_HEIGHT - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_NUM_READ_MAX - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_PE_OVERLAP - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_READ_HEIGHT - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_READ_MARGIN - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_REVERSE_READ_HISTOGRAM - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_REVERSE_READ_TRACK - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_SHOW_BASE_QUALITY - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_SHOW_LABELS - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_SHOW_STRAND - Static variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
CONFIG_TRACK_BASE_URL - Static variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
CONFIG_TRACK_HEIGHT - Static variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
CONFIG_TRACK_TYPE - Static variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
ConfigInputForm - Class in org.utgenome.gwt.utgb.client.track.lib.old.datatype
 
ConfigInputForm() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ConfigInputForm
 
connect(T, String, U) - Method in class org.utgenome.format.ObjectStreamReader.TextReader
 
ConnectionInfo - Class in org.utgenome.config
The connection tag in track-config.xml
ConnectionInfo() - Constructor for class org.utgenome.config.ConnectionInfo
 
consume(Reader, Writer) - Method in class org.utgenome.format.blast.Blast2Silk.Blast2SilkConverter
 
consume(Reader, Writer) - Method in class org.utgenome.format.FormatConversionReader.PipeConsumer
Read the data from in, then output the data to out
consume(InputStream, Writer) - Method in class org.utgenome.format.FormatConversionReader.PipeConsumer
 
contains(int) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
contains(Interval) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
contains(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
contains(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
contains(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChange
Test whether the property of the given key has been changed
contains(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
containsChr(String) - Method in class org.utgenome.format.fasta.CompactFASTA
Test the specified chromosome name is in this FASTA
containsOneOf(String[]) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
containsOneOf(String[]) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
containsOneOf(String[]) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChange
Test at least one of properties among the given key set has changed
containsOneOf(Iterable<String>) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChange
 
Content - Class in org.utgenome.gwt.utgb.client.bean.track
Content descriptor in the track
Content() - Constructor for class org.utgenome.gwt.utgb.client.bean.track.Content
 
contextDestroyed(ServletContextEvent) - Method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
contextInitialized(ServletContextEvent) - Method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
convert() - Method in class org.utgenome.config.TrackConfiguration
 
Convert - Class in org.utgenome.core.cui
 
Convert() - Constructor for class org.utgenome.core.cui.Convert
 
convert(ObjectStreamHandler) - Method in class org.utgenome.format.axt.AXTLens
 
convert() - Method in class org.utgenome.format.fastq.FastqToBAM
 
convert(Reader, Reader) - Method in class org.utgenome.format.fastq.FastqToBAM
 
convert(BufferedReader, Writer) - Method in class org.utgenome.format.illumina.QSeqToFASTQ
 
convert(BufferedReader, Writer) - Static method in class org.utgenome.format.illumina.Seq2Fastq
 
convert(File, Writer) - Method in class org.utgenome.format.sam.Sam2WigConverter
Convert the input SAM file records into WIG format of read depth
convert(File, String, int, int) - Method in class org.utgenome.format.sam.Sam2WigConverter
 
convert(char) - Static method in enum org.utgenome.gwt.utgb.client.bio.CIGAR.Type
 
convert(Exception) - Static method in exception org.utgenome.UTGBException
 
convertResolution(WigGraphData, ChrLoc, int) - Static method in class org.utgenome.format.wig.WIGDatabaseReader
 
convertToFastq(String) - Method in class org.utgenome.format.illumina.QSeqToFASTQ
 
convertToFastq(String) - Static method in class org.utgenome.format.illumina.Seq2Fastq
 
convertToGenomePosition(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
convertToPixelLength(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
convertToPixelX(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
calculate the X position (pixel address) in a track window of a given index on genome.
convertToPixelXDouble(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
convertToSAMRead(SAMRecord) - Static method in class org.utgenome.format.sam.SAM2SilkReader
convert a SAMRecord into a SAMRead, which can be used in GWT code.
convertToSAMReadLight(SAMRecord) - Static method in class org.utgenome.format.sam.SAM2SilkReader
convert a SAMRecord into a SAMRead, which can be used in GWT code.
convertTrackGroupPropertyToXML(TrackGroupProperty) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
convertTrackGroupPropertyToXML(TrackGroupProperty, Set<String>) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
Coordinate - Class in org.utgenome.format.silk.read
Coordinate
Coordinate() - Constructor for class org.utgenome.format.silk.read.Coordinate
 
Coordinate - Class in org.utgenome.gwt.utgb.client.bio
Coordinate system
Coordinate() - Constructor for class org.utgenome.gwt.utgb.client.bio.Coordinate
 
Coordinate(String, String, String, String) - Constructor for class org.utgenome.gwt.utgb.client.bio.Coordinate
 
coordinate - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.TrackGroup
 
coordinateParameters - Static variable in interface org.utgenome.gwt.utgb.client.track.UTGBProperty
 
copyFile(InputStream, File) - Static method in class org.utgenome.shell.ScaffoldGenerator
 
copyScaffold(String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
Creates the folder structure for the Tomcat
correctInterval() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
count - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult
 
countNucleotides(String) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
countOverlap(int) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
countOverlap(int, int) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
coverage - Variable in class org.utgenome.gwt.utgb.client.bio.ReadCoverage
Coverage of each pixel position
coverageStyle - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
Create - Class in org.utgenome.shell
Create sub command
Create() - Constructor for class org.utgenome.shell.Create
 
Create.CreateAllScaffoldFileFilter - Class in org.utgenome.shell
 
Create.CreateAllScaffoldFileFilter() - Constructor for class org.utgenome.shell.Create.CreateAllScaffoldFileFilter
 
Create.OverwriteMode - Enum in org.utgenome.shell
 
Create.ScaffoldFileFilter - Interface in org.utgenome.shell
 
createClusters(DisjointSet<RepeatChainFinder.Interval2D>) - Method in class org.utgenome.util.repeat.RepeatChainFinder
 
createContextXML(String, String, boolean) - Method in class org.utgenome.shell.UTGBShellCommand
 
createDB(Reader, Connection) - Method in class org.utgenome.format.cseg.CSEGDatabase
 
createDB(Reader, SQLiteAccess) - Method in class org.utgenome.format.fasta.FASTADatabase
 
createDB(FASTAPullParser, SQLiteAccess) - Method in class org.utgenome.format.fasta.FASTADatabase
 
createEclipseLaunchFile(String, String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createFileFromTemplate(Class<?>, String, String, Properties) - Method in class org.utgenome.shell.UTGBShellCommand
 
createFileFromTemplate(Class<?>, String, String, String, Properties, boolean) - Static method in class org.utgenome.shell.UTGBShellCommand
 
createFromResultSet(String, ResultSet) - Static method in class org.utgenome.format.bed.BEDEntry
 
createFromString(String) - Static method in class org.utgenome.format.fasta.CompactACGT
 
createGWTModuleScaffold(UTGBConfig) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createInstance() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry.TabEntryFactory
 
createLocalLayout(int) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
Creates an X-Y layout of the given intervals, then return the max depth of the intervals
createNewValueDomain(String[]) - Static method in class org.utgenome.gwt.utgb.client.db.ValueDomain
 
createProjectScaffold(UTGBConfig) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createReadAlignmentImage(ChrLoc, String) - Method in class org.utgenome.core.cui.ScreenShot
 
createScaffold(UTGBConfig, String, Create.ScaffoldFileFilter) - Static method in class org.utgenome.shell.Create
 
createSQL(String, Object...) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Create an SQL from a given template and variable assignments.
createSQLFromFile(String, Object...) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Create an SQL from a given file (relative to the caller class) and variable assignments.
createSQLStatement(String, Object...) - Static method in class org.utgenome.gwt.utgb.server.WebTrackBase
 
createTempDir() - Static method in class org.utgenome.util.TestHelper
 
createTempFileFrom(Class<T>, String) - Static method in class org.utgenome.util.TestHelper
Create a temporary file
createTempFileFrom(Class<T>, String, File) - Static method in class org.utgenome.util.TestHelper
 
createTitledBorder(String) - Static method in class org.utgenome.shell.UTGBPortableWidget
 
createTrackGroup(TrackView) - Static method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Create a track group from a given TrackView
createTrackView(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
createTrackView(String, AsyncCallback<TrackView>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
createTrackView(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
createWindow() - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
CSEGDatabase - Class in org.utgenome.format.cseg
 
CSEGDatabase() - Constructor for class org.utgenome.format.cseg.CSEGDatabase
 
CSEGDatabase.Config - Class in org.utgenome.format.cseg
 
CSEGDatabase.Config() - Constructor for class org.utgenome.format.cseg.CSEGDatabase.Config
 
CSEGTrack - Class in org.utgenome.gwt.utgb.client.track.lib
Track for displaying read data in SEG format.
CSEGTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.CSEGTrack
 
CSEGViewer - Class in org.utgenome.gwt.utgb.server.app
 
CSEGViewer() - Constructor for class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
CSEGViewer.GraphicalOutput - Class in org.utgenome.gwt.utgb.server.app
 
CSEGViewer.GraphicalOutput(HttpServletResponse, long, long, int, int) - Constructor for class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
CSEGViewer.SEGData - Class in org.utgenome.gwt.utgb.server.app
A holder for retrieving compressed genome sequence
CSEGViewer.SEGData() - Constructor for class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
CSEGViewer.SEGData(String, int, int, String, String) - Constructor for class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
CSS_BACKGROUND_COLOR - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_BACKGROUND_IMAGE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_BACKGROUND_POSITION - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_BACKGROUND_REPEAT - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_BORDER - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_BORDER_COLLAPSE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_CURSOR - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_DISPLAY - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_FONT_COLOR - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_FONT_FAMILY - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_FONT_SIZE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_FONT_WEIGHT - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_MARGIN - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_NOWRAP - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_OVERFLOW_X - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_OVERFLOW_Y - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_PADDING - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_VERTICAL_ALIGN - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_WHITESPACE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CSS_Z_INDEX - Static variable in class org.utgenome.gwt.widget.client.Style
 
CUBIC - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
currentDescriptionURLInfo - Variable in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
cursor(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
CURSOR_AUTO - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_CROSSHAIR - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_HELP - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_MOVE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_POINTER - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_RESIZE_E - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_RESIZE_N - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_RESIZE_SE - Static variable in class org.utgenome.gwt.widget.client.Style
 
CURSOR_TEXT - Static variable in class org.utgenome.gwt.widget.client.Style
 
CytoBand - Class in org.utgenome.gwt.utgb.client.bio
CytoBand
CytoBand() - Constructor for class org.utgenome.gwt.utgb.client.bio.CytoBand
 
CytoBand(String, int, int, String, String) - Constructor for class org.utgenome.gwt.utgb.client.bio.CytoBand
 

D

d_chr - Variable in class org.utgenome.format.axt.AXTAlignment
 
d_end - Variable in class org.utgenome.format.axt.AXTAlignment
 
d_start - Variable in class org.utgenome.format.axt.AXTAlignment
 
dasBaseURL - Variable in class org.utgenome.gwt.utgb.server.app.DASViewer
 
DASDsn - Class in org.utgenome.gwt.utgb.server.app
Read DAS DSN
DASDsn() - Constructor for class org.utgenome.gwt.utgb.server.app.DASDsn
 
DASDsn.DSN - Class in org.utgenome.gwt.utgb.server.app
 
DASDsn.DSN() - Constructor for class org.utgenome.gwt.utgb.server.app.DASDsn.DSN
 
DASDsn.DSNQuery - Class in org.utgenome.gwt.utgb.server.app
 
DASDsn.DSNQuery() - Constructor for class org.utgenome.gwt.utgb.server.app.DASDsn.DSNQuery
 
DASDsn.DSNSource - Class in org.utgenome.gwt.utgb.server.app
 
DASDsn.DSNSource() - Constructor for class org.utgenome.gwt.utgb.server.app.DASDsn.DSNSource
 
DASLocation - Class in org.utgenome.gwt.utgb.client.bio
DAS information
DASLocation() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASLocation
 
DASLocation(GenomeDB, String) - Constructor for class org.utgenome.gwt.utgb.client.bio.DASLocation
 
DASResult - Class in org.utgenome.gwt.utgb.client.bio
DAS Result
DASResult() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult
 
DASResult.DASFeature - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature
 
DASResult.DASFeature.FeatureType - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature.FeatureType() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.FeatureType
 
DASResult.DASFeature.Group - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature.Group() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group
 
DASResult.DASFeature.Group.Link - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature.Group.Link() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group.Link
 
DASResult.DASFeature.Method - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature.Method() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Method
 
DASResult.DASFeature.Target - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASFeature.Target() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Target
 
DASResult.DASGFF - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.DASGFF() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.DASGFF
 
DASResult.Segment - Class in org.utgenome.gwt.utgb.client.bio
 
DASResult.Segment() - Constructor for class org.utgenome.gwt.utgb.client.bio.DASResult.Segment
 
DASTrack - Class in org.utgenome.gwt.utgb.client.track.lib
DASTrack is for visualizing data that can be located on das data.
DASTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.DASTrack
 
dasType - Variable in class org.utgenome.gwt.utgb.client.bio.DASLocation
 
dasType - Variable in class org.utgenome.gwt.utgb.server.app.DASViewer
 
DASViewer - Class in org.utgenome.gwt.utgb.server.app
Request handler
DASViewer() - Constructor for class org.utgenome.gwt.utgb.server.app.DASViewer
 
data - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
DATA_SPLIT_UNIT - Static variable in class org.utgenome.format.wig.WIGDatabaseGenerator
 
database - Variable in class org.utgenome.config.UTGBConfig
 
DatabaseCatalog - Class in org.utgenome.gwt.utgb.client.db
read a JSON description of database catalog, a list of database relations.
DatabaseCatalog(String) - Constructor for class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
 
DatabaseCatalog() - Constructor for class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
 
DatabaseEntry - Class in org.utgenome.gwt.utgb.client.bean
 
DatabaseEntry() - Constructor for class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
DatabaseInfo - Class in org.utgenome.config
Database tag in track-config.xml
DatabaseInfo() - Constructor for class org.utgenome.config.DatabaseInfo
 
databaseName - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult
 
DatabaseTable - Class in org.utgenome.gwt.utgb.client.db
A DatabaseTable makes easier to display table data, the schema of which is given by a Relation object, and its raw data are described with the JSON format.
DatabaseTable() - Constructor for class org.utgenome.gwt.utgb.client.db.DatabaseTable
 
DatabaseTable(Relation) - Constructor for class org.utgenome.gwt.utgb.client.db.DatabaseTable
 
DataType - Interface in org.utgenome.gwt.utgb.client.db.datatype
A common interface for data types of configuration parameters, database contents etc.
DataTypeBase - Class in org.utgenome.gwt.utgb.client.db.datatype
 
DataTypeBase(String) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
DataTypeBase(String, boolean) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
DataTypeBase(String, boolean, boolean) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
db - Variable in class org.utgenome.format.bed.BEDTrack
 
db - Variable in class org.utgenome.gwt.utgb.client.view.TrackDisplay.Track
 
db - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer
 
DB_GROUP - Static variable in interface org.utgenome.gwt.utgb.client.track.UTGBProperty
 
DB_NAME - Static variable in interface org.utgenome.gwt.utgb.client.track.UTGBProperty
 
dbGroup - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView
 
dbGroup - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
dbGroup - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
dbms - Variable in class org.utgenome.config.UTGBConfig.Database
 
dbName - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView
 
dbName - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
dbPath(String) - Method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
Path to the specified database file in this database folder
DBSelectTrack - Class in org.utgenome.gwt.utgb.client.track.lib
 
DBSelectTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.DBSelectTrack
 
DebugToolBoxTrack - Class in org.utgenome.gwt.utgb.client.track.lib.debug
A tool box for debug purpose tracks
DebugToolBoxTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.debug.DebugToolBoxTrack
 
decode(byte) - Static method in enum org.utgenome.gwt.utgb.client.bio.IUPAC
 
DEFAULT_HEIGHT - Static variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
DEFAULT_HEIGHT - Static variable in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
DEFAULT_HEIGHT_PER_SAMPLE - Static variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
DEFAULT_KEY_COLUMN_NAME - Static variable in class org.utgenome.gwt.utgb.client.util.TableData
 
DEFAULT_MIN_TRACKFRAME_HEIGHT - Static variable in class org.utgenome.gwt.utgb.client.track.TrackFrameState
 
DefaultRequestMap - Class in org.utgenome.gwt.utgb.server
DefaultRequestMap provides a search function to find a request handler that matches the given web request.
DefaultRequestMap() - Constructor for class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
defaultSetUp() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrackGroup
 
defaultStyle() - Static method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
delete(int, int) - Method in class org.utgenome.format.fasta.Kmer
 
Deploy - Class in org.utgenome.shell
 
Deploy() - Constructor for class org.utgenome.shell.Deploy
 
depthCoverage(ChrLoc, int, List<SAMRecord>, CloseableIterator<SAMRecord>) - Static method in class org.utgenome.format.sam.SAMReader
 
depthCoverage(File, ChrLoc, int, ReadQueryConfig) - Static method in class org.utgenome.format.sam.SAMReader
 
depthCoverageInWIG(File, ChrLoc, int, ReadQueryConfig) - Static method in class org.utgenome.format.sam.SAMReader
 
depthFirstSearch(PrioritySearchTree.Visitor<IntervalLayout.LocusLayout>) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
depthFirstSearch(PrioritySearchTree.Visitor<E>) - Method in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree
 
Description - Static variable in class org.utgenome.format.bed.BEDLexer
 
Description - Static variable in class org.utgenome.format.bed.BEDParser
 
description() - Method in class org.utgenome.format.bed.BEDParser
 
description - Variable in class org.utgenome.format.bed.BEDTrack
 
description - Variable in class org.utgenome.format.fasta.CompactFASTAIndex
Full description written in FASTA file ( > chr1 ...
Description - Static variable in class org.utgenome.format.wig.WIGLexer
 
Description - Static variable in class org.utgenome.format.wig.WIGParser
 
description() - Method in class org.utgenome.format.wig.WIGParser
 
description - Variable in class org.utgenome.gwt.utgb.server.app.DASDsn.DSN
 
description - Variable in enum org.utgenome.util.sv.EnhancedGeneticVariation.MutationPosition
 
description - Variable in enum org.utgenome.util.sv.EnhancedGeneticVariation.MutationType
 
descriptionName() - Method in class org.utgenome.format.bed.BEDParser
 
descriptionName() - Method in class org.utgenome.format.wig.WIGParser
 
descriptionURLList - Variable in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
Design - Class in org.utgenome.gwt.utgb.client.track
Design class gathers image file names
destroy() - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
detectFileType(String) - Static method in class org.utgenome.shell.Import
 
dfa12 - Variable in class org.utgenome.format.bed.BEDLexer
 
dfa12 - Variable in class org.utgenome.format.wig.WIGLexer
 
dfa14 - Variable in class org.utgenome.format.bed.BEDLexer
 
dfa14 - Variable in class org.utgenome.format.wig.WIGLexer
 
Digit - Static variable in class org.utgenome.format.bed.BEDLexer
 
Digit - Static variable in class org.utgenome.format.bed.BEDParser
 
Digit - Static variable in class org.utgenome.format.wig.WIGLexer
 
Digit - Static variable in class org.utgenome.format.wig.WIGParser
 
disableClose() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
disableConfig() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
disabledIcon() - Method in interface org.utgenome.gwt.widget.client.UTGBImageBundle
 
disableEdit(int) - Method in class org.utgenome.gwt.utgb.client.ui.EditableTable
 
disableHide() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
disablePack() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
disableResize() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
disableScroll(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
DisjointSet<E> - Class in org.utgenome.util.repeat
Union-Find disjoint set implementation
DisjointSet() - Constructor for class org.utgenome.util.repeat.DisjointSet
 
disjointSetOf(E) - Method in class org.utgenome.util.repeat.DisjointSet
 
dispalyHelp - Variable in class org.utgenome.format.cseg.CSEGDatabase.Config
 
dispalyHelp - Variable in class org.utgenome.format.fasta.FASTADatabase.Config
 
dispatch(TouchCancelHandler) - Method in class org.utgenome.gwt.ipad.event.TouchCancelEvent
Should only be called by HandlerManager.
dispatch(TouchEndHandler) - Method in class org.utgenome.gwt.ipad.event.TouchEndEvent
Should only be called by HandlerManager.
dispatch(TouchMoveHandler) - Method in class org.utgenome.gwt.ipad.event.TouchMoveEvent
Should only be called by HandlerManager.
dispatch(TouchStartHandler) - Method in class org.utgenome.gwt.ipad.event.TouchStartEvent
Should only be called by HandlerManager.
dispatchRequest(RequestURI, HttpServletRequest, HttpServletResponse, FilterChain) - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
DISPLAY_BLOCK - Static variable in class org.utgenome.gwt.widget.client.Style
 
displayInfo(int, int, GenomeRange) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
displayTrackView() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
displayType - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
dispose() - Method in class org.utgenome.format.bed.BEDDatabase.DBBuilder
 
DispType - Class in org.utgenome.gwt.utgb.client.track.lib.old.datatype
 
DispType(String, String[]) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.datatype.DispType
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.HelloServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.RequestHandlerBase
 
DOMUtil - Class in org.utgenome.gwt.utgb.client.util.xml
Utilities to traverse DOM elements
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.RequestHandlerBase
 
Dot - Static variable in class org.utgenome.format.bed.BEDLexer
 
Dot - Static variable in class org.utgenome.format.bed.BEDParser
 
Dot - Static variable in class org.utgenome.format.wig.WIGLexer
 
Dot - Static variable in class org.utgenome.format.wig.WIGParser
 
DotPlot - Class in org.utgenome.gwt.utgb.server.app
Web action: DotPlot
DotPlot() - Constructor for class org.utgenome.gwt.utgb.server.app.DotPlot
 
Double - Static variable in class org.utgenome.format.bed.BEDLexer
 
Double - Static variable in class org.utgenome.format.bed.BEDParser
 
Double - Static variable in class org.utgenome.format.wig.WIGLexer
 
Double - Static variable in class org.utgenome.format.wig.WIGParser
 
doubleStrandXOR(int) - Method in class org.utgenome.util.kmer.KmerIntegerFactory
Return the XOR value of the double strand reads of a given k-mer sequence.
DoubleType - Class in org.utgenome.gwt.utgb.client.db.datatype
 
DoubleType(String) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.DoubleType
 
DoubleType.DoubleTypeForm - Class in org.utgenome.gwt.utgb.client.db.datatype
 
DoubleType.DoubleTypeForm() - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.DoubleType.DoubleTypeForm
 
downstreamRegion(int) - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
DraggableTable - Class in org.utgenome.gwt.utgb.client.ui
DraggabeleTable supports drag & drop replacement of internal widgets.
DraggableTable() - Constructor for class org.utgenome.gwt.utgb.client.ui.DraggableTable
 
DragListener - Class in org.utgenome.gwt.widget.client
Mouse drag listener support
DragListener(PopupPanel) - Constructor for class org.utgenome.gwt.widget.client.DragListener
 
draw(List<E>) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
draw(List<E>) - Method in class org.utgenome.graphics.GeneCanvas
 
draw(GenomeRange, int) - Method in class org.utgenome.graphics.GeneCanvas
 
draw(Gene, List<Exon>, CDS, int) - Method in class org.utgenome.graphics.GeneCanvas
 
draw(Gene, int) - Method in class org.utgenome.graphics.GeneCanvas
 
draw(Gene, Exon, CDS, int) - Method in class org.utgenome.graphics.GeneCanvas
 
draw(List<GenomeRange>) - Method in class org.utgenome.graphics.ReadCanvas
 
draw(Read) - Method in class org.utgenome.graphics.RibbonCanvas
 
draw(List<CompactWIGData>, GWTGraphCanvas.GraphStyle) - Method in class org.utgenome.gwt.utgb.client.canvas.BarGraphCanvas
 
draw(GWTGraphCanvas.GraphStyle, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.canvas.GraphScale
 
draw() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
draw(Gene, List<Exon>, CDS, int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
draw(Interval, int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
draw(Gene, int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.BEDTrack
Deprecated.  
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.CSEGTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.debug.PropertyEditTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.debug.URLQueryArgumentTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.KeywordSearchTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.RefSeqTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.ToolBoxTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
draw() - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
draw() - Method in interface org.utgenome.gwt.utgb.client.track.Track
draw the track widget
draw() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
drawBase(String, long, long, int, float, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawBase(char, int, int, Color) - Method in class org.utgenome.graphics.ReadCanvas
 
drawBases(int, int, String, String) - Method in class org.utgenome.graphics.ReadCanvas
 
drawBlock(ReadCoverage) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
drawChrName(String, Integer) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawCytoBand(CytoBand, ChromosomeWindow) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawCytoBandName(CytoBand, ChromosomeWindow) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawExon(Gene, Exon, CDS, int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
drawFrame() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
drawGene(Gene, int) - Method in class org.utgenome.graphics.ReadCanvas
 
drawGeneRect(long, long, int, Color) - Method in class org.utgenome.graphics.GeneCanvas
 
drawGeneRect(long, long, int, int, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawGeneRect(int, int, int, Color) - Method in class org.utgenome.graphics.ReadCanvas
 
drawGeneRect(int, int, int, Color, boolean) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
drawGenomeWindow(String, long, long) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
DrawHistogram - Class in org.utgenome.core.cui
 
DrawHistogram() - Constructor for class org.utgenome.core.cui.DrawHistogram
 
drawLabel(GenomeRange, int) - Method in class org.utgenome.graphics.ReadCanvas
 
drawLabelPanel(int, SAMRead, AbsolutePanel, int) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
drawLabelPanel(List<SAMRead>, AbsolutePanel, int) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
drawLine(long, long, long, long, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawLocusLabel(String, long, long, int, float, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawMapping(String[]) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawMapping(String, int, int) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawMapping(String, int, int, char) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawPadding(int, int, int, Color) - Method in class org.utgenome.graphics.ReadCanvas
 
drawPadding(int, int, int, Color, boolean) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
drawRect(int, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawRect(int, int, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawRect(int, int, int, int, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawRegion(GenomeRange, int) - Method in class org.utgenome.graphics.ReadCanvas
 
drawRegion(int, int, int, Color, boolean) - Method in class org.utgenome.graphics.ReadCanvas
 
drawRuler() - Method in class org.utgenome.graphics.ReadCanvas
 
drawSAMCanvas(int, SAMRead) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
drawSAMRead(SAMReadLight, int) - Method in class org.utgenome.graphics.ReadCanvas
 
drawSAMRead(int, SAMRead) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
drawSAMRead(List<SAMRead>) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
drawScale - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
drawScaleLabel() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
drawShadow - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
drawShadow - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
drawTag(long, long) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawTag(long, long, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawText(String, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawText(String, long, long, int, float, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawText(String, long, long, int, int, Color) - Method in class org.utgenome.graphics.GenomeCanvas
 
drawText(String, long, long, int, int, Color) - Method in class org.utgenome.graphics.RibbonCanvas
 
drawTriangle(int, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
drawWidget() - Method in class org.utgenome.gwt.widget.client.HorizontalTrackFrame
 
drawWidget() - Method in class org.utgenome.gwt.widget.client.TrackTitleBar
 
drawWidget() - Method in class org.utgenome.gwt.widget.client.TrackWindowPanel
 
drawWidget() - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
 
drawWigGraph(List<CompactWIGData>, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
drawWigGraph(GWTGraphCanvas.GraphCanvas) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
drawZeroValue - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
driver - Variable in class org.utgenome.config.UTGBConfig.Database
 
DRIVER_NAME - Static variable in class org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess
 
dsn - Variable in class org.utgenome.gwt.utgb.server.app.DASDsn.DSNQuery
 
DynamicForm - Class in org.utgenome.gwt.utgb.client.db
A DynamicForm class creates a data input form organized according to a given reltaion
DynamicForm() - Constructor for class org.utgenome.gwt.utgb.client.db.DynamicForm
 

E

EagyGeneLine - Class in org.utgenome.format.egt
 
EagyGeneLine(String) - Constructor for class org.utgenome.format.egt.EagyGeneLine
 
EAST - Static variable in class org.utgenome.gwt.utgb.client.ui.RoundCornerFrame
 
EAST - Static variable in class org.utgenome.gwt.widget.client.FrameBorder
 
EchoBackView - Class in org.utgenome.gwt.utgb.server.app
Request handler
EchoBackView() - Constructor for class org.utgenome.gwt.utgb.server.app.EchoBackView
 
Eclipse - Class in org.utgenome.shell
A sub command to generate Eclipse project files
Eclipse() - Constructor for class org.utgenome.shell.Eclipse
 
EditableLabel - Class in org.utgenome.gwt.utgb.client.ui
This class is used to implement EditableTable.
EditableLabel(CellReference, String) - Constructor for class org.utgenome.gwt.utgb.client.ui.EditableLabel
 
EditableTable - Class in org.utgenome.gwt.utgb.client.ui
You can insert table data into a EditableTable.
EditableTable(String[]) - Constructor for class org.utgenome.gwt.utgb.client.ui.EditableTable
 
EditableTable(String[], int) - Constructor for class org.utgenome.gwt.utgb.client.ui.EditableTable
 
EGTXMLReader - Class in org.utgenome.format.egt
 
EGTXMLReader(String[]) - Constructor for class org.utgenome.format.egt.EGTXMLReader
 
EGTXMLReader.Opt - Enum in org.utgenome.format.egt
 
elem - Variable in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree.Node
 
element() - Method in class org.utgenome.gwt.utgb.client.bio.CIGAR
 
element(String, XMLAttribute, String) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLWriter
 
element(String, XMLAttribute) - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLWriter
 
elementList() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
return the elements in the tree
empty() - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
 
empty() - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
 
enableClose(int, boolean) - Method in class org.utgenome.gwt.widget.client.TabbedTrackFrame
 
enableCloseButton(boolean) - Method in class org.utgenome.gwt.widget.client.Tab
 
enableConfig() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
enableInsertionOfNewRow() - Method in class org.utgenome.gwt.utgb.client.ui.EditableTable
 
enableResize() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
enableResizeHeight(boolean) - Method in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
enableResizeHeight(boolean) - Method in class org.utgenome.gwt.widget.client.TrackFrame
Enable resize of the track height
enableResizeWidth(boolean) - Method in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
enableResizeWidth(boolean) - Method in class org.utgenome.gwt.widget.client.TrackFrame
Enable resize of the track width
encode(char) - Static method in enum org.utgenome.gwt.utgb.client.bio.IUPAC
 
end - Variable in class org.utgenome.config.OldViewXML.TrackWindow
 
end - Variable in class org.utgenome.format.gff3.GFF3Entry
 
end - Variable in class org.utgenome.format.keyword.GenomeKeywordEntry
 
end - Variable in class org.utgenome.format.silk.read.Read
 
end - Variable in class org.utgenome.gwt.ribbon.client.model.Ribbon.RibbonSegment
end position on the reference genome
end - Variable in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
end - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
end - Variable in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
end - Variable in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
end() - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLWriter
 
end - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.Coordinate
1-based end position (inclusive)
end - Variable in class org.utgenome.gwt.utgb.server.app.BEDViewer
 
end - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
end - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
end - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
end - Variable in class org.utgenome.gwt.utgb.server.app.DASViewer
 
end - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer
 
end - Variable in class org.utgenome.gwt.utgb.server.app.ReadView
 
end - Variable in class org.utgenome.gwt.utgb.server.app.SAMViewer
 
end - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
END - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
endDocument() - Method in class org.utgenome.gwt.utgb.client.util.xml.XMLWriter
 
endIndexOnGenome - Variable in class org.utgenome.graphics.GenomeWindow
 
endOffset - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
endOffset - Variable in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
endPoint() - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
endX - Variable in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
endY - Variable in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
EnhancedGeneticVariation - Class in org.utgenome.util.sv
 
EnhancedGeneticVariation(GeneticVariation) - Constructor for class org.utgenome.util.sv.EnhancedGeneticVariation
 
EnhancedGeneticVariation.MutationPosition - Enum in org.utgenome.util.sv
 
EnhancedGeneticVariation.MutationType - Enum in org.utgenome.util.sv
mutation types (e.g., non-coding, missense, synonymous, non-sense, frame-shift, splice-site mutation, etc.)
entries - Variable in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
environment - Variable in class org.utgenome.shell.UTGBShell.UTGBShellOption
 
EOF - Static variable in class org.utgenome.format.bed.BEDLexer
 
EOF - Static variable in class org.utgenome.format.bed.BEDParser
 
EOF - Static variable in class org.utgenome.format.wig.WIGLexer
 
EOF - Static variable in class org.utgenome.format.wig.WIGParser
 
Eq - Static variable in class org.utgenome.format.bed.BEDLexer
 
Eq - Static variable in class org.utgenome.format.bed.BEDParser
 
Eq - Static variable in class org.utgenome.format.wig.WIGLexer
 
Eq - Static variable in class org.utgenome.format.wig.WIGParser
 
equals(Object) - Method in class org.utgenome.format.axt.AXTAlignment
 
equals(Object) - Method in class org.utgenome.format.fasta.Kmer
 
equals(Object) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
equals(Object) - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
eraseMessage() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
eraseMessage(boolean) - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
error(String) - Method in interface org.utgenome.gwt.utgb.client.track.Track
Report an error
error(String) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
error(String) - Method in class org.utgenome.gwt.utgb.client.ui.Message
 
escape(String) - Static method in class org.utgenome.gwt.utgb.client.util.xml.XMLWriter
 
EscapeSequence - Static variable in class org.utgenome.format.bed.BEDLexer
 
EscapeSequence - Static variable in class org.utgenome.format.bed.BEDParser
 
EscapeSequence - Static variable in class org.utgenome.format.wig.WIGLexer
 
EscapeSequence - Static variable in class org.utgenome.format.wig.WIGParser
 
estimiateLabelWidth(GenomeRange, int) - Static method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
eValue - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult.BlastAlignment
 
eValue - Variable in class org.utgenome.gwt.utgb.client.bio.BlastResult
 
evalue - Variable in class org.utgenome.gwt.utgb.client.bio.BSSRead
 
evalue - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment
 
EventImpl - Class in org.utgenome.gwt.utgb.client.track.operation
 
EventImpl() - Constructor for class org.utgenome.gwt.utgb.client.track.operation.EventImpl
 
exec(String) - Static method in class org.utgenome.shell.Maven.CommandExecutor
 
exec(String, String[], File) - Static method in class org.utgenome.shell.Maven.CommandExecutor
 
execCommand(String, String[], File) - Method in class org.utgenome.shell.Maven.CommandExecutor
 
execute(String[]) - Method in class org.utgenome.core.cui.Convert
 
execute() - Method in class org.utgenome.core.cui.DrawHistogram
 
execute(String[]) - Method in class org.utgenome.core.cui.DrawHistogram
 
execute(String[]) - Method in class org.utgenome.core.cui.ImportBustard
 
execute(String[]) - Method in class org.utgenome.core.cui.ReadStat
 
execute(String[]) - Method in class org.utgenome.core.cui.SAM2Silk
 
execute(String[]) - Method in class org.utgenome.core.cui.ScreenShot
 
execute(String[]) - Method in class org.utgenome.core.cui.Snappy
 
execute(String[]) - Method in class org.utgenome.core.cui.UTGBCommandBase
 
execute(GlobalCommandOption, String[]) - Method in class org.utgenome.core.cui.UTGBCommandBase
 
execute(String[]) - Static method in class org.utgenome.format.fastq.FastqToBAM
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameMoveAbsCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameMoveRelCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameParameterSetCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameRevCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetEndCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetStartCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameZoomAbsCommand
 
execute(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBSubOperationImpl
 
execute(Track) - Method in interface org.utgenome.gwt.utgb.client.track.operation.FrameCommand
 
execute(Track) - Method in class org.utgenome.gwt.utgb.client.track.operation.FrameCommandImpl
 
execute(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.operation.FrameOperation
 
execute(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.operation.LinkOperation
 
execute(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.operation.MenuOperation
 
execute(Widget, int, int) - Method in interface org.utgenome.gwt.utgb.client.track.operation.Operation
 
execute(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.operation.SubOperation
 
execute() - Method in class org.utgenome.gwt.utgb.client.util.Worker
 
execute() - Method in class org.utgenome.gwt.utgb.client.util.WorkQueue
 
execute(String[]) - Method in class org.utgenome.shell.AddAction
 
execute(String[]) - Method in class org.utgenome.shell.Clean
 
execute(String[]) - Method in class org.utgenome.shell.Compile
 
execute(String[]) - Method in class org.utgenome.shell.Create
 
execute(String[]) - Method in class org.utgenome.shell.Deploy
 
execute(String[]) - Method in class org.utgenome.shell.Eclipse
 
execute(String[]) - Method in class org.utgenome.shell.FastqRename
 
execute(String[]) - Method in class org.utgenome.shell.FastqToFasta
 
execute(String[]) - Method in class org.utgenome.shell.FastqToSAM
 
execute(String[]) - Method in class org.utgenome.shell.GWT
 
execute(String[]) - Method in class org.utgenome.shell.GWTCompile
 
execute(String[]) - Method in class org.utgenome.shell.Illumina2Fastq
 
execute(String[]) - Method in class org.utgenome.shell.Import
 
execute(String[]) - Method in class org.utgenome.shell.Keyword
 
execute(String[]) - Method in class org.utgenome.shell.Maven
 
execute(String[]) - Method in class org.utgenome.shell.Pack
 
execute(String[]) - Method in class org.utgenome.shell.QSeqToFastq
 
execute(String[]) - Method in class org.utgenome.shell.Repair
 
execute(String[]) - Method in class org.utgenome.shell.Sam2Wig
 
execute(String[]) - Method in class org.utgenome.shell.SAMToFastq
 
execute(String[]) - Method in class org.utgenome.shell.Sequence
 
execute(String[]) - Method in class org.utgenome.shell.Server
 
execute(String[]) - Method in class org.utgenome.shell.SVNAdd
 
execute(String[]) - Method in class org.utgenome.shell.Upgrade
 
execute(UTGBShell.UTGBShellOption, String[]) - Method in class org.utgenome.shell.UTGBShellCommand
 
execute(String[]) - Method in class org.utgenome.shell.UTGBShellCommand
 
execute(GlobalCommandOption, String[]) - Method in class org.utgenome.shell.UTGBShellCommandBase
 
execute(String[]) - Method in class org.utgenome.util.repeat.RepeatChainFinder
 
execute() - Method in class org.utgenome.util.sv.VariationAnnotator
 
Exon - Class in org.utgenome.format.egt
 
Exon() - Constructor for class org.utgenome.format.egt.Exon
 
Exon - Class in org.utgenome.gwt.utgb.client.bio
Exon
Exon() - Constructor for class org.utgenome.gwt.utgb.client.bio.Exon
 
Exon(int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.Exon
 
Exp - Static variable in class org.utgenome.format.bed.BEDLexer
 
Exp - Static variable in class org.utgenome.format.bed.BEDParser
 
Exp - Static variable in class org.utgenome.format.wig.WIGLexer
 
Exp - Static variable in class org.utgenome.format.wig.WIGParser
 
EXPLODED_WEBAPP_DIR - Static variable in class org.utgenome.shell.UTGBShellCommand
 
exponent - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
extractTarGZ(URL, File) - Static method in class org.utgenome.util.FileUtil
 

F

factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.BEDTrack
Deprecated.  
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.CSEGTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.DASTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.DBSelectTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.debug.DebugToolBoxTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.debug.PropertyEditTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.debug.URLQueryArgumentTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.KeywordSearchTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBAddTrackTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBPropertyTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBRulerTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrackGroup
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
factory(String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.RefSeqTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.RibbonRulerTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.SAMTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ScaleBarTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ScrollButtonTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ToolBoxTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.TrackGenTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.ViewLoaderTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.WIGGraphCanvasTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.lib.WindowControlTrack
 
factory() - Static method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
fade() - Method in class org.utgenome.gwt.ribbon.client.ui.WeaverCanvas
 
FASTA - Class in org.utgenome.format.fasta
 
FASTA(File) - Constructor for class org.utgenome.format.fasta.FASTA
 
FASTA.RawStringWrapper - Class in org.utgenome.format.fasta
 
FASTA.RawStringWrapper(String) - Constructor for class org.utgenome.format.fasta.FASTA.RawStringWrapper
 
FASTADatabase - Class in org.utgenome.format.fasta
Fasta2DB creates a SQLite database file from a given FASTA format file
FASTADatabase() - Constructor for class org.utgenome.format.fasta.FASTADatabase
 
FASTADatabase.Config - Class in org.utgenome.format.fasta
 
FASTADatabase.Config() - Constructor for class org.utgenome.format.fasta.FASTADatabase.Config
 
FASTADatabase.NSeq - Class in org.utgenome.format.fasta
A holder for retrieving compressed genome sequence
FASTADatabase.NSeq() - Constructor for class org.utgenome.format.fasta.FASTADatabase.NSeq
 
FASTADatabase.NSeq(int, int, byte[]) - Constructor for class org.utgenome.format.fasta.FASTADatabase.NSeq
 
FASTADatabase.TextOutput - Class in org.utgenome.format.fasta
 
FASTADatabase.TextOutput(PrintWriter, int, int, boolean) - Constructor for class org.utgenome.format.fasta.FASTADatabase.TextOutput
 
FASTAPullParser - Class in org.utgenome.format.fasta
A pull parser for FASTA format files
FASTAPullParser(Reader) - Constructor for class org.utgenome.format.fasta.FASTAPullParser
Create a pull parser from a given text reader
FASTAPullParser(File) - Constructor for class org.utgenome.format.fasta.FASTAPullParser
Create a pull parse for the given FASTA file.
FASTAPullParser(File, int) - Constructor for class org.utgenome.format.fasta.FASTAPullParser
 
FASTAPullParser(String, InputStream, int) - Constructor for class org.utgenome.format.fasta.FASTAPullParser
 
FASTASequence - Class in org.utgenome.format.fasta
A FASTASequence represents an entry in FASTA files
FASTASequence(String, String) - Constructor for class org.utgenome.format.fasta.FASTASequence
 
FASTASequence() - Constructor for class org.utgenome.format.fasta.FASTASequence
 
FASTASequence - Class in org.utgenome.gwt.utgb.client.bio
Genome sequence
FASTASequence() - Constructor for class org.utgenome.gwt.utgb.client.bio.FASTASequence
 
FastqRead - Class in org.utgenome.format.fastq
An entry of FASTQ format
FastqRead() - Constructor for class org.utgenome.format.fastq.FastqRead
 
FastqRead(String, String, String) - Constructor for class org.utgenome.format.fastq.FastqRead
 
FastqReader - Class in org.utgenome.format.fastq
FASTQ format file reader.
FastqReader(Reader) - Constructor for class org.utgenome.format.fastq.FastqReader
 
FastqRename - Class in org.utgenome.shell
 
FastqRename() - Constructor for class org.utgenome.shell.FastqRename
 
FastqSplitReader - Class in org.utgenome.format.fastq
Read FASTQ file fragment
FastqSplitReader() - Constructor for class org.utgenome.format.fastq.FastqSplitReader
 
FastqToBAM - Class in org.utgenome.format.fastq
Converting Illumina's FASTQ read data (single or paired-end) into BAM format, which can be used BLOAD's GATK pipeline.
FastqToBAM() - Constructor for class org.utgenome.format.fastq.FastqToBAM
 
FastqToFasta - Class in org.utgenome.shell
fastq2fasta command
FastqToFasta() - Constructor for class org.utgenome.shell.FastqToFasta
 
FastqToSAM - Class in org.utgenome.shell
 
FastqToSAM() - Constructor for class org.utgenome.shell.FastqToSAM
 
FastqToSilkReader - Class in org.utgenome.format.fastq
Read the FASTQ file input from the given reader as if it were a Silk
FastqToSilkReader(Reader) - Constructor for class org.utgenome.format.fastq.FastqToSilkReader
 
feature - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.Segment
 
file - Variable in class org.utgenome.format.FileBlock
 
FileBlock - Class in org.utgenome.format
A block in a file
FileBlock(File, int, long) - Constructor for class org.utgenome.format.FileBlock
 
fileName - Variable in class org.utgenome.gwt.utgb.server.app.BEDViewer
 
fileName - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
FileUtil - Class in org.utgenome.util
 
FileUtil() - Constructor for class org.utgenome.util.FileUtil
 
fillPixelsWithMedian(CompactWIGData, int, int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
fillQueue(Deque<Object>) - Method in class org.utgenome.format.ObjectStreamReader.TextReader
Fill the destination queue
fillRect(int, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
fillRect(int, int, int, int, Color) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
filter(String) - Method in class org.utgenome.gwt.utgb.server.util.xml.HTMLContentFilter
replaces &, <, >, ", ' characters into corresponding entity references
filter(String) - Method in interface org.utgenome.gwt.utgb.server.util.xml.TextContentFilter
 
find(String) - Static method in enum org.utgenome.gwt.utgb.client.bio.IUPAC
 
find(String, String, boolean) - Method in class org.utgenome.gwt.utgb.server.util.WebApplicationResource
Retrieves web application resources from the ServletContext
find(ServletContext, String, String, boolean) - Static method in class org.utgenome.gwt.utgb.server.util.WebApplicationResource
Retrieves web application resources from the ServletContext
find(E) - Method in class org.utgenome.util.repeat.DisjointSet
Find the disjoint set ID of the given element
findDir(String) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
findHandler(String) - Method in class org.utgenome.gwt.utgb.server.RequestHandlerTable
 
findOverlap(GenomeRange) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
findRequestHandler(String) - Static method in class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
findRequestHandlerClass(String) - Static method in class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
finish() - Method in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
finish() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
finish() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.JSONOutput
 
finish() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
finish() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.XMLOutput
 
FixedWidthLabel - Class in org.utgenome.gwt.utgb.client.ui
A text label that fits a specified with
FixedWidthLabel(int) - Constructor for class org.utgenome.gwt.utgb.client.ui.FixedWidthLabel
 
FixedWidthLabel(String, int) - Constructor for class org.utgenome.gwt.utgb.client.ui.FixedWidthLabel
 
flag - Variable in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
FLAG_FAILS_QUALITY_CHECK - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_IS_FIRST_READ - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_IS_SECOND_READ - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_MAPPED_IN_A_PROPER_PAIR - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_MATE_IS_UNMAPPED - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_NOT_PRIMARY - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_PAIRED_READ - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_PCR_OR_OPTICAL_DUPLICATE - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_QUERY_IS_UNMAPPED - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_STRAND_OF_MATE - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FLAG_STRAND_OF_QUERY - Static variable in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
FloatType - Class in org.utgenome.gwt.utgb.client.db.datatype
 
FloatType(String) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.FloatType
 
FloatType.FloatTypeForm - Class in org.utgenome.gwt.utgb.client.db.datatype
 
FloatType.FloatTypeForm() - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.FloatType.FloatTypeForm
 
flush() - Method in class org.utgenome.format.sam.Sam2WigConverter.CoverageWriter
 
FOLLOW_attribute_in_description419 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_attribute_in_description426 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_attributeValue_in_attribute461 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_attributeValue_in_attribute468 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_descriptionName_in_description417 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_descriptionName_in_description424 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_Eq_in_attribute459 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_Eq_in_attribute466 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_Number_in_attributeValue488 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_Number_in_attributeValue495 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_QName_in_attribute457 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_QName_in_attribute464 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_QName_in_attributeValue480 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_QName_in_attributeValue487 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_QName_in_descriptionName443 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_QName_in_descriptionName450 - Static variable in class org.utgenome.format.wig.WIGParser
 
FOLLOW_String_in_attributeValue484 - Static variable in class org.utgenome.format.bed.BEDParser
 
FOLLOW_String_in_attributeValue491 - Static variable in class org.utgenome.format.wig.WIGParser
 
follows(Interval) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
FONT_SIZE - Static variable in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
fontColor(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
fontFamily(Widget, String[]) - Static method in class org.utgenome.gwt.widget.client.Style
 
fontFamily(Widget, String) - Static method in class org.utgenome.gwt.widget.client.Style
 
FontMetric - Class in org.utgenome.gwt.utgb.server.app
Request handler
FontMetric() - Constructor for class org.utgenome.gwt.utgb.server.app.FontMetric
 
FontPanel - Class in org.utgenome.gwt.utgb.server.app
Font panel
FontPanel() - Constructor for class org.utgenome.gwt.utgb.server.app.FontPanel
 
FontPanel.FontInfo - Class in org.utgenome.gwt.utgb.server.app
 
FontPanel.FontInfo() - Constructor for class org.utgenome.gwt.utgb.server.app.FontPanel.FontInfo
 
fontSize - Variable in class org.utgenome.gwt.utgb.server.app.FontMetric
 
fontSize - Variable in class org.utgenome.gwt.utgb.server.app.FontPanel
 
fontSize(Widget, int) - Static method in class org.utgenome.gwt.widget.client.Style
 
fontWidth - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
fontWidth - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
FormatConversionReader - Class in org.utgenome.format
A base class for converting an input format into another through a pipe.
FormatConversionReader(Reader, FormatConversionReader.PipeConsumer) - Constructor for class org.utgenome.format.FormatConversionReader
 
FormatConversionReader(InputStream, FormatConversionReader.PipeConsumer) - Constructor for class org.utgenome.format.FormatConversionReader
 
FormatConversionReader.PipeConsumer - Class in org.utgenome.format
 
FormatConversionReader.PipeConsumer() - Constructor for class org.utgenome.format.FormatConversionReader.PipeConsumer
 
formatNumber(int) - Static method in class org.utgenome.gwt.utgb.client.util.StringUtil
insert commas to the given number for the readability
FormLabel - Class in org.utgenome.gwt.utgb.client.ui
 
FormLabel() - Constructor for class org.utgenome.gwt.utgb.client.ui.FormLabel
 
FormLabel(String) - Constructor for class org.utgenome.gwt.utgb.client.ui.FormLabel
 
FormLabel(String, boolean) - Constructor for class org.utgenome.gwt.utgb.client.ui.FormLabel
 
forwardDistance(RepeatChainFinder.Interval2D) - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
Frac - Static variable in class org.utgenome.format.bed.BEDLexer
 
Frac - Static variable in class org.utgenome.format.bed.BEDParser
 
Frac - Static variable in class org.utgenome.format.wig.WIGLexer
 
Frac - Static variable in class org.utgenome.format.wig.WIGParser
 
fraction - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
Frame - Class in org.utgenome.gwt.utgb.client.bean.track
Track frame settings
Frame() - Constructor for class org.utgenome.gwt.utgb.client.bean.track.Frame
 
frame - Variable in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
frame - Variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
Frame - Interface in org.utgenome.gwt.utgb.client.ui
Frame interface for Window, Track, Tab, etc.
FrameBorder - Class in org.utgenome.gwt.widget.client
Bordered Window
FrameBorder(String) - Constructor for class org.utgenome.gwt.widget.client.FrameBorder
 
FrameBorder(String, int) - Constructor for class org.utgenome.gwt.widget.client.FrameBorder
 
FrameBorder(int, int) - Constructor for class org.utgenome.gwt.widget.client.FrameBorder
 
FrameBorder(String, String, int, int) - Constructor for class org.utgenome.gwt.widget.client.FrameBorder
 
FrameButtonListener - Interface in org.utgenome.gwt.utgb.client.ui
Event handler interface when frame buttons are clicked
FrameCommand - Interface in org.utgenome.gwt.utgb.client.track.operation
 
FrameCommandImpl - Class in org.utgenome.gwt.utgb.client.track.operation
 
FrameCommandImpl(Node) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.FrameCommandImpl
 
frameConfig - Variable in class org.utgenome.gwt.utgb.client.track.TrackBase
 
FrameOperation - Class in org.utgenome.gwt.utgb.client.track.operation
 
FrameOperation(Node, Track) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.FrameOperation
 
frequency - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
 
fullBlock(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
fullHeight(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
fullName - Variable in enum org.utgenome.gwt.utgb.client.bio.AminoAcid
 
fullSize(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
fullWidth(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 

G

Gap - Class in org.utgenome.gwt.utgb.client.bio
Gap of paired-end, mate-pair reads
Gap() - Constructor for class org.utgenome.gwt.utgb.client.bio.Gap
 
Gap(int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.Gap
 
Gene - Class in org.utgenome.format.egt
 
Gene() - Constructor for class org.utgenome.format.egt.Gene
 
Gene - Class in org.utgenome.gwt.utgb.client.bio
Gene with Exon and CDS regions
Gene() - Constructor for class org.utgenome.gwt.utgb.client.bio.Gene
 
Gene(Gene) - Constructor for class org.utgenome.gwt.utgb.client.bio.Gene
 
Gene(int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.Gene
 
Gene(String, int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.Gene
 
GeneCanvas - Class in org.utgenome.graphics
Browser-side graphic canvas for drawing gene objects
GeneCanvas() - Constructor for class org.utgenome.graphics.GeneCanvas
 
GeneCanvas(int, int, GenomeWindow) - Constructor for class org.utgenome.graphics.GeneCanvas
 
GeneCanvas.LocusLayout - Class in org.utgenome.graphics
 
GeneCanvas.LocusLayout(GenomeRange, int) - Constructor for class org.utgenome.graphics.GeneCanvas.LocusLayout
 
geneHeight - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
geneList - Variable in class org.utgenome.format.bed.BEDDatabase.BEDRangeQuery
 
geneMargin - Variable in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
geneName - Variable in class org.utgenome.util.sv.EnhancedGeneticVariation
 
generateCharTo2BitACGTTable() - Static method in class org.utgenome.format.fasta.CompactACGTWriter
This method is used to generate source code for the charToACGTCodeTable
generateServerURLLinkHTML() - Method in class org.utgenome.shell.UTGBPortableConfig
 
GeneticVariation - Class in org.utgenome.util.sv
genetic variation location [start, end), chr and allele (genotype) information
GeneticVariation() - Constructor for class org.utgenome.util.sv.GeneticVariation
 
GeneticVariation(String, int, String) - Constructor for class org.utgenome.util.sv.GeneticVariation
 
GeneticVariation(GeneticVariation) - Constructor for class org.utgenome.util.sv.GeneticVariation
 
GeneticVariation.VariationType - Enum in org.utgenome.util.sv
 
GeneViewer - Class in org.utgenome.gwt.utgb.server.app
Gene Viewer
GeneViewer() - Constructor for class org.utgenome.gwt.utgb.server.app.GeneViewer
 
genome - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
 
GenomeCanvas - Class in org.utgenome.graphics
A canvas class for drawing genes.
GenomeCanvas(int, int, GenomeWindow) - Constructor for class org.utgenome.graphics.GenomeCanvas
 
GenomeCoordinate - Class in org.utgenome.gwt.ribbon.client.model
Coordinate system
GenomeCoordinate() - Constructor for class org.utgenome.gwt.ribbon.client.model.GenomeCoordinate
 
GenomeDB - Class in org.utgenome.gwt.utgb.client.bio
Database locator.
GenomeDB() - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeDB
 
GenomeDB(GenomeDB) - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeDB
 
GenomeDB(String, String) - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeDB
 
GenomeDB(GenomeDB.DBType, String, String) - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeDB
 
GenomeDB.DBType - Enum in org.utgenome.gwt.utgb.client.bio
 
GenomeKeywordEntry - Class in org.utgenome.format.keyword
Keyword associated to a genome region
GenomeKeywordEntry(String, String, String, int, int) - Constructor for class org.utgenome.format.keyword.GenomeKeywordEntry
 
GenomeKeywordEntry.KeywordAlias - Class in org.utgenome.format.keyword
Alias is a keyword
GenomeKeywordEntry.KeywordAlias(String, String) - Constructor for class org.utgenome.format.keyword.GenomeKeywordEntry.KeywordAlias
 
GenomeRange - Interface in org.utgenome.gwt.utgb.client.bio
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
GenomeRangeDataSet - Class in org.utgenome.gwt.utgb.client.bio
A set of on-genome data used for transferring genome data between server and client (GWT)
GenomeRangeDataSet() - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeRangeDataSet
 
GenomeRangeVisitor - Interface in org.utgenome.gwt.utgb.client.bio
Visitor interface for traversing data mapped onto a genome sequence
GenomeRangeVisitorBase - Class in org.utgenome.gwt.utgb.client.bio
Refereece implementation of the GenomeRangeVisitor.
GenomeRangeVisitorBase() - Constructor for class org.utgenome.gwt.utgb.client.bio.GenomeRangeVisitorBase
 
GenomeSequence - Interface in org.utgenome.format.fasta
A common interface of genome sequences
GenomeTrack - Class in org.utgenome.gwt.utgb.client.track.lib
GenomeTrack for visualizing data on genome sequences using an image URL or an HTML page embedded in IFRAME tag.
GenomeTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
GenomeTrack(String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
GenomeTrackTextTest - Class in org.utgenome.gwt.utgb.client.track.lib
GenomeTrack is for visualizing data that can be located on genome sequences.
GenomeTrackTextTest() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
GenomeWindow - Class in org.utgenome.graphics
 
GenomeWindow(long, long) - Constructor for class org.utgenome.graphics.GenomeWindow
 
get(String) - Method in class org.utgenome.format.egt.ParameterMap
 
get(int) - Method in class org.utgenome.gwt.utgb.client.bio.CIGAR
 
get(String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
get(String, String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
Gets the String value associated with the given key.
get() - Method in class org.utgenome.gwt.utgb.client.util.Optional
 
get(String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
get(String, String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
Gets the String value associated with the given key.
get(long) - Method in interface org.utgenome.util.aligner.RandomAccess
 
getAbsoluteFocusPanel() - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
getAbsoluteFocusPanel() - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
getAbsoluteFocusPanel() - Method in interface org.utgenome.gwt.utgb.client.track.RangeSelectable
 
getAccept_species() - Method in class org.utgenome.format.legacy.OldDescriptionXML
 
getActionList() - Method in class org.utgenome.config.TrackConfiguration
 
getActionPackage() - Method in class org.utgenome.config.ImportStmt
 
getActionPrefix(HttpServletRequest) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Return the action prefix of the request
getActionSuffix(HttpServletRequest) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Return the action suffix attached to the request
getAddress() - Method in class org.utgenome.config.ConnectionInfo
 
getAdjustHightButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getAdjustHightSwitch() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getAjp13port() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getAlias() - Method in class org.utgenome.config.ImportStmt
 
getAlignment() - Method in class org.utgenome.gwt.utgb.client.bio.AlignmentResult
 
getAllTrackList() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the list of tracks containd in this group, including tracks within the sub groups.
getAltBase() - Method in class org.utgenome.util.sv.GeneticVariation
 
getAssociatedType() - Method in class org.utgenome.gwt.ipad.event.TouchCancelEvent
 
getAssociatedType() - Method in class org.utgenome.gwt.ipad.event.TouchEndEvent
 
getAssociatedType() - Method in class org.utgenome.gwt.ipad.event.TouchMoveEvent
 
getAssociatedType() - Method in class org.utgenome.gwt.ipad.event.TouchStartEvent
 
getAttributeValue(Node, String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
getAttributeValue(Node, String, String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
getAttributeValue(Node, String) - Static method in class org.utgenome.gwt.utgb.client.util.xml.DOMUtil
 
getAttributeValue(Node, String, String) - Static method in class org.utgenome.gwt.utgb.client.util.xml.DOMUtil
 
getAuthorList() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getBamIndexFile(File) - Static method in class org.utgenome.format.sam.SAMReader
 
getBaseColor(char) - Method in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
getBaseColor(char) - Method in class org.utgenome.graphics.RibbonCanvas
 
getBasePackage() - Method in class org.utgenome.config.ActionInfo
 
getBasePanel() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
getBaseURL() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getBaseURL() - Method in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
getBlockCount() - Method in class org.utgenome.format.psl.PSLLine
 
getBlockCount() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getBlockList() - Method in class org.utgenome.format.BlockwiseFileReader
 
getBlockSizes() - Method in class org.utgenome.format.psl.PSLLine
 
getBlockSizes() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getBoolean(String, boolean) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
getBoolean(String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
getBoolean(String, boolean) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
Gets the boolean value associated with the given key.
getBoolean(String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
getBoolean(String, boolean) - Method in class org.utgenome.gwt.utgb.client.util.Properties
Gets the boolean value associated with the given key.
getBooleanAttributeValue(Node, String, boolean) - Static method in class org.utgenome.gwt.utgb.client.util.xml.DOMUtil
 
getBoolValue(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
getBoolValue(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
getBrowser() - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getBrowser() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getBrowser() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getBrowserService() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
Get the RPC service for communicating with the server
getBrowserService() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getBrowserType() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
Retrieve a short name, suitable for use in a tab or filename, for a given user agent.
getBufferedImage() - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
getBufferedImage() - Method in class org.utgenome.graphics.GenomeCanvas
 
getBufferedImage() - Method in class org.utgenome.graphics.ReadCanvas
 
getCatalinaBase() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getCDS() - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
getCDSColor(GenomeRange) - Method in class org.utgenome.graphics.GeneCanvas
 
getCDSColor(Interval, float) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getCDSColor(Interval) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getCellReference() - Method in class org.utgenome.gwt.utgb.client.ui.EditableLabel
 
getChangedParamSet() - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
getChangedParamSet() - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
getChildDBGroups(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getChildDBGroups(String, AsyncCallback<List<String>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getChildDBGroups(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getChildNodeList(Node, String) - Static method in class org.utgenome.gwt.utgb.client.util.xml.DOMUtil
 
getChrList(File) - Method in class org.utgenome.format.sam.SAMReader
 
getChrom() - Method in class org.utgenome.gwt.utgb.client.bio.CytoBand
 
getChromList() - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getChromosomeEnd() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getChromosomeRange() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getChromosomeStart() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getChrRegion(String, String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getChrRegion(String, String, AsyncCallback<ChrRange>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getChrRegion(String, String) - Static method in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
getChrRegion(String, String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getChrSet() - Method in class org.utgenome.format.fasta.CompactFASTA
Get the set of chromosome names
getClassName() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getClassName() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
getClassName() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getClassName() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getClientX() - Method in class org.utgenome.gwt.ipad.event.Touch
 
getClientY() - Method in class org.utgenome.gwt.ipad.event.Touch
 
getClippedReadColor(GenomeRange) - Method in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
getClippedReadColor(GenomeRange) - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
getCloseButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getColor() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
getColor() - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
getColor(String, float) - Static method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getColor(char) - Method in class org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput
 
getColorMode() - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
getColumnCount() - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
getColumnLabel() - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
getColumnLabel(int) - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
getCompactWigData(int, int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getCompactWigDataList(File, int, ChrLoc, GraphWindow) - Static method in class org.utgenome.format.wig.WIGDatabaseReader
 
getCompactWigDataList(String, int, ChrLoc, GraphWindow) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getCompactWigDataList(String, int, ChrLoc, GraphWindow, AsyncCallback<List<CompactWIGData>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getCompactWigDataList(String, int, ChrLoc, GraphWindow) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getComparator() - Static method in class org.utgenome.gwt.utgb.client.track.TrackComparator
 
getComplement(char) - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
getConfig() - Method in class org.utgenome.gwt.utgb.client.track.lib.DBSelectTrack
 
getConfig() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
getConfig() - Method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
getConfig() - Method in interface org.utgenome.gwt.utgb.client.track.Track
Get the TrackConfig panel.
getConfig() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getConfigButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getConfigFile() - Method in class org.utgenome.shell.UTGBShellCommand
 
getConnectionList() - Method in class org.utgenome.config.DatabaseInfo
 
getContent() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getContent() - Method in class org.utgenome.gwt.utgb.client.ui.WindowBox
 
getContent(ServletContext, String) - Static method in class org.utgenome.gwt.utgb.server.util.WebApplicationResource
 
getContentHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
getContextPath() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getContextProperty(String, String) - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getCoordinate() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
Get the current genome coordinate
getCount() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getCreaseInRange(int, int) - Method in class org.utgenome.gwt.utgb.client.ribbon.Ribbon
 
getCSS3DOMprefix() - Static method in class org.utgenome.gwt.widget.client.Style
 
getCSS3prefix() - Static method in class org.utgenome.gwt.widget.client.Style
 
getCurrentView() - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getCytoBandColor(CytoBand) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
getCytoBandNameColor(CytoBand) - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
getData(int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getData(int, int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getData(int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getData() - Method in class org.utgenome.gwt.utgb.client.bean.track.SEGRecord
 
getData() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getData() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getDatabase(String) - Method in class org.utgenome.config.TrackConfiguration
 
getDatabase(String) - Method in class org.utgenome.config.UTGBConfig
 
getDatabaseAccess(UTGBConfig.Database) - Static method in class org.utgenome.gwt.utgb.server.JDBCService
 
getDatabaseAccess(String, UTGBConfig.Database) - Static method in class org.utgenome.gwt.utgb.server.JDBCService
 
getDatabaseAccess(String) - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getDatabaseAccess(String) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Retrieves the database access
getDatabaseAccessInternal(String) - Method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getDatabaseCatalog(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getDatabaseCatalog(String, AsyncCallback<String>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getDatabaseCatalog(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getDatabaseList() - Method in class org.utgenome.config.TrackConfiguration
 
getDataModelParameter(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getDataType(String, String) - Static method in class org.utgenome.gwt.utgb.client.db.Relation
 
getDataType(int) - Method in class org.utgenome.gwt.utgb.client.db.Relation
 
getDataTypeList() - Method in class org.utgenome.gwt.utgb.client.db.Relation
 
getDBEntry(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getDBEntry(String, AsyncCallback<List<DatabaseEntry>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getDBEntry(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getDbms() - Method in class org.utgenome.config.ConnectionInfo
 
getDBNames(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getDBNames(String, AsyncCallback<List<String>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getDBNames(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getDBTypeList() - Static method in enum org.utgenome.gwt.utgb.client.bio.GenomeDB.DBType
 
getDefault() - Method in class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
getDefault() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getDefaultMaxValue() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
getDefaultMinValue() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.debug.PropertyEditTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBRulerTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.ScrollButtonTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.ToolBoxTrack
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
getDefaultWindowHeight() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getDefaultWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getDescription() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getDescription() - Method in class org.utgenome.gwt.utgb.client.bio.FASTASequence
 
getDescription() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getDescription() - Method in class org.utgenome.gwt.utgb.client.track.TrackInfo
 
getDescription() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry.TabEntryFactory
 
getDescriptionLine() - Method in class org.utgenome.format.fasta.FASTASequence
 
getDescriptionXML() - Method in class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
getDeveloper() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getDisplayName() - Method in class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
getDisplayName() - Method in class org.utgenome.gwt.utgb.client.bean.track.Option
 
getDisplayName() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getDisplayType() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
getDocURL() - Method in class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
getDraggableWidget() - Method in class org.utgenome.gwt.widget.client.HorizontalTrackFrame
 
getDraggableWidget() - Method in class org.utgenome.gwt.widget.client.TrackFrame
Get the draggable part of this widget
getDraggableWidget() - Method in class org.utgenome.gwt.widget.client.TrackWindowPanel
 
getEnd() - Method in class org.utgenome.format.egt.Exon
 
getEnd() - Method in class org.utgenome.format.egt.Gene
 
getEnd() - Method in class org.utgenome.format.egt.Range
 
getEnd() - Method in class org.utgenome.format.fasta.FASTADatabase.NSeq
 
getEnd() - Method in class org.utgenome.gwt.utgb.client.bean.track.SEGRecord
 
getEnd() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getEnd() - Method in class org.utgenome.gwt.utgb.client.bio.CytoBand
 
getEnd() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
return 1-based end position of the data.
getEnd() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
Get the end position of the locus (start <= end)
getEnd() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getEnd() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackWindowBean
 
getEnd() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
getEndIndex(String, int, int, int, int) - Method in class org.utgenome.graphics.GenomeCanvas
 
getEndOnGenome() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getEndX() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getEndY() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getEntry() - Method in class org.utgenome.format.legacy.AcceptSpecies
 
getErrorCode() - Method in exception org.utgenome.gwt.utgb.client.UTGBClientException
 
getErrorCode() - Method in exception org.utgenome.UTGBException
 
getExon() - Method in class org.utgenome.format.egt.Gene
 
getExon() - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
getExon(int) - Method in class org.utgenome.gwt.utgb.client.bio.Gene
 
getExonColor(GenomeRange) - Method in class org.utgenome.graphics.GeneCanvas
 
getExonColor(Gene) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getExonColorText(GenomeRange) - Method in class org.utgenome.graphics.GeneCanvas
 
getExtension(String) - Static method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
getFileSize() - Method in class org.utgenome.format.BlockwiseFileReader
 
getFirst() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPair
 
getFirstChild() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
getFixedHightButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getFloat(String, float) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
getFloat(String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
getFloat(String, float) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
Gets the float value associated with the given key.
getFloat(String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
getFloat(String, float) - Method in class org.utgenome.gwt.utgb.client.util.Properties
Gets the float value associated with the given key.
getFloatValue(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
getFloatValue(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
getFocusPanel() - Method in class org.utgenome.gwt.utgb.client.ui.AbsoluteFocusPanel
 
getFontInfo(float) - Static method in class org.utgenome.gwt.utgb.server.app.FontPanel
 
getFontWidth(String) - Method in class org.utgenome.graphics.GenomeCanvas
 
getFrame() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getFrame() - Method in interface org.utgenome.gwt.utgb.client.track.Track
Get the frame of this track
getFrame() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getFrameBar() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
getFrameColor() - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
getFullName() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Get the full path of the action request
getGap() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPair
 
getGap() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
 
getGeneColor(GenomeRange) - Method in class org.utgenome.graphics.GeneCanvas
 
getGeneColor(GenomeRange, float) - Method in class org.utgenome.graphics.GeneCanvas
 
getGeneColor(Interval) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getGeneColor(Interval, float) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getGeneList(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getGenomeDB() - Method in class org.utgenome.gwt.utgb.client.track.lib.DASTrack
 
getGenomeDB() - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
Override this method to extend db info parameters
getGenomeRange() - Method in class org.utgenome.graphics.GenomeWindow
 
getGenomeWindow() - Method in class org.utgenome.graphics.GenomeCanvas
 
getGenotype() - Method in class org.utgenome.util.sv.GeneticVariation
 
getGieStain() - Method in class org.utgenome.gwt.utgb.client.bio.CytoBand
 
getGlobalWindow() - Method in class org.utgenome.gwt.utgb.client.canvas.TrackWindowChain
 
getGrammarFileName() - Method in class org.utgenome.format.bed.BEDLexer
 
getGrammarFileName() - Method in class org.utgenome.format.bed.BEDParser
 
getGrammarFileName() - Method in class org.utgenome.format.wig.WIGLexer
 
getGrammarFileName() - Method in class org.utgenome.format.wig.WIGParser
 
getGraphData() - Method in class org.utgenome.gwt.utgb.client.canvas.BarGraphCanvas
 
getGraphics() - Method in class org.utgenome.graphics.GenomeCanvas
 
getGraphics() - Method in class org.utgenome.graphics.ReadCanvas
 
getGraphics(BufferedImage) - Static method in class org.utgenome.gwt.utgb.server.util.graphic.GraphicUtil
 
getGroup() - Method in class org.utgenome.config.TrackConfiguration
 
getGroup() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getGroup() - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getGroupProperties() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
getGWTModuleName() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getHandlerName() - Method in class org.utgenome.gwt.utgb.server.RequestURI
 
getHash() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getHeight() - Method in class org.utgenome.gwt.utgb.client.bean.track.Frame
 
getHeight() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout
 
getHeight() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getHeight() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getHeight() - Method in class org.utgenome.gwt.utgb.server.app.TextLabel
 
getHeight() - Method in class org.utgenome.gwt.widget.client.ImageHandle
 
getHelpMessageResource() - Method in class org.utgenome.core.cui.UTGBCommandBase
 
getHelpMessageResource() - Method in class org.utgenome.shell.UTGBShellCommand
 
getHiddenParameterList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
getHiddenParamList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getHideButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getHit() - Method in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
getHost() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getHostName() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getHref() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getHTTPContent(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getHTTPContent(String, AsyncCallback<String>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getHTTPContent(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getHTTPRequestQueryString(HttpServletRequest) - Static method in class org.utgenome.gwt.utgb.server.WebTrackBase
 
getIconImage(int) - Static method in class org.utgenome.gwt.utgb.client.track.Design
Get the icon image URL
getIconImage() - Method in class org.utgenome.gwt.widget.client.Icon
 
getIconSetPanel() - Method in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
getId() - Method in class org.utgenome.config.DatabaseInfo
 
getId() - Method in class org.utgenome.gwt.utgb.client.bean.track.SEGRecord
 
getId() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getImage(int) - Static method in class org.utgenome.gwt.utgb.client.ui.WidgetDesign
 
getImagePath(String) - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
Get the path to the image file for the selected theme
getImageURL() - Method in class org.utgenome.gwt.utgb.client.ui.IconImage
 
getImageURL(int) - Static method in class org.utgenome.gwt.utgb.client.ui.WidgetDesign
 
getImportList() - Method in class org.utgenome.config.TrackConfiguration
 
getIndentString(int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
getIndentValue(int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
getIndex(Widget) - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
Get the index of the specified child widget position
getIndex(Widget) - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
Get the index of the specified child widget position
getInputData() - Method in class org.utgenome.gwt.utgb.client.db.DynamicForm
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType
 
getInputForm() - Method in interface org.utgenome.gwt.utgb.client.db.datatype.DataType
Get a user interface for retrieving the data of this data type
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ColorType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.DispType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.GradationType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.LowerBoundType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.SelectType
 
getInputForm() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.UpperBoundType
 
getInstance() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry.TabEntryFactory
 
getInstance() - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getInt(String, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
getInt(String) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
 
getInt(String, int) - Method in class org.utgenome.gwt.utgb.client.util.CanonicalProperties
Gets the integer value associated with the given key.
getInt(String) - Method in class org.utgenome.gwt.utgb.client.util.Properties
 
getInt(String, int) - Method in class org.utgenome.gwt.utgb.client.util.Properties
Gets the integer value associated with the given key.
getIntAttributeValue(Node, String, int) - Static method in class org.utgenome.gwt.utgb.client.util.xml.DOMUtil
 
getIntronColor(GenomeRange) - Method in class org.utgenome.graphics.GeneCanvas
 
getIntValue(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
getIntValue(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
getIteratorOnChr(File, String) - Static method in class org.utgenome.format.sam.SAMReadIterator
 
getJavaClass(ClassLoader, VirtualFile, String) - Static method in class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType.BooleanTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType.DoubleTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType.FloatTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.InputForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeListBox
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType.PasswordTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeForm
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeListBox
 
getJSONValue() - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType.TextTypeForm
 
getKey() - Method in class org.utgenome.gwt.utgb.client.track.bean.Tag
 
getKeyAndValueString(String, String, String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
Gets the key and value string
getKeyAndValueString(String, String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
Gets the key and value string
getKeyColumn() - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
getKeywordList() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getKmerIterator(int) - Method in class org.utgenome.format.fasta.CompactACGT
 
getLabel() - Method in class org.utgenome.gwt.utgb.client.db.Value
 
getLayerList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
getLeftMargin() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getLeftMargin() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
getLength() - Method in class org.utgenome.format.fasta.FASTADatabase.NSeq
 
getLength() - Method in class org.utgenome.gwt.utgb.client.util.xml.NodeListImpl
 
getLighterRate() - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
getLines() - Method in class org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
 
getLinkURL() - Method in class org.utgenome.gwt.utgb.client.track.TrackInfo
 
getLocForPositiveStrand() - Method in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
getLocus() - Method in class org.utgenome.graphics.GeneCanvas.LocusLayout
 
getLocus() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout
 
getLocusList(String, String, ChrLoc) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getLogValue(float, float) - Static method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
getLogValue(float) - Method in class org.utgenome.gwt.utgb.client.canvas.Scale
 
getMappedRate() - Method in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
getMatches() - Method in class org.utgenome.format.psl.PSLLine
 
getMax() - Method in class org.utgenome.gwt.utgb.client.canvas.Scale
 
getMaxpage() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getMaxValue() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getMaxValue() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getMessage() - Method in exception org.utgenome.UTGBException
 
getMessageLabel() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
GETMethodURL - Class in org.utgenome.gwt.utgb.client.util
 
GETMethodURL(String) - Constructor for class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
getMin() - Method in class org.utgenome.gwt.utgb.client.canvas.Scale
 
getMinFrameHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrameState
 
getMinimumWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBAddTrackTrack
 
getMinimumWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBRulerTrack
 
getMinimumWindowHeight() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getMinimumWindowHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getMinValue() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getMinValue() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getMisMatches() - Method in class org.utgenome.format.psl.PSLLine
 
getMouseOverIconImage() - Method in class org.utgenome.gwt.widget.client.Icon
 
getMouseOverImageURL() - Method in class org.utgenome.gwt.utgb.client.ui.IconImage
 
getMPos() - Method in class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
list of C-C and C-T positions
getMutationType() - Method in class org.utgenome.util.sv.EnhancedGeneticVariation
 
getName() - Method in class org.utgenome.format.egt.Gene
 
getName() - Method in class org.utgenome.format.legacy.OldDescriptionXML
 
getName() - Method in class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
getName() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getName() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getName() - Method in class org.utgenome.gwt.utgb.client.bean.track.Species
 
getName() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.CytoBand
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.FASTASequence
 
getName() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.ReadCoverage
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.ReadList
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.ReferenceSequence
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPair
 
getName() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
 
getName() - Method in interface org.utgenome.gwt.utgb.client.db.datatype.DataType
parameter name of this type
getName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
getName() - Method in class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
getName() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getName() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getName() - Method in interface org.utgenome.gwt.utgb.client.track.TrackEntry
Get the entry name
getName() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getName() - Method in class org.utgenome.gwt.utgb.server.app.Hello
 
getName() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Get the leaf name of the action request
getNCount() - Method in class org.utgenome.format.psl.PSLLine
 
getNextSibling() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
getNowLoadingIcon() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getNumMatch() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getNumMisMatch() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getNumN() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getNumRepMatch() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getObsolteConfigurationFile() - Method in class org.utgenome.shell.UTGBShellCommand
 
getOffset(String, int, long, long, int) - Method in class org.utgenome.graphics.GenomeCanvas
 
getOneLineDescription() - Method in class org.utgenome.core.cui.Convert
 
getOneLineDescription() - Method in class org.utgenome.core.cui.DrawHistogram
 
getOneLineDescription() - Method in class org.utgenome.core.cui.ImportBustard
 
getOneLineDescription() - Method in class org.utgenome.core.cui.ReadStat
 
getOneLineDescription() - Method in class org.utgenome.core.cui.SAM2Silk
 
getOneLineDescription() - Method in class org.utgenome.core.cui.ScreenShot
 
getOneLineDescription() - Method in class org.utgenome.core.cui.Snappy
 
getOneLineDescription() - Method in class org.utgenome.core.cui.UTGBCommandBase
 
getOneLineDescription() - Method in class org.utgenome.shell.UTGBShellCommand
 
getOneLinerDescription() - Method in class org.utgenome.shell.AddAction
 
getOneLinerDescription() - Method in class org.utgenome.shell.Clean
 
getOneLinerDescription() - Method in class org.utgenome.shell.Compile
 
getOneLinerDescription() - Method in class org.utgenome.shell.Create
 
getOneLinerDescription() - Method in class org.utgenome.shell.Deploy
 
getOneLinerDescription() - Method in class org.utgenome.shell.Eclipse
 
getOneLinerDescription() - Method in class org.utgenome.shell.FastqRename
 
getOneLinerDescription() - Method in class org.utgenome.shell.FastqToFasta
 
getOneLinerDescription() - Method in class org.utgenome.shell.FastqToSAM
 
getOneLinerDescription() - Method in class org.utgenome.shell.GWT
 
getOneLinerDescription() - Method in class org.utgenome.shell.GWTCompile
 
getOneLinerDescription() - Method in class org.utgenome.shell.Illumina2Fastq
 
getOneLinerDescription() - Method in class org.utgenome.shell.Import
 
getOneLinerDescription() - Method in class org.utgenome.shell.Keyword
 
getOneLinerDescription() - Method in class org.utgenome.shell.Maven
 
getOneLinerDescription() - Method in class org.utgenome.shell.Pack
 
getOneLinerDescription() - Method in class org.utgenome.shell.QSeqToFastq
 
getOneLinerDescription() - Method in class org.utgenome.shell.Repair
 
getOneLinerDescription() - Method in class org.utgenome.shell.Sam2Wig
 
getOneLinerDescription() - Method in class org.utgenome.shell.SAMToFastq
 
getOneLinerDescription() - Method in class org.utgenome.shell.Sequence
 
getOneLinerDescription() - Method in class org.utgenome.shell.Server
 
getOneLinerDescription() - Method in class org.utgenome.shell.SVNAdd
 
getOneLinerDescription() - Method in class org.utgenome.shell.Upgrade
 
getOneLinerDescription() - Method in class org.utgenome.shell.UTGBShellCommand
 
getOnGenomeData(GenomeDB, ChrLoc, ReadQueryConfig) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
Get read data from the specified DB and location
getOnGenomeData(GenomeDB, ChrLoc, ReadQueryConfig, AsyncCallback<List<GenomeRange>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getOnGenomeData(GenomeDB, ChrLoc, ReadQueryConfig) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getOpenButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getOpenHideSwith() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getOptattr() - Method in class org.utgenome.format.legacy.OldDescriptionXML
 
getOptionHolder() - Method in class org.utgenome.core.cui.ReadStat
 
getOptionHolder() - Method in class org.utgenome.core.cui.UTGBCommandBase
 
getOptionHolder() - Method in class org.utgenome.shell.Server
 
getOptionHolder() - Method in class org.utgenome.shell.UTGBShellCommand
 
getOptionList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getOSType() - Static method in enum org.utgenome.shell.OSType
Gets the current OS type
getOverlappingIterator(File, ChrLoc) - Static method in class org.utgenome.format.sam.SAMReadIterator
 
getPack() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getPackage() - Method in class org.utgenome.config.TrackConfiguration
 
getPaddingColor() - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
getPage() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getPagewidth() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getParameter(String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
getParameter(HttpServletRequest, String, String) - Static method in class org.utgenome.gwt.utgb.server.util.ServletUtil
Gets the http request parameter
getParameterList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
getParameterTrack() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
getParamList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getParentTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Return the current parent trackgroup.
getParser() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBOperationParser
 
getParser() - Static method in class org.utgenome.gwt.utgb.client.track.operation.OperationParser
 
getPass() - Method in class org.utgenome.config.ConnectionInfo
 
getPath() - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
getPath() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getPath(File) - Static method in class org.utgenome.shell.ScaffoldGenerator
 
getPath(File) - Static method in class org.utgenome.shell.UTGBShellCommand
 
getPathComponentList() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Return the path component.
getPixelLengthPerBase() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getPixelSize() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getPixelWidth() - Method in class org.utgenome.graphics.ReadCanvas
 
getPixelWidth() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getPort() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getPort() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getPortNumber() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getPrefetchFactor() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getPrefetchWindow() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getPrefix() - Method in class org.utgenome.config.ActionInfo
 
getPrefix() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Get the prefix before the handler name
getPrettyAlignment() - Method in class org.utgenome.gwt.utgb.client.bio.AlignmentResult
 
getPreviousFrameHeight() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrameState
 
getProgramInfo() - Static method in class org.utgenome.shell.UTGBShell
 
getProjectConfigDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getProjectName() - Method in class org.utgenome.config.TrackConfiguration
 
getProjectResourcePath(String) - Method in class org.utgenome.shell.UTGBShellCommand
 
getProjectRoot() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getProjectRoot() - Method in class org.utgenome.shell.UTGBShellCommand
 
getProjectRootFolder() - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getProjectRootPath() - Static method in class org.utgenome.gwt.utgb.server.WebTrackBase
Returns the path to the project root folder
getProperties() - Method in class org.utgenome.shell.POM
 
getProperty(String) - Method in class org.utgenome.config.OldViewXML.TrackGroup
 
getProperty(String, String) - Method in class org.utgenome.config.TrackConfiguration
 
getProperty(String) - Method in class org.utgenome.config.UTGBConfig
 
getProperty(String, String) - Method in class org.utgenome.config.UTGBConfig
 
getProperty() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackBean
 
getProperty() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
getProperty() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupPropertyBean
 
getProperty(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
getProperty(String, String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
getProperty(String) - Method in class org.utgenome.gwt.utgb.client.track.Track.TrackFactory
get a property value.
getProperty(String, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getProperty(String) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getProperty(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupProperty
get a property value of a given key
getProperty(String, String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupProperty
get a property value of a given key.
getPropertyNameArray() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBProperty
 
getPropertyNameList() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBProperty
 
getPropertyNameSet() - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBProperty
 
getPropertyReader() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the TrackGroupProperty of this track group
getPropertyWriter() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the TrackGroupPropertyWriter of this track group.
getPropertyXMLTag(String, String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
getProtocol() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getQBaseInsert() - Method in class org.utgenome.format.psl.PSLLine
 
getQEnd() - Method in class org.utgenome.format.psl.PSLLine
 
getQName() - Method in class org.utgenome.format.psl.PSLLine
 
getQNumInsert() - Method in class org.utgenome.format.psl.PSLLine
 
getQSize() - Method in class org.utgenome.format.psl.PSLLine
 
getQStart() - Method in class org.utgenome.format.psl.PSLLine
 
getQStarts() - Method in class org.utgenome.format.psl.PSLLine
 
getQuery() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getQueryEnd() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getQueryLen() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getQueryName() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getQueryStart() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getQueryStarts() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getQueryString() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getQV() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
getQV() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
getRange() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getRank() - Method in class org.utgenome.graphics.ChromosomeWindow
 
getRawSequence(String) - Method in class org.utgenome.format.fasta.FASTA
 
getRead() - Method in class org.utgenome.gwt.utgb.client.bio.ReadList
 
getReadColor(GenomeRange) - Method in class org.utgenome.graphics.ReadCanvas.DrawStyle
 
getReadColor(GenomeRange) - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
getReadColor(GenomeRange, float) - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
getReadWidth(String) - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
getRealInstance(String, String, String, String[], String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBOptionAttribute
 
getRefSeq(String, String, int, int) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getRefSeq(String, String, int, int, AsyncCallback<String>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getRefSeq(String, String, int, int) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getRelation(String) - Method in class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
 
getRelationList() - Method in class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
 
getRelativeX(Element) - Method in class org.utgenome.gwt.ipad.event.Touch
 
getRelativeY(Element) - Method in class org.utgenome.gwt.ipad.event.Touch
 
getReloadButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getRepeatMappedRate() - Method in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
getRepMathces() - Method in class org.utgenome.format.psl.PSLLine
 
getResizeButton() - Method in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
getResoruceFile(ServletContext, String) - Static method in class org.utgenome.gwt.utgb.server.util.WebApplicationResource
 
getResult() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getReverse() - Method in class org.utgenome.graphics.GenomeWindow
 
getRevision() - Method in class org.utgenome.format.legacy.SpeciesEntry
 
getRevision() - Method in class org.utgenome.gwt.utgb.client.bean.track.Species
 
getRevision() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getRevision() - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getRevision() - Method in class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
getRevision() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getRevision() - Method in class org.utgenome.shell.POM
Retrieves Subversion's revision number from the pom.xml file
getRevision() - Method in class org.utgenome.shell.POMProperties
 
getRevisionList() - Method in class org.utgenome.gwt.utgb.client.track.bean.SequenceInfo
 
getRoot() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreeView
 
getRootTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the root TrackGroup
getRoughCompactWigDataList(File, int, ChrLoc, GraphWindow) - Static method in class org.utgenome.format.wig.WIGDatabaseReader
 
getRow(Object) - Method in class org.utgenome.gwt.utgb.client.util.TableData
 
getRPCService() - Static method in class org.utgenome.gwt.utgb.client.RPCServiceManager
 
getSAMReadColor(SAMReadLight) - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
getSAMReadList(String, String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getSAMReadList(String, String, AsyncCallback<List<SAMRead>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getSAMReadList(String, String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getSAMRecordReader(InputStream) - Static method in class org.utgenome.format.sam.SAMReader
 
getScope() - Method in class org.utgenome.config.ConnectionInfo
 
getScrollPanel() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ConfigInputForm
 
getSecond() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadPair
 
getSelectInstance(String, String[], String[], String) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBOptionAttribute
 
getSequence(String, int, int) - Method in class org.utgenome.format.fasta.CompactFASTA
Retrieves a genome sequence of the specified range [start, end)
getSequence(String, int, int, boolean) - Method in class org.utgenome.format.fasta.CompactFASTA
 
getSequence(String, int) - Method in class org.utgenome.format.fasta.CompactFASTA
 
getSequence(String) - Method in class org.utgenome.format.fasta.CompactFASTA
 
getSequence(String) - Method in class org.utgenome.format.fasta.FASTA
 
getSequence() - Method in class org.utgenome.format.fasta.FASTADatabase.NSeq
 
getSequence() - Method in class org.utgenome.format.fasta.FASTASequence
 
getSequence() - Method in class org.utgenome.gwt.utgb.client.bio.FASTASequence
 
getSequence() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
getSequence() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
getSequenceLength() - Method in class org.utgenome.format.fasta.CompactACGTWriter
 
getSequenceLength(String) - Method in class org.utgenome.format.fasta.CompactFASTA
 
getSequenceLength() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getSequenceName() - Method in class org.utgenome.format.fasta.FASTASequence
Extract a sequence name from the description line
getServerURL() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getSilk() - Method in class org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
 
getSize() - Method in class org.utgenome.gwt.utgb.server.app.TextLabel
 
getSortby() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getSpan() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getSpecies() - Method in class org.utgenome.format.legacy.SpeciesEntry
 
getSpecies() - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getSpecies() - Method in class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
getSpecies() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getSpecies() - Method in class org.utgenome.gwt.utgb.client.track.bean.SequenceInfo
 
getSpeciesList() - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
getStart() - Method in class org.utgenome.format.egt.Exon
 
getStart() - Method in class org.utgenome.format.egt.Gene
 
getStart() - Method in class org.utgenome.format.egt.Range
 
getStart() - Method in class org.utgenome.format.fasta.FASTADatabase.NSeq
 
getStart() - Method in class org.utgenome.gwt.utgb.client.bean.track.SEGRecord
 
getStart() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getStart() - Method in class org.utgenome.gwt.utgb.client.bio.CytoBand
 
getStart() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
return 1-based start position of the data.
getStart() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
Get the start position of the locus.
getStart() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getStart() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackWindowBean
 
getStart() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
getStartOnGenome() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getStartX() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getStartY() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getStrand() - Method in class org.utgenome.format.egt.Gene
 
getStrand() - Method in class org.utgenome.format.psl.PSLLine
 
getStrand() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getStrand() - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
getString(String, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
getStyle() - Method in class org.utgenome.graphics.ReadCanvas
 
getStyle() - Method in class org.utgenome.gwt.utgb.client.bean.track.Frame
 
getStyle() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getStyle() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
getSubCommandNameSet() - Static method in class org.utgenome.shell.UTGBShell
 
getSubSequence(int, int) - Method in class org.utgenome.format.fasta.FASTADatabase.NSeq
extract sub sequence (0-origin)
getSuffix() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Get the suffix of the action request
getTabCloseButton() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getTabContent(int) - Method in class org.utgenome.gwt.widget.client.TabbedTrackFrame
 
getTableData(String, String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getTableData(String, String, AsyncCallback<String>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getTableData(String, String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getTableNameList() - Method in class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
 
getTabName() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry.TabEntryFactory
 
getTagChildNodes(Node) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.Utilities
 
getTarget() - Method in class org.utgenome.format.egt.Gene
 
getTarget() - Method in class org.utgenome.gwt.utgb.client.track.bean.Result
 
getTargetEnd() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getTargetName() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getTargetProperty() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
getTargetSize() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getTargetStart() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getTargetStarts() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
getTBaseInsert() - Method in class org.utgenome.format.psl.PSLLine
 
getTEnd() - Method in class org.utgenome.format.psl.PSLLine
 
getText() - Method in class org.utgenome.gwt.utgb.server.app.TextLabel
 
getTitleBar() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
getTitleBar() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
getTName() - Method in class org.utgenome.format.psl.PSLLine
 
getTNumInsert() - Method in class org.utgenome.format.psl.PSLLine
 
getTokenNames() - Method in class org.utgenome.format.bed.BEDParser
 
getTokenNames() - Method in class org.utgenome.format.wig.WIGParser
 
getTotalcount() - Method in class org.utgenome.gwt.utgb.client.track.bean.SearchResult
 
getTrack(int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getTrack() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getTrack() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getTrack() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
getTrack() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationImpl
 
getTrack() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
getTrack_id() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
getTrack_id() - Method in class org.utgenome.gwt.utgb.client.bio.WigGraphData
 
getTrackBaseURL() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
getTrackConfigProperty(String, String) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Get the property written in the track-config.xml file
getTrackEntryList() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the list of TrackEntrys, including both of Track and TrackGroup.
getTrackFactory(String) - Static method in class org.utgenome.gwt.utgb.client.track.TrackFactoryHolder
 
getTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupBean
 
getTrackGroup() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getTrackGroup() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
getTrackGroupFactory(String) - Static method in class org.utgenome.gwt.utgb.client.track.TrackFactoryHolder
 
getTrackGroupList() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the list of track groups containd in this group, excluding track groups within the sub groups.
getTrackGroupName() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
getTrackGroupProperty(String, String) - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getTrackGroupProperty(String) - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getTrackGroupProperty(String) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getTrackGroupProperty(String, String) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getTrackIdList(String) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getTrackIdList() - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getTrackIndex(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Return the index of the given track in the group.
getTrackIndex(Track) - Method in interface org.utgenome.gwt.utgb.client.track.TrackLayoutManager
Return the index of the given track
getTrackIndex(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
getTrackInfo() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getTrackInfo() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getTrackList(int, int) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getTrackList(String, int, int) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getTrackList(int, int, AsyncCallback<List<TrackBean>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getTrackList(String, int, int, AsyncCallback<List<TrackBean>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getTrackList() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the list of tracks containd in this group, excluding tracks within the sub groups.
getTrackList(int, int) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getTrackList(String, int, int) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getTrackName() - Method in class org.utgenome.gwt.utgb.client.track.TrackInfo
 
getTrackQueue() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
getTrackTitle() - Method in class org.utgenome.gwt.widget.client.HorizontalTrackFrame
 
getTrackTitle() - Method in class org.utgenome.gwt.widget.client.TrackFrame
Gets the track title
getTrackTitle() - Method in class org.utgenome.gwt.widget.client.TrackWindowPanel
 
getTrackURL(String, Map) - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getTrackURL(String) - Method in class org.utgenome.gwt.utgb.client.bio.Coordinate
 
getTrackURL() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
getTrackURL() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
getTrackURL() - Method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
getTrackURL(String) - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
getTrackView(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getTrackView(String, AsyncCallback<TrackView>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getTrackView(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getTrackWindow() - Method in class org.utgenome.gwt.utgb.client.canvas.BarGraphCanvas
 
getTrackWindow() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackGroupPropertyBean
 
getTrackWindow() - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
getTrackWindow() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
getTrackWindow() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Get the TrackWindow of this track group
getTrackWindow() - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupProperty
 
getTrackWindowList() - Method in class org.utgenome.gwt.utgb.client.canvas.TrackWindowChain
 
getTransparentBufferedImage(int, int) - Static method in class org.utgenome.gwt.utgb.server.util.graphic.GraphicUtil
Generates a BufferedImage instance whose background is transparent.
getTree() - Method in class org.utgenome.format.bed.BEDParser.attribute_return
 
getTree() - Method in class org.utgenome.format.bed.BEDParser.attributeValue_return
 
getTree() - Method in class org.utgenome.format.bed.BEDParser.description_return
 
getTree() - Method in class org.utgenome.format.bed.BEDParser.descriptionName_return
 
getTree() - Method in class org.utgenome.format.wig.WIGParser.attribute_return
 
getTree() - Method in class org.utgenome.format.wig.WIGParser.attributeValue_return
 
getTree() - Method in class org.utgenome.format.wig.WIGParser.description_return
 
getTree() - Method in class org.utgenome.format.wig.WIGParser.descriptionName_return
 
getTreeAdaptor() - Method in class org.utgenome.format.bed.BEDParser
 
getTreeAdaptor() - Method in class org.utgenome.format.wig.WIGParser
 
getTSize() - Method in class org.utgenome.format.psl.PSLLine
 
getTStart() - Method in class org.utgenome.format.psl.PSLLine
 
getTStarts() - Method in class org.utgenome.format.psl.PSLLine
 
getType() - Static method in class org.utgenome.gwt.ipad.event.TouchCancelEvent
 
getType() - Static method in class org.utgenome.gwt.ipad.event.TouchEndEvent
 
getType() - Static method in class org.utgenome.gwt.ipad.event.TouchMoveEvent
 
getType() - Static method in class org.utgenome.gwt.ipad.event.TouchStartEvent
 
getType() - Method in class org.utgenome.gwt.utgb.client.bean.track.Content
 
getType() - Method in class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
getType() - Method in class org.utgenome.gwt.utgb.client.bean.track.Layer
 
getType() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType
 
getTypeName() - Method in interface org.utgenome.gwt.utgb.client.db.datatype.DataType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringListType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ColorType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.DispType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.GradationType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.LowerBoundType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.SelectType
 
getTypeName() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.UpperBoundType
 
getUniquelyMapppedRate() - Method in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
getURI() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Get the original URI
getUrl() - Method in class org.utgenome.format.egt.Gene
 
getURL() - Method in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
getURL(Map<String, String>) - Method in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
getUrl() - Method in class org.utgenome.gwt.widget.client.ImageHandle
 
getURLQueryRequestParameters() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getUser() - Method in class org.utgenome.config.ConnectionInfo
 
getUserAgent() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.BooleanType.BooleanTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DoubleType.DoubleTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.FloatType.FloatTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.InputForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeListBox
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.PasswordType.PasswordTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeForm
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.StringType.StringTypeListBox
 
getUserInput() - Method in class org.utgenome.gwt.utgb.client.db.datatype.TextType.TextTypeForm
 
getUTGBConfig() - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getUTGBImageBundle() - Method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getValue(String) - Method in class org.utgenome.format.egt.EagyGeneLine
 
getValue() - Method in class org.utgenome.gwt.utgb.client.bean.track.Option
 
getValue(String) - Method in class org.utgenome.gwt.utgb.client.db.DynamicForm
 
getValue() - Method in class org.utgenome.gwt.utgb.client.db.Value
 
getValue() - Method in class org.utgenome.gwt.utgb.client.track.bean.Tag
 
getValue(String) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackConfigChangeImpl
 
getValue(String) - Method in interface org.utgenome.gwt.utgb.client.track.TrackConfigChange
 
getValue(String) - Method in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
getValueList() - Method in class org.utgenome.gwt.utgb.client.db.ValueDomain
 
getVariable(String) - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
getVersion() - Method in class org.utgenome.config.TrackConfiguration
 
getVersion() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getVersion() - Method in class org.utgenome.shell.POM
 
getVersion() - Static method in class org.utgenome.shell.UTGBShell
 
getViewEndOnGenome() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getViewStartOnGenome() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
getViewWindow() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
getViewWindow() - Method in class org.utgenome.gwt.utgb.client.canvas.TrackWindowChain
 
getWebAppDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getWebsite() - Method in class org.utgenome.gwt.utgb.client.bean.track.TrackDescription
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.DBSelectTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.debug.PropertyEditTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.debug.URLQueryArgumentTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.KeywordSearchTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBAddTrackTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBPropertyTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.RibbonRulerTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ScrollButtonTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ToolBoxTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackGenTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.ViewLoaderTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
getWidget() - Method in class org.utgenome.gwt.utgb.client.track.lib.WindowControlTrack
 
getWidget(PopupPanel) - Method in class org.utgenome.gwt.utgb.client.track.operation.MenuOperationItem
 
getWidget() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
getWidth() - Method in class org.utgenome.graphics.GenomeCanvas
 
getWidth() - Method in class org.utgenome.gwt.utgb.client.track.bean.TrackWindowBean
 
getWidth() - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
getWidth() - Method in class org.utgenome.gwt.utgb.server.app.TextLabel
 
getWidth() - Method in class org.utgenome.gwt.widget.client.ImageHandle
 
getWigData(int, int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigData(int, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigData(int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigDataList(int, String, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigDataList(String, int, int) - Method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigDataList(File, int, ChrLoc, GraphWindow) - Static method in class org.utgenome.format.wig.WIGDatabaseReader
 
getWigDataList(String, int, ChrLoc) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
getWigDataList(String, int, ChrLoc, AsyncCallback<List<WigGraphData>>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
getWigDataList(String, int, ChrLoc) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
getWIGPath() - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
getWindowBorderColor() - Static method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getWindowBorderColorDark() - Static method in class org.utgenome.gwt.widget.client.UTGBDesignFactory
 
getWorkDir() - Method in class org.utgenome.format.fasta.CompactFASTAGenerator
 
getWorkingDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getXOnCanvas(Event) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getXOnCanvas(int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getXPosOnWindow(long, int) - Method in class org.utgenome.graphics.ChromosomeWindow
 
getXPosOnWindow(long) - Method in class org.utgenome.graphics.GenomeCanvas
 
getXPosOnWindow(long, int) - Method in class org.utgenome.graphics.GenomeWindow
 
getYear() - Method in class org.utgenome.gwt.utgb.server.app.Hello
 
getYOffset() - Method in class org.utgenome.graphics.GeneCanvas.LocusLayout
 
getYOffset() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout
 
getYOnCanvas(int) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getYOnCanvas(Event) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
getYPosition(float) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
gff - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult
 
GFF3Entry - Class in org.utgenome.format.gff3
GFF3 entry
GFF3Entry() - Constructor for class org.utgenome.format.gff3.GFF3Entry
 
GFF3Reader - Class in org.utgenome.format.gff3
GFF3 Format has
GFF3Reader(Reader) - Constructor for class org.utgenome.format.gff3.GFF3Reader
 
globalOption - Variable in class org.utgenome.shell.UTGBShellCommandBase
 
GradationType - Class in org.utgenome.gwt.utgb.client.track.lib.old.datatype
 
GradationType(String, double, double, String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.datatype.GradationType
 
GraphData - Interface in org.utgenome.gwt.utgb.client.bio
A common interface for graph data
GraphicUtil - Class in org.utgenome.gwt.utgb.server.util.graphic
Utilities for manipulating Graphics in Java
GraphicUtil() - Constructor for class org.utgenome.gwt.utgb.server.util.graphic.GraphicUtil
 
GraphScale - Class in org.utgenome.gwt.utgb.client.canvas
Scale for graph data
GraphScale() - Constructor for class org.utgenome.gwt.utgb.client.canvas.GraphScale
 
GraphWindow - Enum in org.utgenome.gwt.utgb.client.bio
Windowing type for graph data
gridPanel - Variable in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
group - Variable in class org.utgenome.config.UTGBConfig
 
group - Variable in class org.utgenome.format.bed.BEDTrack
 
group - Variable in class org.utgenome.format.silk.read.Coordinate
 
group - Variable in class org.utgenome.gwt.ribbon.client.model.GenomeCoordinate
group name of this coordinate
group - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature
 
GROUP - Static variable in interface org.utgenome.gwt.utgb.client.track.UTGBProperty
 
groupProperties - Variable in class org.utgenome.config.OldViewXML.TrackGroup
 
GWT - Class in org.utgenome.shell
A sub command for creating a GWT interface
GWT() - Constructor for class org.utgenome.shell.GWT
 
GWTCompile - Class in org.utgenome.shell
 
GWTCompile() - Constructor for class org.utgenome.shell.GWTCompile
 
GWTGenomeCanvas - Class in org.utgenome.gwt.utgb.client.canvas
Browser-side graphic canvas for drawing gene objects
GWTGenomeCanvas() - Constructor for class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
GWTGenomeCanvas.CoverageStyle - Enum in org.utgenome.gwt.utgb.client.canvas
 
GWTGenomeCanvas.DragPoint - Class in org.utgenome.gwt.utgb.client.canvas
 
GWTGenomeCanvas.DragPoint(int, int) - Constructor for class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas.DragPoint
 
GWTGraphCanvas - Class in org.utgenome.gwt.utgb.client.canvas
GWT Canvas for drawing bar graph, heat map, etc.
GWTGraphCanvas() - Constructor for class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
GWTGraphCanvas.GraphStyle - Class in org.utgenome.gwt.utgb.client.canvas
Graph Drawing Configurations
GWTGraphCanvas.GraphStyle() - Constructor for class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
GWTGraphCanvas.Indent - Class in org.utgenome.gwt.utgb.client.canvas
 
GWTGraphCanvas.Indent(float, float, GWTGraphCanvas.GraphStyle) - Constructor for class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 

H

handle(int, Collection<T>) - Method in interface org.utgenome.format.sam.ReadSweeper.ReadSetHandler
 
handle(E) - Method in interface org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree.ResultHandler
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.ACGT
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.BEDViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.BSSReadView
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
handle(CSEGViewer.SEGData) - Method in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.DASDsn
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.DASViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.DotPlot
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.EchoBackView
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.example.UsingTemplate
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.FontMetric
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.FontPanel
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.GeneViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.Hello
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.KeywordSearch
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.LoadView
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.MethylViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.ReadView
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.RoundCircle
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.SAMViewer
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.ScaleBar
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.Sequence
 
handle(FASTADatabase.NSeq) - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.SnappyVersion
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.SQLiteAccessSample
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.TextLabel
 
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.app.Transparent
 
handle(HttpServletRequest, HttpServletResponse) - Method in interface org.utgenome.gwt.utgb.server.RequestHandler
Handles the HTTP request
handle(HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.RequestHandlerBase
 
handleException(Exception) - Method in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
handleException(Exception) - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
handleFailure(Throwable) - Method in class org.utgenome.gwt.utgb.client.util.Worker
 
handleSuccess() - Method in class org.utgenome.gwt.utgb.client.util.Worker
 
hasCacheCovering(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
hasCanvasSupport - Variable in class org.utgenome.gwt.utgb.client.bio.ReadQueryConfig
 
hasEnoughHeightForLabels() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
hashCode() - Method in class org.utgenome.format.fasta.Kmer
 
hashCode() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
hashCode() - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
hasNext() - Method in class org.utgenome.format.ObjectStreamReader
 
hasNext() - Method in class org.utgenome.format.sam.Sam2WigConverter.SAMRecordCursor
 
hasNext() - Method in class org.utgenome.format.sam.SAMReadIterator
 
hasNextWorker() - Method in class org.utgenome.gwt.utgb.client.util.WorkQueue
 
hasOverlap(long, long) - Method in class org.utgenome.graphics.GenomeWindow
 
hasOverlap(GenomeRange) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
hasProperties() - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
hasPropertyOf(String) - Method in class org.utgenome.config.UTGBConfig
 
hasSameScaleWith(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
hasSuffix() - Method in class org.utgenome.gwt.utgb.server.RequestURI
Has suffix in the action request? e.g., .xml, .json, etc.
HasTouchHandlers - Interface in org.utgenome.gwt.ipad.event
If something has all the touch handlers.
header - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult
 
height - Variable in class org.utgenome.config.OldViewXML.Track
 
height - Variable in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
height - Variable in class org.utgenome.gwt.utgb.client.track.TrackBase.TrackFrameConfig
 
height - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.Track
 
height - Variable in class org.utgenome.gwt.utgb.server.app.ACGT
 
height - Variable in class org.utgenome.gwt.utgb.server.app.FontPanel.FontInfo
 
height - Variable in class org.utgenome.gwt.utgb.server.app.ScaleBar
 
Hello - Class in org.utgenome.gwt.utgb.server.app
Request handler that simply returns hello + name
Hello() - Constructor for class org.utgenome.gwt.utgb.server.app.Hello
 
HelloServlet - Class in org.utgenome.gwt.utgb.server
 
HelloServlet() - Constructor for class org.utgenome.gwt.utgb.server.HelloServlet
 
HexDigit - Static variable in class org.utgenome.format.bed.BEDLexer
 
HexDigit - Static variable in class org.utgenome.format.bed.BEDParser
 
HexDigit - Static variable in class org.utgenome.format.wig.WIGLexer
 
HexDigit - Static variable in class org.utgenome.format.wig.WIGParser
 
hexValue2Color(String, float) - Method in class org.utgenome.graphics.GeneCanvas
 
HiddenParameter - Class in org.utgenome.gwt.utgb.client.bean.track
Hidden parameter in the track
HiddenParameter() - Constructor for class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
hideHorizontalScrollBar(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
hideLoadingMessage() - Static method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
hideVerticalScrollBar(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
highlightImproperMate() - Static method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
HorizontalBorder - Class in org.utgenome.gwt.widget.client
Horizontal Border for FrameBorder
HorizontalBorder(int, int, int, String) - Constructor for class org.utgenome.gwt.widget.client.HorizontalBorder
 
HorizontalTrackFrame - Class in org.utgenome.gwt.widget.client
Track panel that has the horizontal layout.
HorizontalTrackFrame() - Constructor for class org.utgenome.gwt.widget.client.HorizontalTrackFrame
 
href - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group.Link
 
href - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASGFF
 
href - Variable in class org.utgenome.gwt.utgb.server.app.DASDsn.DSN
 
HTMLContentFilter - Class in org.utgenome.gwt.utgb.server.util.xml
Removes illegal characters that cannot be used as XML text contents into entity references.
HTMLContentFilter() - Constructor for class org.utgenome.gwt.utgb.server.util.xml.HTMLContentFilter
 
htmlUrl - Variable in class org.utgenome.format.bed.BEDTrack
 

I

Icon - Class in org.utgenome.gwt.utgb.client.ui
 
Icon(IconImage) - Constructor for class org.utgenome.gwt.utgb.client.ui.Icon
 
Icon - Class in org.utgenome.gwt.widget.client
Icon image which flips on mouse over events
Icon(Image, Image) - Constructor for class org.utgenome.gwt.widget.client.Icon
 
ICON_CLOSE - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_CONFIG - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_HIDE - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_PACK - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_SHOW - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_UNKNOWN - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ICON_UNPACK - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
IconImage - Class in org.utgenome.gwt.utgb.client.ui
IconImage image URL holder
IconImage(String, String) - Constructor for class org.utgenome.gwt.utgb.client.ui.IconImage
 
iconSet - Variable in class org.utgenome.gwt.widget.client.impl.TrackPanelBase
 
IconSetPanel - Class in org.utgenome.gwt.widget.client.impl
Icon set
IconSetPanel(TrackFrame) - Constructor for class org.utgenome.gwt.widget.client.impl.IconSetPanel
 
id - Variable in class org.utgenome.config.UTGBConfig.Database
 
id - Variable in class org.utgenome.format.FileBlock
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.FeatureType
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Method
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Target
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.Segment
 
id - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
id - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.TrackGroup
ID of this track group
id - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer.SEGData
 
id - Variable in class org.utgenome.gwt.utgb.server.app.DASDsn.DSNSource
 
id - Variable in class org.utgenome.util.repeat.RepeatChainFinder.IntervalCluster
 
identifier() - Method in class org.utgenome.gwt.ipad.event.Touch
 
identity - Variable in class org.utgenome.gwt.utgb.client.bio.BlastResult
 
Illumina2Fastq - Class in org.utgenome.shell
 
Illumina2Fastq() - Constructor for class org.utgenome.shell.Illumina2Fastq
 
IMAGE_DELETE_BUTTON - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
IMAGE_NOT_AVAILABLE - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
IMAGE_NOW_LOADING - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
IMAGE_RULER_TICK - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
IMAGE_TRANSPARENT - Static variable in class org.utgenome.gwt.utgb.client.track.Design
 
ImageHandle - Class in org.utgenome.gwt.widget.client
If I say an image element is a JavascriptObject...
ImageHandle() - Constructor for class org.utgenome.gwt.widget.client.ImageHandle
 
ImageLoader - Class in org.utgenome.gwt.widget.client
Provides a mechanism for deferred execution of a callback method once all specified Images are loaded.
ImageLoader.CallBack - Interface in org.utgenome.gwt.widget.client
Interface to allow anonymous instantiation of a CallBack Object with method that gets invoked when all the images are loaded.
Import - Class in org.utgenome.shell
import command
Import() - Constructor for class org.utgenome.shell.Import
 
Import.FileType - Enum in org.utgenome.shell
 
ImportBustard - Class in org.utgenome.core.cui
 
ImportBustard() - Constructor for class org.utgenome.core.cui.ImportBustard
 
importFromBAM(String, InputStream) - Method in class org.utgenome.format.keyword.KeywordDB
 
importFromBED(String, Reader) - Method in class org.utgenome.format.keyword.KeywordDB
 
importFromFASTAIndex(String, Reader) - Method in class org.utgenome.format.keyword.KeywordDB
 
importFromTAB(String, Reader) - Method in class org.utgenome.format.keyword.KeywordDB
 
importKeywordAliasFile(Reader) - Method in class org.utgenome.format.keyword.KeywordDB
 
ImportStmt - Class in org.utgenome.config
This is the import statement in the track-config.xml, which is used to load a UTGB action package from the class loader.
ImportStmt() - Constructor for class org.utgenome.config.ImportStmt
 
inactiveImageURL - Variable in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
indelLength - Variable in class org.utgenome.util.sv.GeneticVariation
 
indexFileName - Variable in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
info(String) - Method in class org.utgenome.gwt.utgb.client.ui.Message
 
INFOPANEL_WIDTH - Static variable in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
InfoSilkGenerator - Class in org.utgenome.gwt.utgb.client.bio
Generating read information in Silk format, which is used for displaying mouse over message
InfoSilkGenerator() - Constructor for class org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
 
init(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
init() - Method in class org.utgenome.gwt.utgb.client.ui.SVGPanel
 
init() - Method in class org.utgenome.gwt.utgb.server.app.CSEGViewer.GraphicalOutput
 
init() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.JSONOutput
 
init() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
init() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.XMLOutput
 
init(FilterConfig) - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
initDB() - Method in class org.utgenome.format.keyword.KeywordDB
 
initialize() - Static method in class org.utgenome.gwt.utgb.client.track.TrackFactorySetup
 
initRequestMap() - Method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
initServices() - Static method in class org.utgenome.gwt.utgb.client.RPCServiceManager
 
inputCSEGFile - Variable in class org.utgenome.format.cseg.CSEGDatabase.Config
 
inputFASTAFile - Variable in class org.utgenome.format.fasta.FASTADatabase.Config
 
InputForm - Class in org.utgenome.gwt.utgb.client.db.datatype
InputForm is an interface of input forms of various data types.
InputForm() - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.InputForm
 
insert(int, String) - Method in class org.utgenome.format.fasta.Kmer
 
insert(E, int, int) - Method in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree
Insert a new node
insert(Widget, Widget, int) - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
Add the widge with the specified drag handle before the location beforeIndex
insert(Widget, Widget, int) - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
Add the widge with the specified drag handle before the location beforeIndex
insertRow(Object[], int) - Method in class org.utgenome.gwt.utgb.client.ui.EditableTable
 
insertTrack(Track, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Insert a new track before the specified index
Int - Static variable in class org.utgenome.format.bed.BEDLexer
 
Int - Static variable in class org.utgenome.format.bed.BEDParser
 
Int - Static variable in class org.utgenome.format.wig.WIGLexer
 
Int - Static variable in class org.utgenome.format.wig.WIGParser
 
Integer - Static variable in class org.utgenome.format.bed.BEDLexer
 
Integer - Static variable in class org.utgenome.format.bed.BEDParser
 
Integer - Static variable in class org.utgenome.format.wig.WIGLexer
 
Integer - Static variable in class org.utgenome.format.wig.WIGParser
 
IntegerType - Class in org.utgenome.gwt.utgb.client.db.datatype
 
IntegerType(String) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.IntegerType
 
IntegerType(String, ValueDomain) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.IntegerType
 
IntegerType(String, boolean, boolean) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.IntegerType
 
IntegerType.IntegerTypeForm - Class in org.utgenome.gwt.utgb.client.db.datatype
 
IntegerType.IntegerTypeForm() - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeForm
 
IntegerType.IntegerTypeListBox - Class in org.utgenome.gwt.utgb.client.db.datatype
 
IntegerType.IntegerTypeListBox(ValueDomain) - Constructor for class org.utgenome.gwt.utgb.client.db.datatype.IntegerType.IntegerTypeListBox
 
interpolate(double) - Method in class org.utgenome.gwt.utgb.client.ui.Animation
Interpolate the linear progress into a more natural easing function.
intersect(Interval) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
Return the intersected interval with the other
intersectsWith(Interval) - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
Interval - Class in org.utgenome.gwt.utgb.client.bio
An interval in a genome sequence.
Interval() - Constructor for class org.utgenome.gwt.utgb.client.bio.Interval
 
Interval(int, int) - Constructor for class org.utgenome.gwt.utgb.client.bio.Interval
 
Interval(Interval) - Constructor for class org.utgenome.gwt.utgb.client.bio.Interval
 
IntervalLayout - Class in org.utgenome.gwt.utgb.client.canvas
On-genome data layout
IntervalLayout() - Constructor for class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
IntervalLayout.IntervalRetriever - Class in org.utgenome.gwt.utgb.client.canvas
Retrieves the interval (x1, x2) and the height of OnGenome objects
IntervalLayout.IntervalRetriever() - Constructor for class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
IntervalLayout.LocusLayout - Class in org.utgenome.gwt.utgb.client.canvas
 
IntervalLayout.LocusLayout(GenomeRange, int) - Constructor for class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout
 
IntervalLayout.LocusLayout(GenomeRange, int, int) - Constructor for class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout
 
IntervalTree<T extends GenomeRange> - Class in org.utgenome.gwt.utgb.client.canvas
Interval layout
IntervalTree() - Constructor for class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
intStartSeq - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
isAdjustable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isAdjustable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
isAntiSense() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
isAntiSense() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isAutoAdjust() - Method in class org.utgenome.gwt.utgb.client.bean.track.Frame
 
isC2T() - Method in class org.utgenome.gwt.utgb.client.canvas.SAMCanvas
 
isCanvasSupported() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
isClosable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isClosable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isConfigurable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isConfigurable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isDefined - Variable in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever
 
isDefined() - Method in class org.utgenome.gwt.utgb.client.util.Optional
 
isDescendant(String) - Static method in class org.utgenome.gwt.utgb.server.app.ReadView
 
isEmpty() - Method in class org.utgenome.gwt.utgb.client.bio.GenomeRangeDataSet
 
isEmpty() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
isFile - Variable in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
isFile() - Method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
isFirstRead(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isFirstRead() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isFolder() - Method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
isForward() - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
isGoogleGearsInstalled() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
isGWTHostedMode() - Static method in class org.utgenome.gwt.utgb.server.RequestDispatcher
 
isHorizontallyResizable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isHorizontallyResizable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isIE() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
isInitialized() - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
isInitialized() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
isInLowerRightRegion() - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
isInProjectRoot() - Method in class org.utgenome.shell.UTGBShellCommand
 
isInstanciated() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry.TabEntryFactory
 
iSize - Variable in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isLighter() - Method in class org.utgenome.graphics.ChromosomeMapCanvas
 
isLoaded() - Method in class org.utgenome.gwt.widget.client.ImageHandle
 
isLoading() - Method in class org.utgenome.gwt.widget.client.NowLoadingIcon
 
isMappedInProperPair(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isMappedInProperPair() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isMate(SAMRead) - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
isMate(SAMReadLight) - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isMateForwardStrand(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isMateUnmapped(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isMinimizable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isMinimizable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isMinimized() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrameState
 
isMobileSafari() - Static method in class org.utgenome.gwt.utgb.client.util.BrowserInfo
 
isNotNull() - Method in interface org.utgenome.gwt.utgb.client.db.datatype.DataType
 
isNotNull - Variable in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
isNotNull() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
isPacked() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
isPacked() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrameState
 
isPairedRead(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isPairedRead() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isPlusStrand() - Method in class org.utgenome.gwt.utgb.client.bio.Alignment
 
isPositiveStrand() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
isPrimaryKey() - Method in interface org.utgenome.gwt.utgb.client.db.datatype.DataType
 
isPrimaryKey - Variable in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
isPrimaryKey() - Method in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
isQueryForwardStrand(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isQueryUnmapped(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isRequired() - Method in class org.utgenome.gwt.utgb.client.bean.track.HiddenParameter
 
isRequired() - Method in class org.utgenome.gwt.utgb.client.bean.track.Parameter
 
isReverseStrand() - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
isReverseStrand() - Method in class org.utgenome.gwt.utgb.server.app.Sequence.SequenceRetrieverBase
 
isReverseYAxis() - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
isSecondRead(int) - Static method in class org.utgenome.gwt.utgb.client.bio.SAMReadFlag
 
isSecondRead() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
isSense() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.Read
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
isSense() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isStopCodon() - Method in enum org.utgenome.gwt.utgb.client.bio.AminoAcid
 
isTrack() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
isTrack() - Method in interface org.utgenome.gwt.utgb.client.track.TrackEntry
Test whether this entry is Track or not.
isTrack() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
isTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
isTrackGroup() - Method in interface org.utgenome.gwt.utgb.client.track.TrackEntry
Test whether this entry is TrackGroup or not
isTrackGroup() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
isUndefined() - Method in class org.utgenome.gwt.utgb.client.util.Optional
 
isUnmapped() - Method in class org.utgenome.gwt.utgb.client.bio.SAMReadLight
 
isUseGUI() - Method in class org.utgenome.shell.UTGBPortableConfig
 
isVerbose() - Method in class org.utgenome.shell.UTGBPortableConfig
 
isVerticallyResizable() - Method in interface org.utgenome.gwt.utgb.client.ui.Frame
 
isVerticallyResizable() - Method in class org.utgenome.gwt.utgb.client.ui.TrackFrame
 
isVisible - Variable in class org.utgenome.gwt.ribbon.client.model.Ribbon.RibbonSegment
true if this segment is visible to the user, otherwise false
isVisible(int) - Method in class org.utgenome.gwt.widget.client.HorizontalTrackFrame
Checks the visibility of the button
isWidgetReady - Variable in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
isWidgetReady - Variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
italic(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
item(int) - Method in class org.utgenome.gwt.utgb.client.util.xml.NodeListImpl
 
itemRgb - Variable in class org.utgenome.format.bed.BEDTrack
 
iterator() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalTree
 
iterator() - Method in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree
 
iterator() - Method in class org.utgenome.gwt.utgb.client.ui.DraggableTable
 
iterator() - Method in class org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel
 
IUPAC - Enum in org.utgenome.gwt.utgb.client.bio
IUPAC: allele variation notation

J

javaPackage - Variable in class org.utgenome.config.UTGBConfig
 
javaPackage - Variable in class org.utgenome.config.UTGBConfig.WebAction
 
jdbcPrefix - Variable in class org.utgenome.config.UTGBConfig.Database
 
JDBCService - Class in org.utgenome.gwt.utgb.server
A support class for acquiring JDBC connections.
JDBCService() - Constructor for class org.utgenome.gwt.utgb.server.JDBCService
 
JDBCService.GenericDBAccess - Class in org.utgenome.gwt.utgb.server
 
JDBCService.GenericDBAccess(UTGBConfig.Database) - Constructor for class org.utgenome.gwt.utgb.server.JDBCService.GenericDBAccess
 
JDBCService.HSQLDBAccess - Class in org.utgenome.gwt.utgb.server
 
JDBCService.HSQLDBAccess() - Constructor for class org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess
open memory database
JDBCService.HSQLDBAccess(String) - Constructor for class org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess
 
JDBCService.HSQLDBAccess(String, String, String) - Constructor for class org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess
 
join(String[], String[]) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
join(String[], String) - Static method in class org.utgenome.gwt.utgb.client.util.StringUtil
Join the given element list with the specified separator
join(List<String>, String) - Static method in class org.utgenome.gwt.utgb.client.util.StringUtil
 
join(String[], String) - Static method in class org.utgenome.gwt.widget.client.StringUtil
Join the given element list with the specified separator
join(List, String) - Static method in class org.utgenome.gwt.widget.client.StringUtil
 
joinIterable(Iterable<String>, String) - Static method in class org.utgenome.gwt.utgb.client.util.StringUtil
 
joinWithWS(String[]) - Static method in class org.utgenome.gwt.utgb.client.util.StringUtil
 
joinWithWS(String[]) - Static method in class org.utgenome.gwt.widget.client.StringUtil
 
JSONUtil - Class in org.utgenome.gwt.utgb.client.util
 

K

keepSpaceForLabels() - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
key - Variable in class org.utgenome.config.OldViewXML.Prop
 
key - Variable in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameParameterSetCommand
 
keySet() - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
 
keySet() - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupProperty
 
keySet() - Method in class org.utgenome.gwt.utgb.client.util.TableData
key set of Integer
keyword - Variable in class org.utgenome.format.keyword.GenomeKeywordEntry.KeywordAlias
 
Keyword - Class in org.utgenome.shell
keyword DB management tool
Keyword() - Constructor for class org.utgenome.shell.Keyword
 
Keyword.SubCommand - Enum in org.utgenome.shell
 
KeywordAliasReader - Class in org.utgenome.format.keyword
keyword alias file is a tab-delimited file, each line of which has a keyword and its aliases.
KeywordAliasReader(String) - Constructor for class org.utgenome.format.keyword.KeywordAliasReader
 
KeywordAliasReader(Reader) - Constructor for class org.utgenome.format.keyword.KeywordAliasReader
 
KeywordDB - Class in org.utgenome.format.keyword
Keyword database generator/query interface
KeywordDB(File) - Constructor for class org.utgenome.format.keyword.KeywordDB
 
KeywordDB(String) - Constructor for class org.utgenome.format.keyword.KeywordDB
 
KeywordDB(SQLiteAccess) - Constructor for class org.utgenome.format.keyword.KeywordDB
 
keywordSearch(String, String, String, int, int) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
keywordSearch(String, String, String, int, int, AsyncCallback<KeywordSearchResult>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
KeywordSearch - Class in org.utgenome.gwt.utgb.server.app
Web action: KeywordSearch
KeywordSearch() - Constructor for class org.utgenome.gwt.utgb.server.app.KeywordSearch
 
keywordSearch(String, String, String, int, int) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
KeywordSearchResult - Class in org.utgenome.gwt.utgb.client.bio
keyword search result
KeywordSearchResult() - Constructor for class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult
 
KeywordSearchResult.Entry - Class in org.utgenome.gwt.utgb.client.bio
 
KeywordSearchResult.Entry() - Constructor for class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
KeywordSearchTrack - Class in org.utgenome.gwt.utgb.client.track.lib
Keyword Search using utgb-keyword service
KeywordSearchTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.KeywordSearchTrack
 
Kmer - Class in org.utgenome.format.fasta
K-mer integer representation of ACGT.
Kmer(Kmer) - Constructor for class org.utgenome.format.fasta.Kmer
 
Kmer(CompactACGT) - Constructor for class org.utgenome.format.fasta.Kmer
 
Kmer(String) - Constructor for class org.utgenome.format.fasta.Kmer
 
KmerIntegerFactory - Class in org.utgenome.util.kmer
Generator of the bit-integer representation of a k-mer sequence
KmerIntegerFactory(int) - Constructor for class org.utgenome.util.kmer.KmerIntegerFactory
 
kmerIntToAminoAcidTable - Static variable in class org.utgenome.gwt.utgb.client.bio.CodonTable
3mer integer (2bit encoding) to amino acid

L

label - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group
 
label - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature
 
LABEL_ROW - Static variable in class org.utgenome.gwt.utgb.client.db.DatabaseTable
 
Layer - Class in org.utgenome.gwt.utgb.client.bean.track
Layer descriptor of the track
Layer() - Constructor for class org.utgenome.gwt.utgb.client.bean.track.Layer
 
layout - Variable in class org.utgenome.gwt.utgb.client.bio.ReadQueryConfig
 
layout - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
layout(Panel) - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
layout() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreeView
 
layout - Variable in class org.utgenome.gwt.utgb.server.app.ReadView
 
layoutFrame - Variable in class org.utgenome.gwt.utgb.client.ui.WindowTitleBar
 
layoutPanel - Variable in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
layoutPanel - Variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
leaf() - Method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
leaf(String) - Static method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
left - Variable in class org.utgenome.gwt.utgb.client.canvas.PrioritySearchTree.Node
 
LEFT - Static variable in class org.utgenome.gwt.utgb.client.ui.Border
 
LEFT - Static variable in class org.utgenome.gwt.widget.client.HorizontalBorder
 
LEFT - Static variable in class org.utgenome.gwt.widget.client.Style
 
leftCorner - Variable in class org.utgenome.gwt.utgb.client.ui.WindowTitleBar
 
leftMargin - Variable in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
LegacyTrackInformation - Class in org.utgenome.gwt.utgb.client.track.bean
 
LegacyTrackInformation() - Constructor for class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation
 
length() - Method in class org.utgenome.format.fasta.CompactACGT
 
length - Variable in class org.utgenome.format.fasta.CompactFASTAIndex
sequence length
length() - Method in class org.utgenome.format.fasta.FASTA.RawStringWrapper
 
length() - Method in interface org.utgenome.format.fasta.GenomeSequence
 
length() - Method in class org.utgenome.format.fasta.Kmer
 
length - Variable in class org.utgenome.gwt.ribbon.client.model.Ribbon.RibbonSegment
the length of this ribbon segment
length() - Method in class org.utgenome.gwt.utgb.client.bio.ChrLoc
 
length - Variable in class org.utgenome.gwt.utgb.client.bio.CIGAR.Element
 
length() - Method in class org.utgenome.gwt.utgb.client.bio.CompactWIGData
 
length() - Method in interface org.utgenome.gwt.utgb.client.bio.GenomeRange
return the length of the data
length() - Method in class org.utgenome.gwt.utgb.client.bio.Interval
 
length - Variable in class org.utgenome.gwt.utgb.client.ribbon.Ribbon.Crease
 
length - Variable in class org.utgenome.util.repeat.RepeatChainFinder.IntervalCluster
 
lens(List<String>) - Static method in class org.utgenome.format.axt.AXTLens
 
lens(BufferedReader) - Static method in class org.utgenome.format.axt.AXTLens
 
lens(BufferedReader, ObjectHandler<AXTAlignment>) - Static method in class org.utgenome.format.axt.AXTLens
 
lens(File, ObjectHandler<AXTAlignment>) - Static method in class org.utgenome.format.axt.AXTLens
 
lines - Variable in class org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
 
LINETO - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
link - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group
 
LinkOperation - Class in org.utgenome.gwt.utgb.client.track.operation
 
LinkOperation(Node) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.LinkOperation
 
load(Reader) - Method in class org.utgenome.format.egt.EGTXMLReader
 
load(URL) - Static method in class org.utgenome.format.fasta.CompactFASTAIndex
 
load(Reader) - Static method in class org.utgenome.format.fasta.CompactFASTAIndex
 
load(TrackConfig) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
Load the parameter values from the configuration panel
load(String) - Method in class org.utgenome.gwt.utgb.client.db.DatabaseCatalog
parsing the given JSONData representing database schema
loadActionPackage(ClassLoader, String, String) - Static method in class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
loadConfig(TrackConfig) - Method in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
loadImages(String[], ImageLoader.CallBack) - Static method in class org.utgenome.gwt.widget.client.ImageLoader
Takes in an array of url Strings corresponding to the images needed to be loaded.
loadingDone() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
loadIntoMemory(String) - Static method in class org.utgenome.format.fasta.CompactFASTA
 
loadJSON(Reader, Class<T>, ObjectHandler<T>) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
Load JSON data from the stream and convert the JSON data into Object of the given resultClass.
loadJSON(Reader, Class<T>) - Method in class org.utgenome.gwt.utgb.server.WebTrackBase
load the json data, and converts them into a list of result class instances
loadUTGBConfig() - Static method in class org.utgenome.gwt.utgb.server.UTGBMaster
 
loadUTGBConfig() - Method in class org.utgenome.shell.UTGBShellCommand
 
loadView(TrackView.Track) - Method in interface org.utgenome.gwt.utgb.client.track.Track
load the track parameters from the view definition
loadView(TrackView.Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
loadView(String) - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
load the view XML file from the public/view folder.
LoadView - Class in org.utgenome.gwt.utgb.server.app
Get the view data from the user's file via POST request, and return the data by embedding it in an HTML.
LoadView() - Constructor for class org.utgenome.gwt.utgb.server.app.LoadView
 
location - Variable in class org.utgenome.gwt.utgb.client.bio.GenomeRangeDataSet
 
LocusClickHandler - Interface in org.utgenome.gwt.utgb.client.canvas
 
logBase - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
logScale - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
LOWER - Static variable in class org.utgenome.gwt.utgb.client.ui.Border
 
LOWER - Static variable in class org.utgenome.gwt.widget.client.HorizontalBorder
 
LowerBoundType - Class in org.utgenome.gwt.utgb.client.track.lib.old.datatype
 
LowerBoundType(String, double, double) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.datatype.LowerBoundType
 

M

main(String[]) - Static method in class org.utgenome.core.cui.DrawHistogram
 
main(String[]) - Static method in class org.utgenome.format.cseg.CSEGDatabase
 
main(String[]) - Static method in class org.utgenome.format.egt.EGTXMLReader
 
main(String[]) - Static method in class org.utgenome.format.fasta.FASTADatabase
 
main(String[]) - Static method in class org.utgenome.format.legacy.OldDescriptionXMLReader
 
main() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
main(String[]) - Static method in class org.utgenome.gwt.utgb.TrackLoaderGenerator
 
main(String[]) - Static method in class org.utgenome.shell.tomcat.TomcatServer
entry point for running Tomcat from CUI
main(String[]) - Static method in class org.utgenome.shell.UTGBPortable
entry point of the UTGBServer
main(String[]) - Static method in class org.utgenome.shell.UTGBPortableWidget
 
main(String[]) - Static method in class org.utgenome.shell.UTGBShell
Run UTGB Shell command.
main(String[]) - Static method in class org.utgenome.util.repeat.RepeatChainFinder
 
main(String[]) - Static method in class org.utgenome.util.sv.VariationAnnotator
 
map(Reader, ObjectStreamHandler) - Method in interface org.utgenome.format.ObjectStreamReader.TextFormatToObjectMapper
 
map(RequestURI, HttpServletRequest, HttpServletResponse) - Method in class org.utgenome.gwt.utgb.server.DefaultRequestMap
 
map(RequestURI, HttpServletRequest, HttpServletResponse) - Method in interface org.utgenome.gwt.utgb.server.RequestMap
 
mapMaster - Variable in class org.utgenome.gwt.utgb.server.app.DASDsn.DSN
 
mapq - Variable in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
margin(Widget, int) - Static method in class org.utgenome.gwt.widget.client.Style
 
margin(Widget, int, int) - Static method in class org.utgenome.gwt.widget.client.Style
 
mark(int) - Method in class org.utgenome.util.ReaderInputStream
Marks the read limit of the StringReader.
markSupported() - Method in class org.utgenome.util.ReaderInputStream
 
mask(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
matchLength - Variable in class org.utgenome.format.blast.Blast2Silk.BlastResult.BlastAlignment
 
matchLength - Variable in class org.utgenome.gwt.utgb.client.bio.BlastResult
 
mateIsMappedToTheSameChr() - Method in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
mateStart - Variable in class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
 
Maven - Class in org.utgenome.shell
Maven utility
Maven() - Constructor for class org.utgenome.shell.Maven
 
maven(String) - Method in class org.utgenome.shell.UTGBShellCommand
 
maven(String, Properties) - Method in class org.utgenome.shell.UTGBShellCommand
 
Maven.CommandExecutor - Class in org.utgenome.shell
 
Maven.CommandExecutor() - Constructor for class org.utgenome.shell.Maven.CommandExecutor
 
max - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
maxDepth(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.canvas.IntervalLayout
 
maxHeight - Variable in class org.utgenome.gwt.utgb.client.bio.ReadCoverage
 
maxLength - Variable in class org.utgenome.gwt.utgb.client.bio.ChrRange
 
maxLength() - Method in class org.utgenome.util.repeat.RepeatChainFinder.Interval2D
 
maxmumNumberOfReadsToDisplay - Variable in class org.utgenome.gwt.utgb.client.bio.ReadQueryConfig
 
maxPage - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult
 
maxValue - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
mDigit() - Method in class org.utgenome.format.bed.BEDLexer
 
mDigit() - Method in class org.utgenome.format.wig.WIGLexer
 
mDot() - Method in class org.utgenome.format.bed.BEDLexer
 
mDot() - Method in class org.utgenome.format.wig.WIGLexer
 
mDouble() - Method in class org.utgenome.format.bed.BEDLexer
 
mDouble() - Method in class org.utgenome.format.wig.WIGLexer
 
MenuOperation - Class in org.utgenome.gwt.utgb.client.track.operation
 
MenuOperation(Node) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.MenuOperation
 
MenuOperation(String) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.MenuOperation
 
MenuOperationItem - Class in org.utgenome.gwt.utgb.client.track.operation
 
MenuOperationItem(Node) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.MenuOperationItem
 
MenuOperationItem(String) - Constructor for class org.utgenome.gwt.utgb.client.track.operation.MenuOperationItem
 
mEq() - Method in class org.utgenome.format.bed.BEDLexer
 
mEq() - Method in class org.utgenome.format.wig.WIGLexer
 
mEscapeSequence() - Method in class org.utgenome.format.bed.BEDLexer
 
mEscapeSequence() - Method in class org.utgenome.format.wig.WIGLexer
 
Message - Class in org.utgenome.gwt.utgb.client.ui
for message
Message() - Constructor for class org.utgenome.gwt.utgb.client.ui.Message
 
Message(String) - Constructor for class org.utgenome.gwt.utgb.client.ui.Message
 
Message(MessageType, String) - Constructor for class org.utgenome.gwt.utgb.client.ui.Message
 
MessageType - Enum in org.utgenome.gwt.utgb.client.ui
Information
method - Variable in class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature
 
MethylViewer - Class in org.utgenome.gwt.utgb.server.app
Request handler
MethylViewer() - Constructor for class org.utgenome.gwt.utgb.server.app.MethylViewer
 
MethylViewer.MethlEntry - Class in org.utgenome.gwt.utgb.server.app
 
MethylViewer.MethlEntry() - Constructor for class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
 
mExp() - Method in class org.utgenome.format.bed.BEDLexer
 
mExp() - Method in class org.utgenome.format.wig.WIGLexer
 
mFrac() - Method in class org.utgenome.format.bed.BEDLexer
 
mFrac() - Method in class org.utgenome.format.wig.WIGLexer
 
mHexDigit() - Method in class org.utgenome.format.bed.BEDLexer
 
mHexDigit() - Method in class org.utgenome.format.wig.WIGLexer
 
min - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
minHeight - Variable in class org.utgenome.gwt.utgb.client.bio.ReadCoverage
 
MiniBrowserTrack - Class in org.utgenome.gwt.utgb.client.track.lib
Track for embedding HTML page via iframe tag.
MiniBrowserTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
minimize() - Method in class org.utgenome.gwt.utgb.client.track.TrackFrame
 
MINIMUM_WINDOW_SIZE - Static variable in class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
minReadHeight - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
mInt() - Method in class org.utgenome.format.bed.BEDLexer
 
mInt() - Method in class org.utgenome.format.wig.WIGLexer
 
mInteger() - Method in class org.utgenome.format.bed.BEDLexer
 
mInteger() - Method in class org.utgenome.format.wig.WIGLexer
 
minValue - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle
 
mkdirs(File) - Static method in class org.utgenome.shell.Create
Create directories including its parent folders if not exist
mkdirs(File) - Static method in class org.utgenome.shell.ScaffoldGenerator
Create directories including its parent folders if not exist
mNumber() - Method in class org.utgenome.format.bed.BEDLexer
 
mNumber() - Method in class org.utgenome.format.wig.WIGLexer
 
MouseClickEventImpl - Class in org.utgenome.gwt.utgb.client.track.operation
 
MouseClickEventImpl() - Constructor for class org.utgenome.gwt.utgb.client.track.operation.MouseClickEventImpl
 
MouseMoveListener - Class in org.utgenome.gwt.utgb.client.ui
 
MouseMoveListener(PopupPanel) - Constructor for class org.utgenome.gwt.utgb.client.ui.MouseMoveListener
 
move() - Method in class org.utgenome.gwt.ribbon.client.ui.WeaverCanvas
 
MOVETO - Static variable in class org.utgenome.gwt.widget.client.impl.PathElement
 
mQName() - Method in class org.utgenome.format.bed.BEDLexer
 
mQName() - Method in class org.utgenome.format.wig.WIGLexer
 
mrnm - Variable in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
mStart - Variable in class org.utgenome.gwt.utgb.client.bio.SAMRead
 
mString() - Method in class org.utgenome.format.bed.BEDLexer
 
mString() - Method in class org.utgenome.format.wig.WIGLexer
 
mStringChar() - Method in class org.utgenome.format.bed.BEDLexer
 
mStringChar() - Method in class org.utgenome.format.wig.WIGLexer
 
mStringChars() - Method in class org.utgenome.format.bed.BEDLexer
 
mStringChars() - Method in class org.utgenome.format.wig.WIGLexer
 
mTokens() - Method in class org.utgenome.format.bed.BEDLexer
 
mTokens() - Method in class org.utgenome.format.wig.WIGLexer
 
mUnicodeChar() - Method in class org.utgenome.format.bed.BEDLexer
 
mUnicodeChar() - Method in class org.utgenome.format.wig.WIGLexer
 
mutationPosition - Variable in class org.utgenome.util.sv.EnhancedGeneticVariation
 
mWhiteSpace() - Method in class org.utgenome.format.bed.BEDLexer
 
mWhiteSpace() - Method in class org.utgenome.format.wig.WIGLexer
 

N

name - Variable in class org.utgenome.config.OldViewXML.Track
 
name() - Method in class org.utgenome.core.cui.Convert
 
name() - Method in class org.utgenome.core.cui.DrawHistogram
 
name() - Method in class org.utgenome.core.cui.ImportBustard
 
name() - Method in class org.utgenome.core.cui.ReadStat
 
name() - Method in class org.utgenome.core.cui.SAM2Silk
 
name() - Method in class org.utgenome.core.cui.ScreenShot
 
name() - Method in class org.utgenome.core.cui.Snappy
 
name() - Method in class org.utgenome.core.cui.UTGBCommandBase
 
Name - Static variable in class org.utgenome.format.bed.BEDLexer
 
Name - Static variable in class org.utgenome.format.bed.BEDParser
 
name - Variable in class org.utgenome.format.bed.BEDTrack
 
name - Variable in class org.utgenome.format.fasta.CompactFASTAIndex
sequence name (e.g., chr1, scaffold2)
name - Variable in class org.utgenome.format.silk.read.Read
 
name - Variable in class org.utgenome.format.silk.read.Reference
 
Name - Static variable in class org.utgenome.format.wig.WIGLexer
 
Name - Static variable in class org.utgenome.format.wig.WIGParser
 
name - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
name - Variable in class org.utgenome.gwt.utgb.client.bio.ReferenceSequence
 
name - Variable in class org.utgenome.gwt.utgb.client.db.datatype.DataTypeBase
 
name - Variable in class org.utgenome.gwt.utgb.client.view.TrackDisplay.Track
 
name - Variable in class org.utgenome.gwt.utgb.client.view.TrackView.Track
 
name - Variable in class org.utgenome.gwt.utgb.server.app.BEDViewer
 
name - Variable in class org.utgenome.gwt.utgb.server.app.BSSReadView
 
name - Variable in class org.utgenome.gwt.utgb.server.app.ChromosomeMap
 
name - Variable in class org.utgenome.gwt.utgb.server.app.CSEGViewer
 
name - Variable in class org.utgenome.gwt.utgb.server.app.DASViewer
 
name - Variable in class org.utgenome.gwt.utgb.server.app.example.UsingTemplate
Use dbGroup, dbName parameters to specify database contents to be accessed
name - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer
 
name - Variable in class org.utgenome.gwt.utgb.server.app.SAMViewer
 
name - Variable in class org.utgenome.gwt.utgb.server.app.Sequence
 
name() - Method in class org.utgenome.shell.AddAction
 
name() - Method in class org.utgenome.shell.Clean
 
name() - Method in class org.utgenome.shell.Compile
 
name() - Method in class org.utgenome.shell.Create
 
name() - Method in class org.utgenome.shell.Deploy
 
name() - Method in class org.utgenome.shell.Eclipse
 
name() - Method in class org.utgenome.shell.FastqRename
 
name() - Method in class org.utgenome.shell.FastqToFasta
 
name() - Method in class org.utgenome.shell.FastqToSAM
 
name() - Method in class org.utgenome.shell.GWT
 
name() - Method in class org.utgenome.shell.GWTCompile
 
name() - Method in class org.utgenome.shell.Illumina2Fastq
 
name() - Method in class org.utgenome.shell.Import
 
name() - Method in class org.utgenome.shell.Keyword
 
name() - Method in class org.utgenome.shell.Maven
 
name() - Method in class org.utgenome.shell.Pack
 
name() - Method in class org.utgenome.shell.QSeqToFastq
 
name() - Method in class org.utgenome.shell.Repair
 
name() - Method in class org.utgenome.shell.Sam2Wig
 
name() - Method in class org.utgenome.shell.SAMToFastq
 
name() - Method in class org.utgenome.shell.Sequence
 
name() - Method in class org.utgenome.shell.Server
 
name() - Method in class org.utgenome.shell.SVNAdd
 
name() - Method in class org.utgenome.shell.Upgrade
 
name() - Method in class org.utgenome.shell.UTGBShellCommand
 
NavigatorTrack - Class in org.utgenome.gwt.utgb.client.track.lib
Navigator of the UTGB
NavigatorTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
newDeletion(int, int) - Static method in class org.utgenome.gwt.utgb.client.ribbon.Ribbon.Crease
 
newFile(String) - Static method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
newFolder(String) - Static method in class org.utgenome.gwt.utgb.client.bean.DatabaseEntry
 
newGZIPFileReader(InputStream) - Static method in class org.utgenome.format.fasta.FASTAPullParser
 
newInsertion(int, int) - Static method in class org.utgenome.gwt.utgb.client.ribbon.Ribbon.Crease
 
newInstance(Node) - Static method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl
 
newInstance(Node) - Static method in class org.utgenome.gwt.utgb.client.track.operation.FrameCommandImpl
 
newInstance(Node) - Static method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
newInstance() - Method in class org.utgenome.gwt.utgb.client.track.Track.TrackFactory
obtain a new factory instance.
newInstance(String) - Static method in class org.utgenome.gwt.utgb.client.util.GETMethodURL
 
newInstance(int) - Static method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
newPixelWidthWindow(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
newSAMRead(SAMRecord) - Method in class org.utgenome.format.sam.SAMReader.CompleteSAMReadFactory
 
newSAMRead(SAMRecord) - Method in class org.utgenome.format.sam.SAMReader.LightWeightSAMReadFactory
 
newSAMRead(SAMRecord) - Method in interface org.utgenome.format.sam.SAMReader.SAMReadFactory
 
newTARFileReader(InputStream) - Static method in class org.utgenome.format.fasta.FASTAPullParser
 
newTARGZFileReader(InputStream) - Static method in class org.utgenome.format.fasta.FASTAPullParser
 
newUTGBCoordinate(String, String, String) - Static method in class org.utgenome.gwt.utgb.client.bio.Coordinate
Create a new coordinate for UTGB
newWindow(int, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackWindow
 
next() - Method in class org.utgenome.format.fastq.FastqReader
Read the next FASTQ read entry.
next() - Method in class org.utgenome.format.keyword.KeywordAliasReader
read a next keyword and its aliases
next() - Method in class org.utgenome.format.ObjectStreamReader
 
next() - Method in class org.utgenome.format.sam.Sam2WigConverter.SAMRecordCursor
 
next() - Method in class org.utgenome.format.sam.SAMReadIterator
 
nextDescriptionLine() - Method in class org.utgenome.format.fasta.FASTAPullParser
 
nextKmer() - Method in interface org.utgenome.format.fasta.OverlappingKmerIterator
Return the next K-mer, or null when no more K-mer can be generated .
nextSequence() - Method in class org.utgenome.format.fasta.FASTAPullParser
read the next fasta sequence;
nextSequenceLine() - Method in class org.utgenome.format.fasta.FASTAPullParser
 
nextWorker() - Method in class org.utgenome.gwt.utgb.client.util.WorkQueue
 
NodeListImpl - Class in org.utgenome.gwt.utgb.client.util.xml
 
NodeListImpl() - Constructor for class org.utgenome.gwt.utgb.client.util.xml.NodeListImpl
 
normal(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
NORTH - Static variable in class org.utgenome.gwt.utgb.client.ui.RoundCornerFrame
 
NORTH - Static variable in class org.utgenome.gwt.widget.client.FrameBorder
 
notifyConfigChange(String) - Method in class org.utgenome.gwt.utgb.client.track.TrackConfig
 
notifyResize() - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
Notify the change of the inner track widget size to this group
notifyTheChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.impl.TrackGroupPropertyImpl
Notify the change to the track group and listeners
NowLoadingIcon - Class in org.utgenome.gwt.widget.client
Now loading button.
NowLoadingIcon(Image, Icon) - Constructor for class org.utgenome.gwt.widget.client.NowLoadingIcon
 
nowrap(Widget) - Static method in class org.utgenome.gwt.widget.client.Style
 
nSteps - Variable in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.Indent
 
num - Variable in class org.utgenome.format.axt.AXTAlignment
 
numAlignedWithSW - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
Number - Static variable in class org.utgenome.format.bed.BEDLexer
 
Number - Static variable in class org.utgenome.format.bed.BEDParser
 
Number - Static variable in class org.utgenome.format.wig.WIGLexer
 
Number - Static variable in class org.utgenome.format.wig.WIGParser
 
numBothEndIsMapped - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numBothEndIsUnmapped - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numChildren() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
numCtoT - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
 
numElements() - Method in class org.utgenome.util.repeat.DisjointSet
 
numHitsOfTracks(String) - Method in interface org.utgenome.gwt.utgb.client.BrowserService
 
numHitsOfTracks(String, AsyncCallback<Integer>) - Method in interface org.utgenome.gwt.utgb.client.BrowserServiceAsync
 
numHitsOfTracks(String) - Method in class org.utgenome.gwt.utgb.server.BrowserServiceImpl
 
numMapped - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numOneEndIsMapped - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numOtherMismatch - Variable in class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry
 
numPairs - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numRead - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numReadsMax - Variable in class org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle
 
numRepeat - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numSiblings() - Method in class org.utgenome.gwt.utgb.client.ui.treeview.TreePanel
 
numUnique - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 
numUnmapped - Variable in class org.utgenome.core.cui.ReadStat.ReadAlignmentStat
 

O

ObjectStreamReader - Class in org.utgenome.format
Text Format -> Object -> Iterator
ObjectStreamReader(Reader, ObjectStreamReader.TextFormatToObjectMapper) - Constructor for class org.utgenome.format.ObjectStreamReader
 
ObjectStreamReader.TextFormatToObjectMapper - Interface in org.utgenome.format
 
ObjectStreamReader.TextReader - Class in org.utgenome.format
 
ObjectStreamReader.TextReader(Reader) - Constructor for class org.utgenome.format.ObjectStreamReader.TextReader
 
offset - Variable in class org.utgenome.format.bed.BEDTrack
 
offset - Variable in class org.utgenome.format.fasta.CompactFASTAIndex
Offset from the beginning of the packed file
offset - Variable in class org.utgenome.format.FileBlock
 
offsets - Variable in class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry
 
OldDescriptionXML - Class in org.utgenome.format.legacy
 
OldDescriptionXML() - Constructor for class org.utgenome.format.legacy.OldDescriptionXML
 
OldDescriptionXMLReader - Class in org.utgenome.format.legacy
 
OldDescriptionXMLReader() - Constructor for class org.utgenome.format.legacy.OldDescriptionXMLReader
 
OldUTGBAddTrackTrack - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBAddTrackTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBAddTrackTrack
 
OldUTGBFrameCommandImpl - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl
 
OldUTGBFrameCommandImpl.FrameMoveAbsCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameMoveAbsCommand(int) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameMoveAbsCommand
 
OldUTGBFrameCommandImpl.FrameMoveRelCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameMoveRelCommand(int) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameMoveRelCommand
 
OldUTGBFrameCommandImpl.FrameParameterSetCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameParameterSetCommand(String, String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameParameterSetCommand
 
OldUTGBFrameCommandImpl.FrameRevCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameRevCommand() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameRevCommand
 
OldUTGBFrameCommandImpl.FrameSetEndCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameSetEndCommand(int) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetEndCommand
 
OldUTGBFrameCommandImpl.FrameSetRevisionCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameSetRevisionCommand(String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetRevisionCommand
 
OldUTGBFrameCommandImpl.FrameSetSpeciesCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameSetSpeciesCommand(String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetSpeciesCommand
 
OldUTGBFrameCommandImpl.FrameSetStartCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameSetStartCommand(int) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetStartCommand
 
OldUTGBFrameCommandImpl.FrameSetTargetCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameSetTargetCommand(String) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameSetTargetCommand
 
OldUTGBFrameCommandImpl.FrameZoomAbsCommand - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBFrameCommandImpl.FrameZoomAbsCommand(int) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBFrameCommandImpl.FrameZoomAbsCommand
 
OldUTGBOperationParser - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBOperationParser() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBOperationParser
 
OldUTGBOptionAttribute - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBOptionAttribute() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBOptionAttribute
 
OldUTGBProperty - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBPropertyTrack - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBPropertyTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBPropertyTrack
 
OldUTGBRulerTrack - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBRulerTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBRulerTrack
 
OldUTGBSubOperationImpl - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBSubOperationImpl(Node, Track) - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBSubOperationImpl
 
OldUTGBTrack - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBTrack() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
OldUTGBTrackGroup - Class in org.utgenome.gwt.utgb.client.track.lib.old
 
OldUTGBTrackGroup() - Constructor for class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrackGroup
 
OldViewXML - Class in org.utgenome.config
For reading view.xml files used in UTGB 1.3.x.
OldViewXML() - Constructor for class org.utgenome.config.OldViewXML
 
OldViewXML.GroupProperties - Class in org.utgenome.config
 
OldViewXML.GroupProperties() - Constructor for class org.utgenome.config.OldViewXML.GroupProperties
 
OldViewXML.Prop - Class in org.utgenome.config
 
OldViewXML.Prop() - Constructor for class org.utgenome.config.OldViewXML.Prop
 
OldViewXML.Track - Class in org.utgenome.config
 
OldViewXML.Track() - Constructor for class org.utgenome.config.OldViewXML.Track
 
OldViewXML.TrackGroup - Class in org.utgenome.config
 
OldViewXML.TrackGroup() - Constructor for class org.utgenome.config.OldViewXML.TrackGroup
 
OldViewXML.TrackWindow - Class in org.utgenome.config
 
OldViewXML.TrackWindow() - Constructor for class org.utgenome.config.OldViewXML.TrackWindow
 
onAddTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onAddTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onAddTrackGroup(TrackGroup) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
 
onAddTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onAttach() - Method in class org.utgenome.gwt.utgb.client.track.lib.old.datatype.ConfigInputForm
 
onBeforeSelection(BeforeSelectionEvent<Integer>) - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabViewer
 
onBrowserEvent(Event) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGenomeCanvas
 
onBrowserEvent(Event) - Method in class org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas
 
onBrowserEvent(Event) - Method in class org.utgenome.gwt.widget.client.Icon
 
onBrowserEvent(Event) - Method in class org.utgenome.gwt.widget.client.Switch
 
onButtonClick(WindowBox, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onButtonClick(WindowBox, int) - Method in interface org.utgenome.gwt.utgb.client.ui.WindowListener
An event handler when a window buton is clicked
onCancel() - Method in class org.utgenome.gwt.utgb.client.ui.Animation
Called immediately after the animation is canceled.
onChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
onChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
onChange(TrackGroupPropertyChange, TrackWindow) - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
onChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
onChange(TrackGroupPropertyChange, TrackWindow) - Method in interface org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChangeListener
Handle change event.
onChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChangeListenerAdapter
 
onChange(TrackInfo) - Method in interface org.utgenome.gwt.utgb.client.track.TrackInfoChangeListener
An event handler when some track information changes
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.BEDTrack
Deprecated.  
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.ChromosomeMapTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.CSEGTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.DASTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.MiniBrowserTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.RefSeqTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
onChangeTrackConfig(TrackConfigChange) - Method in interface org.utgenome.gwt.utgb.client.track.Track
An event handler when some cofigurations of the track changes
onChangeTrackConfig(TrackConfigChange) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.DBSelectTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBPropertyTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.ParameterTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.ValueSelectorTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in interface org.utgenome.gwt.utgb.client.track.Track
An event handler when some properties shared within the track group has changed
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
onChangeTrackGroupProperty(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChangeListenerAdapter
 
onChangeTrackHeight(int) - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
onChangeTrackHeight(int) - Method in interface org.utgenome.gwt.utgb.client.track.Track
 
onChangeTrackHeight(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.GenomeTrackTextTest
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBPropertyTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OperationTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.ReadTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.RibbonRulerTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMQueryTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.SAMTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.lib.WIGTrack
 
onChangeTrackWindow(TrackWindow) - Method in interface org.utgenome.gwt.utgb.client.track.Track
An event handler when the track window location has changed
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackBase
 
onChangeTrackWindow(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroupPropertyChangeListenerAdapter
 
onChangeWidgetSize(int, int) - Method in interface org.utgenome.gwt.utgb.client.ui.WidgetSizeChangeListener
 
onClick(int, int, GenomeRange) - Method in interface org.utgenome.gwt.utgb.client.canvas.LocusClickHandler
 
onClick(ClickEvent) - Method in class org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBAddTrackTrack
 
onClick(ClickEvent) - Method in class org.utgenome.gwt.utgb.client.track.operation.MenuOperationItem
 
onClick(ClickEvent) - Method in class org.utgenome.gwt.utgb.client.track.operation.MouseClickEventImpl
 
onClick() - Method in class org.utgenome.gwt.widget.client.Icon
Called when the user finishes clicking on this button.
onClick() - Method in class org.utgenome.gwt.widget.client.Switch
Called when the user finishes clicking on this button.
onClickAdjust(Frame) - Method in interface org.utgenome.gwt.utgb.client.ui.FrameButtonListener
When clicked the adjust button
onClickAdjustHightButton(TrackFrame) - Method in interface org.utgenome.gwt.widget.client.TrackButtonListener
 
onClickAdjustHightButton(TrackFrame) - Method in class org.utgenome.gwt.widget.client.TrackButtonListenerAdapter
 
onClickCancel() - Method in class org.utgenome.gwt.widget.client.Icon
Called when the user aborts a click in progress; for example, by dragging the mouse outside of the button before releasing the mouse button.
onClickCancel() - Method in class org.utgenome.gwt.widget.client.Switch
Called when the user aborts a click in progress; for example, by dragging the mouse outside of the button before releasing the mouse button.
onClickClose(Frame) - Method in interface org.utgenome.gwt.utgb.client.ui.FrameButtonListener
When clicked the close button
onClickCloseButton(TrackFrame) - Method in interface org.utgenome.gwt.widget.client.TrackButtonListener
 
onClickCloseButton(TrackFrame) - Method in class org.utgenome.gwt.widget.client.TrackButtonListenerAdapter
 
onClickConfig(Frame) - Method in interface org.utgenome.gwt.utgb.client.ui.FrameButtonListener
When clicked the configuration button
onClickConfigButton(TrackFrame) - Method in interface org.utgenome.gwt.widget.client.TrackButtonListener
 
onClickConfigButton(TrackFrame) - Method in class org.utgenome.gwt.widget.client.TrackButtonListenerAdapter
 
onClickMinimize(Frame) - Method in interface org.utgenome.gwt.utgb.client.ui.FrameButtonListener
When clicked the minimize button
onClickMinimizeButton(TrackFrame) - Method in interface org.utgenome.gwt.widget.client.TrackButtonListener
 
onClickMinimizeButton(TrackFrame) - Method in class org.utgenome.gwt.widget.client.TrackButtonListenerAdapter
 
onClickReloadButton(TrackFrame) - Method in interface org.utgenome.gwt.widget.client.TrackButtonListener
 
onClickReloadButton(TrackFrame) - Method in class org.utgenome.gwt.widget.client.TrackButtonListenerAdapter
 
onClickStart() - Method in class org.utgenome.gwt.widget.client.Icon
Called when the user begins to click on this button.
onClickStart() - Method in class org.utgenome.gwt.widget.client.Switch
Called when the user begins to click on this button.
onComplete() - Method in class org.utgenome.gwt.utgb.client.ui.Animation
Called immediately after the animation completes.
onDeleteRow(Object) - Method in interface org.utgenome.gwt.utgb.client.ui.TableChangeListener
 
onDetachedFromTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onDetachedFromTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onDrop(DragContext) - Method in class org.utgenome.gwt.widget.client.impl.TabDropController
 
oneEnd - Variable in class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
 
onEnter(DragContext) - Method in class org.utgenome.gwt.widget.client.impl.TabDropController
 
onFailure(Throwable) - Method in class org.utgenome.gwt.utgb.client.util.Worker.WorkerCallback
 
onFocus() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry
 
onFocus() - Method in interface org.utgenome.gwt.utgb.client.ui.tab.TabEventListener
 
onImagesLoaded(ImageHandle[]) - Method in interface org.utgenome.gwt.widget.client.ImageLoader.CallBack
 
onInsertNewRow(Object[]) - Method in interface org.utgenome.gwt.utgb.client.ui.TableChangeListener
 
onInsertTrack(Track, int) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onInsertTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onInsertTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onInsertTrack(Track, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onInsertTrack(Track) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
When a new track is inserted to the group
onInsertTrack(Track, int) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
When a new track is inserted to the group
onInsertTrack(Track, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onInsertTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onLoad() - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onLostFocus() - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabEntry
 
onLostFocus() - Method in interface org.utgenome.gwt.utgb.client.ui.tab.TabEventListener
 
onModuleLoad() - Method in class org.utgenome.gwt.ribbon.client.RibbonBrowser
 
onModuleLoad() - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase
 
onMouseDown(MouseDownEvent) - Method in class org.utgenome.gwt.utgb.client.track.TrackRangeSelector
 
onMouseDown(Element, int, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackRangeSelector
 
onMouseDown(MouseDownEvent) - Method in class org.utgenome.gwt.utgb.client.ui.MouseMoveListener
 
onMouseDown(Widget, int, int) - Method in class org.utgenome.gwt.widget.client.DragListener
 
onMouseDownFromChild(Widget, int, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackRangeSelector
An event handler when a mouse down event is reported from a child widget of the trackPanel.
onMouseDownFromChild(MouseDownEvent) - Method in class org.utgenome.gwt.utgb.client.track.TrackRangeSelector
 
onMouseEnter(Widget) - Method in class org.utgenome.gwt.widget.client.DragListener
 
onMouseLeave(Widget) - Method in class org.utgenome.gwt.widget.client.DragListener
 
onMouseMove(MouseMoveEvent) - Method in class org.utgenome.gwt.utgb.client.track.TrackRangeSelector
 
onMouseMove(MouseMoveEvent) - Method in class org.utgenome.gwt.utgb.client.ui.MouseMoveListener
 
onMouseMove(Widget, int, int) - Method in class org.utgenome.gwt.widget.client.DragListener
 
onMouseOut(MouseOutEvent) - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
onMouseOut(MouseOutEvent) - Method in class org.utgenome.gwt.utgb.client.ui.Icon
 
onMouseOut(MouseOutEvent) - Method in class org.utgenome.gwt.widget.client.Tab
 
onMouseOver(MouseOverEvent) - Method in class org.utgenome.gwt.utgb.client.track.operation.OperationArea
 
onMouseOver(MouseOverEvent) - Method in class org.utgenome.gwt.utgb.client.ui.Icon
 
onMouseOver(MouseOverEvent) - Method in class org.utgenome.gwt.widget.client.Tab
 
onMouseUp(MouseUpEvent) - Method in class org.utgenome.gwt.utgb.client.ui.MouseMoveListener
 
onMouseUp(Widget, int, int) - Method in class org.utgenome.gwt.widget.client.DragListener
 
onParentChange(TrackGroupPropertyChange, TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
 
onParentTrackGroupPropertyChange(TrackGroupPropertyChange) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
An event handler when the TrackGroupProperty of the parent group has changed.
onParentTrackWindowChange(TrackWindow) - Method in class org.utgenome.gwt.utgb.client.track.TrackGroup
An event handler when the TrackWindow of this group has changed.
onPreviewNativeEvent(Event.NativePreviewEvent) - Method in class org.utgenome.gwt.utgb.client.UTGBEntryPointBase.KeyboardShortcut
 
onRangeSelect(int, int) - Method in class org.utgenome.gwt.utgb.client.track.lib.RulerTrack
 
onRangeSelect(int, int) - Method in class org.utgenome.gwt.utgb.client.track.lib.SequenceRulerTrack
 
onRangeSelect(int, int) - Method in interface org.utgenome.gwt.utgb.client.track.RangeSelectable
 
onRemoveTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onRemoveTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onRemoveTrack(Track) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
When the track is removed from the group
onRemoveTrack(Track) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onRemoveTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onRemoveTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onRemoveTrackGroup(TrackGroup) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
 
onRemoveTrackGroup(TrackGroup) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onResizeTrack() - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onResizeTrack() - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onResizeTrack() - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
When the size of a track changes
onResizeTrack() - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onResizeTrackWindow(int) - Method in class org.utgenome.gwt.utgb.client.track.lib.TrackTreeTrack
 
onResizeTrackWindow(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onResizeTrackWindow(int) - Method in interface org.utgenome.gwt.utgb.client.track.TrackUpdateListener
 
onResizeTrackWindow(int) - Method in class org.utgenome.gwt.utgb.client.track.TrackUpdateListenerAdapter
 
onResizeWindow(WindowBox, int) - Method in class org.utgenome.gwt.utgb.client.track.TrackQueue
 
onResizeWindow(WindowBox, int) - Method in interface org.utgenome.gwt.utgb.client.ui.WindowListener
 
onSelection(SelectionEvent<Integer>) - Method in class org.utgenome.gwt.utgb.client.ui.tab.TabViewer
 
onStart() - Method in class org.utgenome.gwt.utgb.client.ui.Animation
Called immediately before the animation starts.
onSuccess(Object) - Method in class org.utgenome.gwt.utgb.client.util.Worker.WorkerCallback
 
onTouchCancel(TouchCancelEven