- a -

• AboutAction() : gov::lbl::genome::gui::action::AboutAction
• AbstractActionDialogPanel() : gov::lbl::genome::gui::panel::AbstractActionDialogPanel
• AbstractCurveModel() : gov::lbl::genome::common::AbstractCurveModel
• ActionDialog() : gov::lbl::genome::gui::dialog::ActionDialog
• actionPerformed() : gov::lbl::genome::gui::action::VAbstractAction, gov::lbl::genome::gui::action::ForwardAction, gov::lbl::genome::gui::action::BackAction, gnu::jpdf::PDFTest
• add() : gov::lbl::genome::gui::panel::GraphViewList, gov::lbl::genome::common::features::ChromSegment, gnu::jpdf::PDFPageList, gnu::jpdf::PDFPage::procset, gnu::jpdf::PDFPage, gnu::jpdf::PDFOutline, gnu::jpdf::PDFDocument, gnu::jpdf::BoundingBox
• Add_ChromSegment() : gov::lbl::genome::common::features::ChromSegments
• AddAction() : gov::lbl::genome::gui::action::AddAction
• addAnnotation() : gnu::jpdf::PDFPage
• addCurve() : gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::GeneralGraphModel
• addCurves() : gov::lbl::genome::gui::panel::DisplayPanel
• addDefaultCurve() : gov::lbl::genome::gui::panel::DisplayPanel
• addElement() : gov::lbl::genome::gui::panel::GraphViewList
• addGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• addImage() : ranab::img::gif::GifImage
• addLayoutComponent() : layout::TableLayout
• addLink() : gnu::jpdf::PDFPage
• addNote() : gnu::jpdf::PDFPage, gnu::jpdf::PDFJob
• addOutline() : gnu::jpdf::PDFPage, gnu::jpdf::PDFJob
• addPoint() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• addPrintedGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• addResource() : gnu::jpdf::PDFPage
• addXObject() : gnu::jpdf::PDFPage
• annotationLegend() : gov::lbl::genome::gui::panel::DisplayPanel
• AnnotationPanel() : gov::lbl::genome::gui::panel::AnnotationPanel
• AnnotationPanelPicture() : gov::lbl::genome::gui::panel::AnnotationPanelPicture
• arc() : gnu::jpdf::PDFGraphics
• ArrowsPanel() : gov::lbl::genome::gui::panel::ArrowsPanel
• AxisPanel() : gov::lbl::genome::gui::panel::AxisPanel
• AxisPanelPicture() : gov::lbl::genome::gui::panel::AxisPanelPicture

- b -

• BackAction() : gov::lbl::genome::gui::action::BackAction
• BadCoordinateTypeException() : gov::lbl::genome::common::BadCoordinateTypeException
• BaseImage() : ranab::img::BaseImage
• BaseInfoPanel() : gov::lbl::genome::gui::panel::BaseInfoPanel
• BoundingBox() : gnu::jpdf::BoundingBox
• boxExists() : gnu::jpdf::BoundingBox
• BrowserInfo() : gov::lbl::genome::common::BrowserInfo

- c -

• calculateSize() : layout::TableLayout
• cancelAction() : gov::lbl::genome::gui::dialog::ActionDialog
• centerDialog() : gov::lbl::genome::gui::dialog::VistaDialog
• changePanel() : gov::lbl::genome::gui::dialog::VistaDialog
• changeSequence() : ranab::util::ByteUtils
• checkCurves() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::common::CommUnit
• checkVisible() : gov::lbl::genome::gui::GeneralGraphView
• ChromInfo() : gov::lbl::genome::common::ChromInfo
• ChromPanel() : gov::lbl::genome::gui::panel::ChromPanel
• ChromPanelPicture() : gov::lbl::genome::gui::panel::ChromPanelPicture
• ChromPosition() : gov::lbl::genome::common::features::ChromPosition
• ChromSegment() : gov::lbl::genome::common::features::ChromSegment
• ChromSegments() : gov::lbl::genome::common::features::ChromSegments
• clear() : gov::lbl::genome::gui::History
• clearAll() : gov::lbl::genome::gui::History
• clearChildren() : gov::lbl::genome::gui::GeneralGraphView
• clearModel() : gov::lbl::genome::gui::CurveParameters
• clearRect() : gnu::jpdf::PDFGraphics
• clearStatus() : gov::lbl::genome::gui::Status
• clearStatusBar() : gov::lbl::genome::gui::VistaApp
• clipPolygon() : gnu::jpdf::PDFGraphics
• clipRect() : gnu::jpdf::PDFGraphics
• clone() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::AnnotationPanel, gov::lbl::genome::gui::AbstractCurveView
• cloneCurve() : gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::AbstractCurveModel
• cloneSegment() : gov::lbl::genome::common::features::ChromSegment
• close() : gnu::jpdf::PDFOutput
• closeBlock() : gnu::jpdf::PDFGraphics
• CodeEntry() : ranab::img::gif::GifImage::CodeEntry
• collectValues() : gov::lbl::genome::gui::panel::StatPanel, gov::lbl::genome::gui::panel::SearchResultsPanel, gov::lbl::genome::gui::panel::SaveAsPanel, gov::lbl::genome::gui::panel::ContigListPanel, gov::lbl::genome::gui::panel::AbstractActionDialogPanel
• Comment() : sjg::xml::Comment
• CommUnit() : gov::lbl::genome::common::CommUnit
• compareTo() : gov::lbl::genome::common::features::ChromSegment
• componentResized() : gov::lbl::genome::gui::panel::DisplayPanel
• contains() : gov::lbl::genome::common::features::ChromSegment
• Contig() : gov::lbl::genome::common::features::Contig
• contigLegend() : gov::lbl::genome::gui::panel::DisplayPanel
• ContigListDialog() : gov::lbl::genome::gui::dialog::ContigListDialog
• ContigListPanel() : gov::lbl::genome::gui::panel::ContigListPanel
• ContigPanel() : gov::lbl::genome::gui::panel::ContigPanel
• convertX() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::ChromPanelPicture, gov::lbl::genome::gui::AbstractCurveView
• convertY() : gov::lbl::genome::gui::AbstractCurveView
• copyArea() : gnu::jpdf::PDFGraphics
• create() : gnu::jpdf::PDFJob::graphic, gnu::jpdf::PDFGraphics
• createBarImage() : gov::lbl::genome::gui::panel::TracerPanel
• createGraphic() : gnu::jpdf::PDFGraphics
• createImage() : gov::lbl::genome::gui::panel::XAxisPanel, gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::panel::ChromPanel, gov::lbl::genome::gui::panel::AxisPanel, gov::lbl::genome::gui::panel::AnnotationPanel, gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::gui::GeneralGraphComp
• createTracerImage() : gov::lbl::genome::gui::panel::TracerPanel
• crossMouseCursor() : gov::lbl::genome::gui::panel::TracerPanel
• CursorInfoPanel() : gov::lbl::genome::gui::panel::CursorInfoPanel
• CurveInfo() : gov::lbl::genome::common::CurveInfo
• CurveParameters() : gov::lbl::genome::gui::CurveParameters
• curveto() : gnu::jpdf::PDFGraphics
• curveto2() : gnu::jpdf::PDFGraphics
• cx() : gnu::jpdf::PDFPage
• cxy() : gnu::jpdf::PDFPage
• cy() : gnu::jpdf::PDFPage

- d -

• Data() : sjg::xml::Data
• Debug() : gov::lbl::genome::gui::panel::VGBPanel
• debug() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::Debug
• debugException() : gov::lbl::genome::gui::Debug
• debugOff() : gov::lbl::genome::gui::Debug
• debugOn() : gov::lbl::genome::gui::Debug
• Decrement_All() : gov::lbl::genome::common::features::ChromSegments
• defaultMouseCursor() : gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::panel::ChromPanel
• deleteColumn() : layout::TableLayout
• deleteRow() : layout::TableLayout
• descendants() : gnu::jpdf::PDFOutline
• DetailsAction() : gov::lbl::genome::gui::action::DetailsAction
• Difference() : gov::lbl::genome::common::features::ChromSegments
• disableCancelBtn() : gov::lbl::genome::gui::dialog::ActionDialog
• disableGUI() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::GeneSearchPanel, gov::lbl::genome::gui::panel::BaseInfoPanel
• disableOKBtn() : gov::lbl::genome::gui::dialog::ActionDialog
• dispatch() : gov::lbl::genome::gui::panel::VGBPanel
• dispatchEvent() : gov::lbl::genome::gui::panel::VGBPanel, gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::GeneralGraphComp
• DisplayPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• dispose() : gnu::jpdf::PDFGraphics
• Document() : sjg::xml::Document
• draw3DRect() : gnu::jpdf::PDFGraphics
• drawArc() : gnu::jpdf::PDFGraphics
• drawBytes() : gnu::jpdf::PDFGraphics
• drawChoppedString() : gnu::jpdf::BoundingBox
• drawContent() : gov::lbl::genome::gui::panel::XAxisPanel, gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::DisplayPanel, gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::panel::ChromPanel, gov::lbl::genome::gui::panel::AxisPanel, gov::lbl::genome::gui::panel::AnnotationPanel, gov::lbl::genome::gui::GeneralGraphComp
• drawGene() : gov::lbl::genome::gui::panel::AnnotationPanelPicture
• drawGreenBar() : gov::lbl::genome::gui::panel::TracerPanel
• drawGrid() : layout::TableLayout
• drawImage() : gnu::jpdf::PDFGraphics
• drawLine() : gnu::jpdf::PDFGraphics
• drawOval() : gnu::jpdf::PDFGraphics
• drawPicture() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::RepeatPanelPicture, gov::lbl::genome::gui::panel::ContigPanelPicture, gov::lbl::genome::gui::panel::ChromPanelPicture, gov::lbl::genome::gui::panel::AxisPanelPicture, gov::lbl::genome::gui::panel::AnnotationPanelPicture
• drawPolygon() : gnu::jpdf::PDFGraphics
• drawPolyline() : gnu::jpdf::PDFGraphics
• drawRect() : gnu::jpdf::PDFGraphics
• drawRoundRect() : gnu::jpdf::PDFGraphics
• drawString() : gnu::jpdf::PDFGraphics
• drawWrappedString() : gnu::jpdf::BoundingBox
• drawWrappedStringTruncate() : gnu::jpdf::BoundingBox

- e -

• eastMouseCursor() : gov::lbl::genome::gui::panel::ChromPanel
• elementAt() : gov::lbl::genome::gui::panel::GraphViewList
• elements() : sjg::xml::Element, gnu::jpdf::PDFOutline
• enableCancelBtn() : gov::lbl::genome::gui::dialog::ActionDialog
• enableDialogButtons() : gov::lbl::genome::gui::panel::AbstractActionDialogPanel
• enableGUI() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::GeneSearchPanel, gov::lbl::genome::gui::panel::BaseInfoPanel
• enableOKBtn() : gov::lbl::genome::gui::dialog::ActionDialog
• enablePrinting() : gov::lbl::genome::gui::VistaApp
• encode() : ranab::img::gif::GifImage, ranab::img::BaseImage
• end() : gnu::jpdf::PDFJob
• equals() : gov::lbl::genome::gui::Status, gov::lbl::genome::gui::CurveParameters, gov::lbl::genome::common::AbstractCurveModel, gnu::jpdf::PDFFont
• equalsIgnoreData() : gov::lbl::genome::gui::Status
• error() : gov::lbl::genome::gui::Debug

- f -

• fill3DRect() : gnu::jpdf::PDFGraphics
• fillAnnotations() : gov::lbl::genome::gui::VistaCurveView
• fillArc() : gnu::jpdf::PDFGraphics
• fillOval() : gnu::jpdf::PDFGraphics
• fillPolygon() : gnu::jpdf::PDFGraphics
• fillRect() : gnu::jpdf::PDFGraphics
• fillRoundRect() : gnu::jpdf::PDFGraphics
• findMatch() : ranab::img::gif::GifImage::GifHash
• findParentFrame() : gov::lbl::genome::gui::panel::VGBPanel
• firstElement() : gov::lbl::genome::gui::panel::GraphViewList
• flipSelected() : gov::lbl::genome::gui::GeneralGraphView
• ForwardAction() : gov::lbl::genome::gui::action::ForwardAction
• freezeCounters() : gov::lbl::genome::gui::VistaApp
• fromString() : gov::lbl::genome::common::features::Gap, gov::lbl::genome::common::features::ChromPosition

- g -

• Gene() : gov::lbl::genome::common::features::Gene
• GeneNotFoundException() : gov::lbl::genome::common::GeneNotFoundException
• GeneralGraphComp() : gov::lbl::genome::gui::GeneralGraphComp
• GeneralGraphModel() : gov::lbl::genome::common::GeneralGraphModel
• GeneralGraphView() : gov::lbl::genome::gui::GeneralGraphView
• GeneSearchPanel() : gov::lbl::genome::gui::panel::GeneSearchPanel
• GenesInfo() : gov::lbl::genome::common::GenesInfo
• GenomeInfo() : gov::lbl::genome::common::GenomeInfo
• Get_ChromSegment() : gov::lbl::genome::common::features::ChromSegments
• getAbsoluteLocation() : gnu::jpdf::BoundingBox
• getAdb() : gov::lbl::genome::common::GenomeInfo
• getAddAction() : gov::lbl::genome::gui::VistaApp
• getAlign() : gov::lbl::genome::common::features::Contig
• getAllCurveInfos() : gov::lbl::genome::gui::panel::DisplayPanel
• getAllCurves() : gov::lbl::genome::gui::panel::DisplayPanel
• getAllGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• getAllPoints() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getAllSelectedGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• getAnno() : gov::lbl::genome::common::CommUnit
• getAnnotation() : gov::lbl::genome::gui::Status
• getAnnotationColor() : gov::lbl::genome::gui::panel::RepeatPanel
• getAnnotationPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• getAnnotations() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::AnnotationPanel, gov::lbl::genome::common::AbstractCurveModel
• getAttribute() : sjg::xml::Element
• getAuthor() : gnu::jpdf::PDFInfo
• getAvailCurves() : gov::lbl::genome::common::CommUnit
• getBase() : gov::lbl::genome::common::CurveInfo
• getBaseFamily() : gov::lbl::genome::common::VistaCurveInfo
• getBaseGenome() : gov::lbl::genome::gui::VistaApp
• getBG() : gov::lbl::genome::gui::VistaApp
• getBlockId() : ranab::img::gif::GifEx
• getBrowsers() : gov::lbl::genome::common::GenomeInfo
• getCalcWindow() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::common::VistaCurveModel
• getCheckedCurves() : gov::lbl::genome::common::GenomeInfo
• getChrom() : gov::lbl::genome::gui::VistaApp
• getChromDX() : gov::lbl::genome::gui::panel::DisplayPanel
• getChromInfo() : gov::lbl::genome::common::CommUnit
• getChromName() : gov::lbl::genome::common::features::ChromSegment
• getChromosome() : gov::lbl::genome::common::features::ChromSegment, gov::lbl::genome::common::features::ChromPosition
• getChromSize() : gov::lbl::genome::gui::VistaApp
• getChromX() : gov::lbl::genome::gui::panel::TracerPanel
• getClip() : gnu::jpdf::PDFGraphics
• getClipBounds() : gnu::jpdf::PDFGraphics
• getCode() : ranab::img::gif::GifImage::CodeEntry, gov::lbl::genome::common::VGBException
• getCodeEntry() : ranab::img::gif::GifImage::GifHash
• getColor() : ranab::img::gif::GifColor, gov::lbl::genome::gui::Parameter, gnu::jpdf::PDFGraphics
• getColorArray() : gov::lbl::genome::gui::Parameter
• getColumn() : layout::TableLayout
• getComment() : ranab::img::gif::GifCommentEx, gov::lbl::genome::common::GenesInfo
• getCommentBlock() : ranab::img::gif::GifImage
• getCommUnit() : gov::lbl::genome::gui::VistaApp
• getComponent() : gov::lbl::genome::gui::dialog::VistaDialog
• getConnection() : gov::lbl::genome::gui::VistaApp
• getConsIdentity() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::common::VistaCurveModel
• getConstraints() : layout::TableLayout
• getConsWidth() : gov::lbl::genome::gui::VistaApp
• getContents() : sjg::xml::Element
• getContig() : gov::lbl::genome::common::GenomeInfo
• getContigName() : gov::lbl::genome::common::features::Contig
• getContigNum() : gov::lbl::genome::common::features::Contig
• getContigPanel() : gov::lbl::genome::gui::GeneralGraphView
• getContigs() : gov::lbl::genome::gui::VistaCurveView, gov::lbl::genome::gui::panel::ContigPanel
• getCoordinate() : gov::lbl::genome::common::features::ChromPosition
• getCreated() : gov::lbl::genome::common::GenesInfo
• getCreator() : gnu::jpdf::PDFInfo
• getCurrentPage() : gnu::jpdf::PDFJob
• getCurrentPageNumber() : gnu::jpdf::PDFJob
• getCurrentPos() : gov::lbl::genome::common::GenomeInfo
• getCurve() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::CommUnit
• getCurveInfo() : gov::lbl::genome::common::AbstractCurveModel
• getCurveModel() : gov::lbl::genome::gui::AbstractCurveView
• getCurveModels() : gov::lbl::genome::common::GraphModel, gov::lbl::genome::common::GeneralGraphModel
• getCurveModelsCollection() : gov::lbl::genome::common::GeneralGraphModel
• getCurveParameters() : gov::lbl::genome::gui::Status
• getCurves() : gov::lbl::genome::common::GenomeInfo
• getCurveViews() : gov::lbl::genome::gui::GeneralGraphView
• getData() : gov::lbl::genome::common::AbstractCurveModel
• getDataInterval() : gov::lbl::genome::gui::VistaApp
• getDataUrl() : gov::lbl::genome::common::GenomeInfo
• getDefaultBaseGenome() : gov::lbl::genome::gui::panel::BaseInfoPanel
• getDefaultGenes() : gov::lbl::genome::gui::VistaApp
• getDefaultGenome() : gov::lbl::genome::gui::panel::BaseInfoPanel
• getDeflate() : gnu::jpdf::PDFStream
• getDefPos() : gov::lbl::genome::common::GenomeInfo
• getDelayTime() : ranab::img::gif::GifGraphicEx
• getDescr() : gov::lbl::genome::common::features::Gene
• getDetailsAction() : gov::lbl::genome::gui::VistaApp
• getDialogElement() : gov::lbl::genome::gui::VistaApp
• getDir() : gov::lbl::genome::common::features::Contig
• getDisplayPanel() : gov::lbl::genome::gui::VistaApp
• getDouble() : gov::lbl::genome::gui::Parameter
• getDoubleArray() : gov::lbl::genome::gui::Parameter
• getDrawingPoint() : gnu::jpdf::BoundingBox
• getDs() : gov::lbl::genome::common::features::Contig
• getDsChrom() : gov::lbl::genome::common::features::Contig
• getDsEnd() : gov::lbl::genome::common::features::Contig
• getDsStart() : gov::lbl::genome::common::features::Contig
• getDsStrand() : gov::lbl::genome::common::features::Contig
• getDX() : gov::lbl::genome::gui::Picture
• getEnabled() : gov::lbl::genome::gui::panel::TracerPanel
• getEnd() : gov::lbl::genome::common::features::ChromSegment
• getEndPoint() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getErrorHandler() : gov::lbl::genome::gui::VistaApp
• getFamily() : gov::lbl::genome::common::BrowserInfo
• getFirstSelectedIndex() : gov::lbl::genome::gui::panel::DisplayPanel
• getFont() : gov::lbl::genome::gui::Parameter, gnu::jpdf::PDFPage, gnu::jpdf::PDFGraphics, gnu::jpdf::PDFFont, gnu::jpdf::PDFDocument
• getFontArray() : gov::lbl::genome::gui::Parameter
• getFontMetrics() : gnu::jpdf::PDFGraphics
• getFormattedNumberString() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel
• getFormattedXDisplayString() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::ChromPanelPicture
• getFullString() : gnu::jpdf::BoundingBox
• getGeneName() : gov::lbl::genome::common::features::Gene
• getGeneralGraphView() : gov::lbl::genome::gui::GeneralGraphView
• getGenes() : gov::lbl::genome::common::CommUnit
• getGenesInfo() : gov::lbl::genome::gui::VistaApp
• getGenesInfos() : gov::lbl::genome::common::GenomeInfo
• getGenesName() : gov::lbl::genome::gui::panel::GeneSearchPanel
• getGenome() : gov::lbl::genome::gui::Status
• getGenomeId() : gov::lbl::genome::common::GenomeInfo
• getGenomesIter() : gov::lbl::genome::gui::panel::BaseInfoPanel
• getGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• getGraphComp() : gov::lbl::genome::gui::GeneralGraphView
• getGraphHeight() : gov::lbl::genome::gui::GeneralGraphView
• getGraphicBlock() : ranab::img::gif::GifImage
• getGraphics() : ranab::img::gif::GifImage, ranab::img::BaseImage, gnu::jpdf::PDFPage, gnu::jpdf::PDFJob
• getGraphModel() : gov::lbl::genome::gui::GeneralGraphView
• getGraphName() : gov::lbl::genome::gui::GeneralGraphView
• getGraphPanelSize() : gov::lbl::genome::gui::panel::DisplayPanel
• getGraphPos() : gov::lbl::genome::gui::GeneralGraphView
• getGraphView() : gov::lbl::genome::gui::CurveView, gov::lbl::genome::gui::AbstractCurveView
• getGraphWidth() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::GeneralGraphView
• getHeader() : sjg::xml::Document
• getHeight() : ranab::img::gif::GifScreenDescriptor, ranab::img::BaseImage, gov::lbl::genome::gui::Picture, gnu::jpdf::PDFImage
• getHistory() : gov::lbl::genome::gui::VistaApp
• getHorizSize() : gov::lbl::genome::gui::panel::VistaPanel
• getID() : gov::lbl::genome::common::CustomCurveModel, gov::lbl::genome::common::AbstractGraphModel, gov::lbl::genome::common::AbstractCurveModel
• getId() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::CurveInfo
• getImage() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::AxisPanel, gov::lbl::genome::gui::panel::AnnotationPanel
• getImageableHeight() : gov::lbl::genome::gui::Picture
• getImageableWidth() : gov::lbl::genome::gui::Picture
• getImageData() : ranab::img::gif::GifEx
• getIndex() : gnu::jpdf::PDFOutline
• getInitInfo() : gov::lbl::genome::common::CommUnit
• getInputStream() : gov::lbl::genome::gui::VistaApp
• getInt() : gov::lbl::genome::gui::Parameter
• getIntArray() : gov::lbl::genome::gui::Parameter
• getInterval() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getIntValue() : sjg::xml::Attribute
• getInvisible() : gov::lbl::genome::gui::panel::GraphViewList
• getIterationCount() : ranab::img::gif::GifNsAppEx
• getKeywords() : gnu::jpdf::PDFInfo
• getLabel() : gov::lbl::genome::common::CurveInfo
• getLast() : gnu::jpdf::PDFOutline
• getLastSelectedIndex() : gov::lbl::genome::gui::panel::DisplayPanel
• getLayoutAlignmentX() : layout::TableLayout
• getLayoutAlignmentY() : layout::TableLayout
• getLongName() : gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::common::VistaCurveInfo, gov::lbl::genome::common::GenesInfo, gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::AbstractGraphModel, gov::lbl::genome::common::AbstractCurveModel
• getMarginBottom() : gov::lbl::genome::gui::Picture
• getMarginLeft() : gov::lbl::genome::gui::Picture
• getMarginRight() : gov::lbl::genome::gui::Picture
• getMarginTop() : gov::lbl::genome::gui::Picture
• getMaxHeight() : gov::lbl::genome::gui::Picture
• getMaxWidth() : gov::lbl::genome::gui::Picture
• getMaxX() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::AbstractGraphModel, gov::lbl::genome::common::AbstractCurveModel
• getMaxY() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::AbstractGraphModel
• getMedia() : gnu::jpdf::PDFPage
• getMethodResult() : gov::lbl::genome::gui::dialog::VistaDialog
• getMimeType() : ranab::img::gif::GifImage, ranab::img::BaseImage
• getMinConsWidth() : gov::lbl::genome::common::VistaCurveModel
• getMinX() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::AbstractGraphModel, gov::lbl::genome::common::AbstractCurveModel
• getMinY() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::AbstractGraphModel
• getMode() : gov::lbl::genome::common::VistaCurveModel
• getName() : sjg::xml::Element, sjg::xml::Attribute, gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::GenesInfo, gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::features::ChromSegment, gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::ChromInfo, gov::lbl::genome::common::BrowserInfo, gov::lbl::genome::common::AbstractGraphModel, gov::lbl::genome::common::AbstractCurveModel, gnu::jpdf::PDFImage, gnu::jpdf::PDFFont
• getNewHeight() : gov::lbl::genome::gui::VistaApp
• getNewWidth() : gov::lbl::genome::gui::VistaApp
• getNext() : gov::lbl::genome::gui::History
• getNode() : gnu::jpdf::PDFOutline
• getNsApplicationBlock() : ranab::img::gif::GifImage
• getNumberOfCurves() : gov::lbl::genome::common::GenomeInfo
• getNumberOfGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• getNumberOfPoints() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getNumberOfRows() : gov::lbl::genome::gui::panel::BaseInfoPanel
• getNumColumn() : layout::TableLayout
• getNumDataPoints() : gov::lbl::genome::gui::VistaApp
• getNumRow() : layout::TableLayout
• getObject() : gov::lbl::genome::gui::Parameter
• getObjectArray() : gov::lbl::genome::gui::Parameter
• getOrganisms() : gov::lbl::genome::gui::Status, gov::lbl::genome::gui::panel::BaseInfoPanel
• getOrgId() : gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::VistaCurveInfo
• getOrientation() : gnu::jpdf::PDFPage
• getOutline() : gnu::jpdf::PDFDocument
• getOutputStream() : gov::lbl::genome::gui::VistaApp, gnu::jpdf::PDFStream
• getPage() : gnu::jpdf::PDFPageList, gnu::jpdf::PDFGraphics, gnu::jpdf::PDFDocument
• getPageDimension() : gnu::jpdf::PDFJob
• getPageResolution() : gnu::jpdf::PDFJob
• getPanel() : gov::lbl::genome::gui::dialog::VistaDialog
• getPanelCapacity() : gov::lbl::genome::gui::panel::DisplayPanel
• getParam() : gov::lbl::genome::gui::VistaApp
• getParameters() : gov::lbl::genome::gui::Resource, gov::lbl::genome::common::AbstractCurveModel
• getParameterString() : gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getParent() : sjg::xml::Element, gnu::jpdf::BoundingBox
• getPassword() : gov::lbl::genome::common::GenesInfo
• getPDFDocument() : gnu::jpdf::PDFObject, gnu::jpdf::PDFJob
• getPDFInfo() : gnu::jpdf::PDFDocument
• getPicture() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::panel::AxisPanel, gov::lbl::genome::gui::panel::AnnotationPanel
• getPopup() : gov::lbl::genome::gui::panel::DisplayPanel
• getPos() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::common::features::ChromSegment
• getPosition() : gov::lbl::genome::gui::Status, gov::lbl::genome::common::AbstractGraphModel
• getPositionString() : gov::lbl::genome::gui::VistaApp
• getPostHeader() : gov::lbl::genome::gui::VistaApp
• getPrev() : gov::lbl::genome::gui::History
• getPrintHeight() : gov::lbl::genome::gui::panel::DisplayPanel
• getPrintJob() : gnu::jpdf::PDFJob::graphic
• getProviderName() : gov::lbl::genome::common::VistaCurveInfo
• getProviderUrl() : gov::lbl::genome::common::VistaCurveInfo
• getPValue() : gov::lbl::genome::common::features::PValue
• getRandomString() : gov::lbl::genome::gui::VistaApp
• getRealEnd() : gov::lbl::genome::common::features::ChromSegment
• getRelX() : gov::lbl::genome::gui::Picture
• getRemoveAction() : gov::lbl::genome::gui::VistaApp
• getRepeatPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• getRepeats() : gov::lbl::genome::gui::Status
• getRoot() : sjg::xml::Document
• getRow() : layout::TableLayout
• GetRun() : gov::lbl::genome::common::GumbyCurveInfo
• getRun() : gov::lbl::genome::common::VistaCurveInfo
• getRunOrg() : gov::lbl::genome::gui::VistaCurveView, gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::VistaCurveInfo
• getRuns() : gov::lbl::genome::gui::VistaApp
• getScore() : gov::lbl::genome::common::features::PValue
• getSecondFamily() : gov::lbl::genome::common::VistaCurveInfo
• getSelectedIndices() : gov::lbl::genome::gui::panel::DisplayPanel
• getSelectedOrg() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::BaseInfoPanel
• getSelectedRadio() : gov::lbl::genome::gui::dialog::VistaDialog
• getSequence() : gov::lbl::genome::common::features::ChromPosition
• getSerialID() : gnu::jpdf::PDFObject
• getSettingsAction() : gov::lbl::genome::gui::VistaApp
• getShow() : gov::lbl::genome::gui::VistaApp
• getSize() : gov::lbl::genome::common::ChromInfo
• getSrcName() : gov::lbl::genome::common::GenesInfo
• getSrcUrl() : gov::lbl::genome::common::GenesInfo
• getStart() : gov::lbl::genome::common::features::ChromSegment
• getStartPoint() : gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getStatAction() : gov::lbl::genome::gui::VistaApp
• getStatistics() : gov::lbl::genome::gui::VistaCurveView, gov::lbl::genome::gui::panel::DisplayPanel, gov::lbl::genome::gui::GeneralGraphView
• getStrand() : gov::lbl::genome::common::features::Contig
• getStream() : gnu::jpdf::PDFStream
• getString() : gov::lbl::genome::gui::Parameter
• getStringArray() : gov::lbl::genome::gui::Parameter, gnu::jpdf::BoundingBox
• getStringBounds() : gnu::jpdf::BoundingBox
• getStringWidth() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel
• getStyle() : gnu::jpdf::PDFFont
• getSubject() : gnu::jpdf::PDFInfo
• getSuperContigNum() : gov::lbl::genome::common::features::SuperContig
• getTableName() : gov::lbl::genome::common::GenesInfo
• getTestgpvParam() : gov::lbl::genome::gui::action::UCSCBrowserAction
• getText() : sjg::xml::ProcessingInstruction, sjg::xml::Comment
• getTextbrowserURL() : gov::lbl::genome::gui::VistaApp
• getTitle() : gnu::jpdf::PDFInfo
• getTracerPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• getType() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::features::Repeat, gov::lbl::genome::common::features::PValue, gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::ChromInfo, gov::lbl::genome::common::BrowserInfo, gnu::jpdf::PDFObject, gnu::jpdf::PDFFont
• getUniqOrganisms() : gov::lbl::genome::gui::panel::DisplayPanel
• getUp2Date() : gov::lbl::genome::common::CommUnit
• getUrl() : gov::lbl::genome::common::BrowserInfo
• getValue() : sjg::xml::Attribute
• getVersion() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::common::CommUnit
• getVertSize() : gov::lbl::genome::gui::panel::VistaPanel
• getVisible() : gov::lbl::genome::gui::panel::GraphViewList
• getVisibleCurveNames() : gov::lbl::genome::gui::panel::DisplayPanel
• getWidth() : ranab::img::gif::GifScreenDescriptor, ranab::img::BaseImage, gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::AbstractCurveView, gnu::jpdf::PDFImage
• getWriter() : gnu::jpdf::PDFStream, gnu::jpdf::PDFGraphics
• getXDisplay() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::ChromPanelPicture
• getXType() : gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getXUnits() : gov::lbl::genome::common::AbstractGraphModel
• getYLabel() : gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::AbstractGraphModel
• getYLabelOrientation() : gov::lbl::genome::common::AbstractGraphModel
• getYType() : gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::CurveModel, gov::lbl::genome::common::AbstractCurveModel
• getYUnits() : gov::lbl::genome::common::AbstractGraphModel
• GifAppEx() : ranab::img::gif::GifAppEx
• GifColor() : ranab::img::gif::GifColor
• GifCommentEx() : ranab::img::gif::GifCommentEx
• GifEx() : ranab::img::gif::GifEx
• GifGraphicEx() : ranab::img::gif::GifGraphicEx
• GifHash() : ranab::img::gif::GifImage::GifHash
• GifImage() : ranab::img::gif::GifImage
• GifImageDescriptor() : ranab::img::gif::GifImageDescriptor
• GifNsAppEx() : ranab::img::gif::GifNsAppEx
• GifScreenDescriptor() : ranab::img::gif::GifScreenDescriptor
• graphic() : gnu::jpdf::PDFJob::graphic
• GraphViewList() : gov::lbl::genome::gui::panel::GraphViewList
• GumbyCurveInfo() : gov::lbl::genome::common::GumbyCurveInfo

- h -

• handle() : gov::lbl::genome::gui::ErrorHandler
• handlePixel() : gnu::jpdf::PDFImage
• hasAttribute() : sjg::xml::Element
• hasParent() : gnu::jpdf::BoundingBox
• HelpAction() : gov::lbl::genome::gui::action::HelpAction
• hidden() : layout::TableLayout
• hide() : gov::lbl::genome::common::AbstractCurveModel
• hideCursor() : gov::lbl::genome::gui::panel::TracerPanel
• hideGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• hideInvisibleElements() : gov::lbl::genome::gui::panel::GraphViewList
• History() : gov::lbl::genome::gui::History

- i -

• imageUpdate() : gnu::jpdf::PDFImage
• Increment_All() : gov::lbl::genome::common::features::ChromSegments
• init() : gov::lbl::genome::gui::VistaApp, gnu::jpdf::PDFGraphics
• insertColumn() : layout::TableLayout
• insertRow() : layout::TableLayout
• intersect() : gov::lbl::genome::common::features::ChromSegment
• invalidateLayout() : layout::TableLayout
• invisibleElementAt() : gov::lbl::genome::gui::panel::GraphViewList
• invisibleMouseCursor() : gov::lbl::genome::gui::panel::TracerPanel
• invisibleSize() : gov::lbl::genome::gui::panel::GraphViewList
• isCheckable() : gov::lbl::genome::common::CurveInfo
• isChrom() : gov::lbl::genome::gui::VistaApp
• isDangerous() : gov::lbl::genome::gui::VistaApp
• isDefault() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::GenesInfo, gov::lbl::genome::common::CurveInfo
• isDefaultVisible() : gov::lbl::genome::gui::VistaApp
• isDelayed() : ranab::img::gif::GifGraphicEx
• isDeleted() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::AbstractCurveModel
• isDownEnabled() : gov::lbl::genome::gui::panel::ArrowsPanel
• isForward() : gov::lbl::genome::common::features::Gene
• isFree() : ranab::img::gif::GifImage::CodeEntry
• isHidden() : gov::lbl::genome::common::AbstractCurveModel
• isIdle1() : gov::lbl::genome::gui::VistaApp
• isIdle2() : gov::lbl::genome::gui::VistaApp
• isIdle3() : gov::lbl::genome::gui::VistaApp
• isInside() : gov::lbl::genome::gui::panel::ChromPanelPicture
• isMatch() : ranab::img::gif::GifImage::CodeEntry
• isNearEast() : gov::lbl::genome::gui::panel::ChromPanelPicture
• isNearWest() : gov::lbl::genome::gui::panel::ChromPanelPicture
• isNextEmpty() : gov::lbl::genome::gui::History
• isPopup() : gov::lbl::genome::gui::panel::TracerPanel
• isPrevEmpty() : gov::lbl::genome::gui::History
• isReady() : gov::lbl::genome::gui::VistaApp
• isRealChrom() : gov::lbl::genome::common::features::ChromSegment
• isSelected() : gov::lbl::genome::gui::GeneralGraphView
• isTemp() : gov::lbl::genome::common::VistaCurveInfo
• isTransparent() : ranab::img::gif::GifGraphicEx
• isUpEnabled() : gov::lbl::genome::gui::panel::ArrowsPanel
• isVisible() : gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::common::CurveInfo
• iterator() : gov::lbl::genome::gui::panel::GraphViewList

- j -

• jbInit() : gov::lbl::genome::gui::panel::StatPanel, gov::lbl::genome::gui::panel::SearchResultsPanel, gov::lbl::genome::gui::panel::SaveAsPanel, gov::lbl::genome::gui::panel::LegendPanel

- l -

• lastElement() : gov::lbl::genome::gui::panel::GraphViewList
• lastPageFirst() : gnu::jpdf::PDFJob
• lastPosition() : gov::lbl::genome::gui::VistaApp
• layoutContainer() : layout::TableLayout
• LegendPanel() : gov::lbl::genome::gui::panel::LegendPanel
• lineto() : gnu::jpdf::PDFGraphics
• LinkLabel() : gov::lbl::genome::gui::LinkLabel
• listIterator() : gov::lbl::genome::gui::panel::GraphViewList
• lockDown() : gov::lbl::genome::gui::panel::ArrowsPanel
• lockUp() : gov::lbl::genome::gui::panel::ArrowsPanel

- m -

• main() : gnu::jpdf::PDFTest, gnu::jpdf::BoundingBox
• makePDFString() : gnu::jpdf::PDFStringHelper
• maximumLayoutSize() : layout::TableLayout
• MergeWith() : gov::lbl::genome::common::features::ChromSegments
• minimumLayoutSize() : layout::TableLayout
• mouseClicked() : gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::LinkLabel
• mouseDragged() : gov::lbl::genome::gui::panel::TracerPanel
• mouseEntered() : gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::LinkLabel
• mouseExited() : gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::LinkLabel
• mouseMoved() : gov::lbl::genome::gui::panel::TracerPanel
• mousePressed() : gov::lbl::genome::gui::panel::TracerPanel
• mouseReleased() : gov::lbl::genome::gui::panel::TracerPanel
• moveMouseCursor() : gov::lbl::genome::gui::panel::ChromPanel
• moveSelectedDown() : gov::lbl::genome::gui::panel::DisplayPanel
• moveSelectedUp() : gov::lbl::genome::gui::panel::DisplayPanel
• moveto() : gnu::jpdf::PDFGraphics
• multiSelectGraphs() : gov::lbl::genome::gui::panel::DisplayPanel

- n -

• newPath() : gnu::jpdf::PDFGraphics
• newTextBlock() : gnu::jpdf::PDFGraphics
• nextPosition() : gov::lbl::genome::gui::VistaApp

- o -

• okAction() : gov::lbl::genome::gui::dialog::StatDialog, gov::lbl::genome::gui::dialog::SearchResultsDialog, gov::lbl::genome::gui::dialog::SaveAsDialog, gov::lbl::genome::gui::dialog::ContigListDialog, gov::lbl::genome::gui::dialog::ActionDialog
• Overlap() : gov::lbl::genome::common::features::ChromSegments
• overlapping() : layout::TableLayout

- p -

• PageSetupAction() : gov::lbl::genome::gui::action::PageSetupAction
• paintComponent() : gov::lbl::genome::gui::VistaLabel, gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::gui::GeneralGraphComp
• Parameter() : gov::lbl::genome::gui::Parameter
• parse() : sjg::xml::Parser
• parsePos() : gov::lbl::genome::common::features::ChromSegment
• parseSpan() : gov::lbl::genome::common::features::ChromSegment
• PCurveModel() : gov::lbl::genome::common::PCurveModel
• PDFAnnot() : gnu::jpdf::PDFAnnot
• PDFBorder() : gnu::jpdf::PDFBorder
• PDFCatalog() : gnu::jpdf::PDFCatalog
• PDFDocument() : gnu::jpdf::PDFDocument
• PDFFont() : gnu::jpdf::PDFFont
• PDFImage() : gnu::jpdf::PDFImage
• PDFInfo() : gnu::jpdf::PDFInfo
• PDFJob() : gnu::jpdf::PDFJob
• PDFObject() : gnu::jpdf::PDFObject
• PDFOutline() : gnu::jpdf::PDFOutline
• PDFOutput() : gnu::jpdf::PDFOutput
• PDFPage() : gnu::jpdf::PDFPage
• PDFPageList() : gnu::jpdf::PDFPageList
• PDFStream() : gnu::jpdf::PDFStream
• PDFXref() : gnu::jpdf::PDFXref
• Picture() : gov::lbl::genome::gui::Picture
• polygon() : gnu::jpdf::PDFGraphics
• popupOff() : gov::lbl::genome::gui::panel::TracerPanel
• positionFormat() : gov::lbl::genome::common::features::ChromSegment
• preferredLayoutSize() : layout::TableLayout
• print() : gov::lbl::genome::gui::panel::VGBPanel, gov::lbl::genome::gui::panel::DisplayPanel
• PrintAction() : gov::lbl::genome::gui::action::PrintAction
• printColor() : ranab::img::gif::GifImage
• PrinterSetupAction() : gov::lbl::genome::gui::action::PrinterSetupAction
• printInfo() : gov::lbl::genome::gui::VistaCurveView, gov::lbl::genome::gui::GeneralGraphComp
• printStatusBar() : gov::lbl::genome::gui::VistaApp
• ProcessingInstruction() : sjg::xml::ProcessingInstruction
• push() : gov::lbl::genome::gui::History
• pushInHistory() : gov::lbl::genome::gui::VistaApp
• PValue() : gov::lbl::genome::common::features::PValue
• PValueCurveView() : gov::lbl::genome::gui::PValueCurveView

- r -

• rebuildPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• redispatchMouseEvent() : gov::lbl::genome::gui::panel::TracerPanel
• refresh() : gov::lbl::genome::gui::GraphView, gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::gui::CurveView, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::CustomCurveModel, gov::lbl::genome::common::CurveModel
• refreshAnnotations() : gov::lbl::genome::gui::panel::DisplayPanel
• refreshGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• refreshOrgList() : gov::lbl::genome::gui::VistaApp
• release() : gov::lbl::genome::gui::VistaApp
• RemoveAction() : gov::lbl::genome::gui::action::RemoveAction
• removeAll() : gov::lbl::genome::gui::panel::GraphViewList
• removeAllElements() : gov::lbl::genome::gui::panel::GraphViewList
• removeAllGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• removeAllSelectedGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• removeBarImage() : gov::lbl::genome::gui::panel::TracerPanel
• removeChromSegment() : gov::lbl::genome::common::features::ChromSegments
• removeCompImage() : gov::lbl::genome::gui::GeneralGraphView
• removeDataImages() : gov::lbl::genome::gui::panel::DisplayPanel
• removeElementAt() : gov::lbl::genome::gui::panel::GraphViewList
• removeGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• removeImage() : gov::lbl::genome::gui::panel::VistaPanel, gov::lbl::genome::gui::panel::TracerPanel, gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::gui::GeneralGraphComp
• removeLayoutComponent() : layout::TableLayout
• render() : gov::lbl::genome::gui::VistaCurveView, gov::lbl::genome::gui::PValueCurveView, gov::lbl::genome::gui::CurveView
• renderInitialize() : gov::lbl::genome::gui::AbstractCurveView
• repaint() : gov::lbl::genome::gui::panel::ChromPanel
• repaintTracerPanels() : gov::lbl::genome::gui::panel::DisplayPanel
• Repeat() : gov::lbl::genome::common::features::Repeat
• repeatLegend() : gov::lbl::genome::gui::panel::DisplayPanel
• RepeatPanel() : gov::lbl::genome::gui::panel::RepeatPanel
• RepeatPanelPicture() : gov::lbl::genome::gui::panel::RepeatPanelPicture
• replaceGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• requestAnnotations() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::AnnotationPanel
• rereadInitInfo() : gov::lbl::genome::gui::panel::BaseInfoPanel
• reRenderOff() : gov::lbl::genome::gui::AbstractCurveView
• reRenderOn() : gov::lbl::genome::gui::AbstractCurveView
• reset() : ranab::img::gif::GifImage::CodeEntry, ranab::img::gif::GifImage::GifHash, gov::lbl::genome::gui::panel::TracerPanel
• resetBaseGenome() : gov::lbl::genome::gui::panel::BaseInfoPanel
• resetConnection() : gov::lbl::genome::gui::VistaApp
• resetCounter1() : gov::lbl::genome::gui::VistaApp
• resetCounter2() : gov::lbl::genome::gui::VistaApp
• resetCounter3() : gov::lbl::genome::gui::VistaApp
• resetDefaultBaseGenome() : gov::lbl::genome::gui::panel::BaseInfoPanel
• resetDelay() : ranab::img::gif::GifImage, ranab::img::gif::GifGraphicEx
• resetOrgList() : gov::lbl::genome::gui::panel::BaseInfoPanel
• resetPicture() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::panel::AnnotationPanel
• resetPrintedGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• resetTransparency() : ranab::img::gif::GifImage
• resetXBorders() : gov::lbl::genome::gui::panel::DisplayPanel
• Resource() : gov::lbl::genome::gui::Resource
• retrieveInitInfo() : gov::lbl::genome::gui::panel::BaseInfoPanel
• run() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::GeneSearchPanel, gov::lbl::genome::gui::action::ZoomOutAction, gov::lbl::genome::gui::action::ZoomInAction, gov::lbl::genome::gui::action::VAbstractAction, gov::lbl::genome::gui::action::UCSCBrowserAction, gov::lbl::genome::gui::action::SwapCurvesAction, gov::lbl::genome::gui::action::StatAction, gov::lbl::genome::gui::action::SettingsAction, gov::lbl::genome::gui::action::ScrollForwardAction, gov::lbl::genome::gui::action::ScrollBackwardAction, gov::lbl::genome::gui::action::SaveAsAction, gov::lbl::genome::gui::action::RemoveAction, gov::lbl::genome::gui::action::PrinterSetupAction, gov::lbl::genome::gui::action::PrintAction, gov::lbl::genome::gui::action::PageSetupAction, gov::lbl::genome::gui::action::HelpAction, gov::lbl::genome::gui::action::ForwardAction, gov::lbl::genome::gui::action::DetailsAction, gov::lbl::genome::gui::action::BackAction, gov::lbl::genome::gui::action::AddAction, gov::lbl::genome::gui::action::AboutAction

- s -

• SaveAsAction() : gov::lbl::genome::gui::action::SaveAsAction
• SaveAsDialog() : gov::lbl::genome::gui::dialog::SaveAsDialog
• SaveAsPanel() : gov::lbl::genome::gui::panel::SaveAsPanel
• saveData() : gov::lbl::genome::gui::action::SaveAsAction
• ScrollBackwardAction() : gov::lbl::genome::gui::action::ScrollBackwardAction
• ScrollForwardAction() : gov::lbl::genome::gui::action::ScrollForwardAction
• SearchResultsDialog() : gov::lbl::genome::gui::dialog::SearchResultsDialog
• SearchResultsPanel() : gov::lbl::genome::gui::panel::SearchResultsPanel
• select() : gov::lbl::genome::gui::GeneralGraphView
• selectChildren() : gov::lbl::genome::gui::GeneralGraphView
• selectGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• sendRequest() : gov::lbl::genome::common::CommUnit
• set() : ranab::img::gif::GifImage::CodeEntry
• Set_ChromSegment() : gov::lbl::genome::common::features::ChromSegments
• setAbsoluteLocation() : gnu::jpdf::BoundingBox
• setAnnotations() : gov::lbl::genome::gui::panel::RepeatPanel, gov::lbl::genome::gui::panel::AnnotationPanel, gov::lbl::genome::common::AbstractCurveModel
• setApplet() : gov::lbl::genome::gui::LinkLabel
• setArrows() : gov::lbl::genome::gui::panel::DisplayPanel
• setAsDefault() : gov::lbl::genome::common::CurveInfo
• setAuthor() : gnu::jpdf::PDFInfo
• setBackground() : ranab::img::gif::GifScreenDescriptor
• setBaseGenome() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::BaseInfoPanel
• setBorder() : gnu::jpdf::PDFAnnot
• setCheckable() : gov::lbl::genome::common::CurveInfo
• setCheckedCurves() : gov::lbl::genome::common::GenomeInfo
• setChrom() : gov::lbl::genome::gui::VistaApp
• setChromosome() : gov::lbl::genome::common::features::ChromSegment
• setClip() : gnu::jpdf::PDFGraphics
• setCodeBaseURL() : gov::lbl::genome::common::CommUnit
• setColor() : gnu::jpdf::PDFGraphics
• setColumn() : layout::TableLayout
• setComment() : ranab::img::gif::GifCommentEx
• setComponent() : gov::lbl::genome::gui::Picture
• setComponentsAction() : gov::lbl::genome::gui::dialog::VistaDialog
• setCompSize() : gov::lbl::genome::gui::GeneralGraphComp
• setConstraints() : layout::TableLayout
• setContig() : gov::lbl::genome::gui::panel::CursorInfoPanel, gov::lbl::genome::gui::panel::BaseInfoPanel, gov::lbl::genome::common::GenomeInfo
• setContigs() : gov::lbl::genome::gui::panel::ContigPanel, gov::lbl::genome::gui::GeneralGraphView
• setCreator() : gnu::jpdf::PDFInfo
• setCurrentPos() : gov::lbl::genome::common::GenomeInfo
• setCurveInfo() : gov::lbl::genome::common::AbstractCurveModel
• setCurveModel() : gov::lbl::genome::gui::CurveView, gov::lbl::genome::gui::AbstractCurveView
• setCurveModels() : gov::lbl::genome::common::GeneralGraphModel
• setDangerous() : gov::lbl::genome::gui::VistaApp
• setData() : gov::lbl::genome::common::AbstractCurveModel
• setDebug() : gov::lbl::genome::gui::Resource, gov::lbl::genome::gui::Picture
• setDebugExceptions() : gov::lbl::genome::gui::Debug
• setDebugLevel() : gov::lbl::genome::gui::VistaApp
• setDebugMode() : gov::lbl::genome::gui::Debug
• setDefaultBaseGenome() : gov::lbl::genome::gui::panel::BaseInfoPanel
• setDefaultLineWidth() : gnu::jpdf::PDFGraphics
• setDeflate() : gnu::jpdf::PDFStream
• setDelay() : ranab::img::gif::GifImage, ranab::img::gif::GifGraphicEx
• setDeleted() : gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::CurveInfo
• setDetails() : gov::lbl::genome::gui::panel::DisplayPanel
• setDetailsActionEnabled() : gov::lbl::genome::gui::VistaApp
• setDragged() : gov::lbl::genome::gui::panel::TracerPanel
• setDsEnd() : gov::lbl::genome::common::features::Contig
• setDsStart() : gov::lbl::genome::common::features::Contig
• setElementAt() : gov::lbl::genome::gui::panel::GraphViewList
• setEnd() : gov::lbl::genome::common::features::ChromSegment
• setFixedRows() : gov::lbl::genome::gui::panel::DisplayPanel
• setFont() : gnu::jpdf::PDFGraphics
• setForwardBackBtns() : gov::lbl::genome::gui::VistaApp
• setFullString() : gnu::jpdf::BoundingBox
• setGraphModel() : gov::lbl::genome::gui::GeneralGraphView
• setGraphPos() : gov::lbl::genome::gui::GeneralGraphView
• setGraphView() : gov::lbl::genome::gui::CurveView, gov::lbl::genome::gui::AbstractCurveView
• setHeight() : gnu::jpdf::PDFImage
• setImage() : gov::lbl::genome::gui::panel::VistaPanel, gnu::jpdf::PDFImage
• setImageableArea() : gov::lbl::genome::gui::Picture
• setImageName() : gnu::jpdf::PDFDocument
• setIterationCount() : ranab::img::gif::GifNsAppEx, ranab::img::gif::GifImage
• setKeywords() : gnu::jpdf::PDFInfo
• setLineNumber() : gov::lbl::genome::gui::AbstractCurveView
• setLineWidth() : gnu::jpdf::PDFGraphics
• setLink() : gov::lbl::genome::gui::LinkLabel
• setLocation() : gov::lbl::genome::gui::SplashWindow, gov::lbl::genome::gui::dialog::VistaDialog, gov::lbl::genome::gui::dialog::ActionDialog
• setLongName() : gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::AbstractGraphModel
• setMarginLeft() : gov::lbl::genome::gui::AbstractCurveView
• setMarginRight() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::AbstractCurveView
• setMargins() : gov::lbl::genome::gui::Picture
• setMarginTop() : gov::lbl::genome::gui::AbstractCurveView
• setMaxX() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::AbstractCurveView
• setMaxY() : gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::AbstractGraphModel
• setMedia() : gnu::jpdf::PDFPage
• setMinMaxX() : gov::lbl::genome::gui::Picture
• setMinX() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::AbstractCurveView
• setMinY() : gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::VistaCurveModel, gov::lbl::genome::common::PCurveModel, gov::lbl::genome::common::AbstractGraphModel
• setName() : gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::common::GeneralGraphModel, gov::lbl::genome::common::AbstractGraphModel, gnu::jpdf::PDFImage
• setNewHeight() : gov::lbl::genome::gui::VistaApp
• setNewSize() : gov::lbl::genome::gui::VistaApp
• setNewWidth() : gov::lbl::genome::gui::VistaApp
• setOrgLabel() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::BaseInfoPanel
• setOrgList() : gov::lbl::genome::gui::panel::BaseInfoPanel
• setOrientation() : gnu::jpdf::PDFPage, gnu::jpdf::PDFGraphics
• setOutline() : gnu::jpdf::PDFCatalog
• setPage() : gov::lbl::genome::gui::Picture
• setPaintMode() : gnu::jpdf::PDFGraphics
• setParam() : gov::lbl::genome::gui::VistaApp
• setParent() : gov::lbl::genome::gui::GeneralGraphView, gnu::jpdf::BoundingBox
• setPDFInfo() : gnu::jpdf::PDFDocument
• setPosition() : gov::lbl::genome::gui::panel::CursorInfoPanel, gov::lbl::genome::common::AbstractGraphModel
• setPositionString() : gov::lbl::genome::gui::VistaApp
• setPrintCapacity() : gov::lbl::genome::gui::panel::DisplayPanel
• setReady() : gov::lbl::genome::gui::VistaApp
• setRealChrom() : gov::lbl::genome::common::features::ChromSegment
• setRegion() : gov::lbl::genome::gui::panel::GeneSearchPanel
• setRow() : layout::TableLayout
• setSelected() : gov::lbl::genome::gui::GeneralGraphView
• setSelectedIndices() : gov::lbl::genome::gui::panel::DisplayPanel
• setServletURL() : gov::lbl::genome::common::CommUnit
• setSettings() : gov::lbl::genome::gui::panel::DisplayPanel
• setSettingsVisible() : gov::lbl::genome::gui::VistaApp
• setSize() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::AbstractCurveView
• setStart() : gov::lbl::genome::common::features::ChromSegment
• setStringArray() : gnu::jpdf::BoundingBox
• setStroke() : gov::lbl::genome::gui::AbstractCurveView
• setSubject() : gnu::jpdf::PDFInfo
• setText() : gov::lbl::genome::gui::LinkLabel
• setThumbnail() : gnu::jpdf::PDFPage
• SettingsAction() : gov::lbl::genome::gui::action::SettingsAction
• setTip() : gov::lbl::genome::gui::action::UCSCBrowserAction
• setTitle() : gnu::jpdf::PDFInfo
• setTracerPanel() : gov::lbl::genome::gui::panel::DisplayPanel
• setTransparency() : ranab::img::gif::GifImage, ranab::img::gif::GifGraphicEx
• setUCSCActionTip() : gov::lbl::genome::gui::VistaApp
• setVisible() : gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::common::CurveInfo
• setWidth() : gnu::jpdf::PDFImage
• setXBorders() : gov::lbl::genome::gui::panel::DisplayPanel
• setXORMode() : gnu::jpdf::PDFGraphics
• setYLabel() : gov::lbl::genome::common::AbstractGraphModel
• setYLabelOrientation() : gov::lbl::genome::common::AbstractGraphModel
• setZ() : gov::lbl::genome::gui::Picture
• shortenString() : gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::panel::VistaPanel
• show() : gov::lbl::genome::common::AbstractCurveModel
• showCursor() : gov::lbl::genome::gui::panel::TracerPanel
• showGraph() : gov::lbl::genome::gui::panel::DisplayPanel
• size() : gov::lbl::genome::gui::panel::GraphViewList
• sort() : gov::lbl::genome::gui::QSortAlgorithm
• SplashWindow() : gov::lbl::genome::gui::SplashWindow
• startProgress() : gov::lbl::genome::gui::VistaApp
• StatAction() : gov::lbl::genome::gui::action::StatAction
• StatDialog() : gov::lbl::genome::gui::dialog::StatDialog
• StatPanel() : gov::lbl::genome::gui::panel::StatPanel
• Status() : gov::lbl::genome::gui::Status
• stopProgress() : gov::lbl::genome::gui::VistaApp
• StringInputStream() : gov::lbl::genome::common::StringInputStream
• StringTooLongException() : gnu::jpdf::StringTooLongException
• subtract() : gnu::jpdf::BoundingBox
• SuperContig() : gov::lbl::genome::common::features::SuperContig
• swapCurves() : gov::lbl::genome::gui::VistaApp
• SwapCurvesAction() : gov::lbl::genome::gui::action::SwapCurvesAction
• swapElements() : gov::lbl::genome::gui::panel::GraphViewList
• swapGraphs() : gov::lbl::genome::gui::panel::DisplayPanel

- t -

• TableLayout() : layout::TableLayout
• TableLayoutConstraints() : layout::TableLayoutConstraints
• testPosition() : gov::lbl::genome::gui::VistaApp
• toArray() : gnu::jpdf::PDFObject
• toString() : sjg::xml::ProcessingInstruction, sjg::xml::Element, sjg::xml::Document, sjg::xml::Data, sjg::xml::Comment, layout::TableLayoutConstraints, layout::TableLayout, gov::lbl::genome::gui::Status, gov::lbl::genome::gui::Picture, gov::lbl::genome::gui::GeneralGraphView, gov::lbl::genome::gui::GeneralGraphComp, gov::lbl::genome::gui::CurveParameters, gov::lbl::genome::gui::AbstractCurveView, gov::lbl::genome::common::VistaCurveInfo, gov::lbl::genome::common::GenomeInfo, gov::lbl::genome::common::GenesInfo, gov::lbl::genome::common::features::SuperContig, gov::lbl::genome::common::features::Repeat, gov::lbl::genome::common::features::PValue, gov::lbl::genome::common::features::Gene, gov::lbl::genome::common::features::Contig, gov::lbl::genome::common::features::ChromSegment, gov::lbl::genome::common::CurveInfo, gov::lbl::genome::common::ChromInfo, gov::lbl::genome::common::BrowserInfo, gnu::jpdf::PDFXref, gnu::jpdf::PDFObject
• touches() : gov::lbl::genome::common::features::ChromSegment
• TracerPanel() : gov::lbl::genome::gui::panel::TracerPanel
• translate() : gov::lbl::genome::gui::Picture, gnu::jpdf::PDFGraphics

- u -

• UCSCBrowserAction() : gov::lbl::genome::gui::action::UCSCBrowserAction
• uiInit() : gov::lbl::genome::gui::panel::GeneSearchPanel, gov::lbl::genome::gui::GeneralGraphView
• Union() : gov::lbl::genome::common::features::ChromSegments
• unlockDown() : gov::lbl::genome::gui::panel::ArrowsPanel
• unlockUp() : gov::lbl::genome::gui::panel::ArrowsPanel
• unselect() : gov::lbl::genome::gui::GeneralGraphView
• unselectAllGraphs() : gov::lbl::genome::gui::panel::DisplayPanel
• unselectChildren() : gov::lbl::genome::gui::GeneralGraphView
• upDate() : gov::lbl::genome::gui::VistaApp
• updateColor() : ranab::img::gif::GifColor
• updateColorTable() : ranab::img::gif::GifImage
• updateContig() : gov::lbl::genome::gui::VistaApp
• updateCurrPosition() : gov::lbl::genome::gui::VistaApp
• updatePosition() : gov::lbl::genome::gui::VistaApp, gov::lbl::genome::gui::panel::DisplayPanel
• updateSelectList() : gov::lbl::genome::gui::panel::DisplayPanel

- v -

• VAbstractAction() : gov::lbl::genome::gui::action::VAbstractAction
• VGBException() : gov::lbl::genome::common::VGBException
• VGBPanel() : gov::lbl::genome::gui::panel::VGBPanel
• visible() : gov::lbl::genome::gui::panel::TracerPanel
• VistaApp() : gov::lbl::genome::gui::VistaApp
• VistaCurveInfo() : gov::lbl::genome::common::VistaCurveInfo
• VistaCurveModel() : gov::lbl::genome::common::VistaCurveModel
• VistaCurveView() : gov::lbl::genome::gui::VistaCurveView
• VistaDialog() : gov::lbl::genome::gui::dialog::VistaDialog
• VistaLabel() : gov::lbl::genome::gui::VistaLabel
• VistaPanel() : gov::lbl::genome::gui::panel::VistaPanel

- w -

• waitMouseCursor() : gov::lbl::genome::gui::panel::TracerPanel
• westMouseCursor() : gov::lbl::genome::gui::panel::ChromPanel
• windowClosing() : gov::lbl::genome::gui::VistaApp
• write() : ranab::img::gif::GifScreenDescriptor, ranab::img::gif::GifNsAppEx, ranab::img::gif::GifImageDescriptor, ranab::img::gif::GifGraphicEx, ranab::img::gif::GifEx, ranab::img::gif::GifCommentEx, ranab::img::gif::GifColor, gnu::jpdf::PDFStream, gnu::jpdf::PDFPageList, gnu::jpdf::PDFPage::procset, gnu::jpdf::PDFPage, gnu::jpdf::PDFOutput, gnu::jpdf::PDFOutline, gnu::jpdf::PDFObject, gnu::jpdf::PDFInfo, gnu::jpdf::PDFImage, gnu::jpdf::PDFFont, gnu::jpdf::PDFDocument, gnu::jpdf::PDFCatalog, gnu::jpdf::PDFBorder, gnu::jpdf::PDFAnnot
• writeblock() : gnu::jpdf::PDFOutput
• writeEnd() : gnu::jpdf::PDFObject
• writeStart() : gnu::jpdf::PDFObject
• writeStream() : gnu::jpdf::PDFStream, gnu::jpdf::PDFImage

- x -

• X() : gov::lbl::genome::gui::Picture
• XAxisPanel() : gov::lbl::genome::gui::panel::XAxisPanel
• xDisplay() : gov::lbl::genome::gui::AbstractCurveView

- y -

• Y() : gov::lbl::genome::gui::Picture

- z -

• ZoomInAction() : gov::lbl::genome::gui::action::ZoomInAction
• ZoomOutAction() : gov::lbl::genome::gui::action::ZoomOutAction

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