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A

ABCD - Static variable in class layout.TableLayoutConstraints
AboutAction - Class in gov.lbl.genome.gui.action: Title: About
AboutAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.AboutAction: AboutAction
AboutAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.AboutAction
AbstractActionDialogPanel - Class in gov.lbl.genome.gui.panel: Title: AbstractActionDialogPanel
AbstractActionDialogPanel(ActionDialog, boolean, boolean) - Constructor for class gov.lbl.genome.gui.panel.AbstractActionDialogPanel: AbstractActionDialogPanel
AbstractCurveModel - Class in gov.lbl.genome.common: Title: AbstractCurveModel
AbstractCurveModel(TreeMap) - Constructor for class gov.lbl.genome.common.AbstractCurveModel: AbstractCurveModel
AbstractCurveView - Class in gov.lbl.genome.gui: Title: AbstractCurveView
AbstractCurveView() - Constructor for class gov.lbl.genome.gui.AbstractCurveView
AbstractGraphModel - Class in gov.lbl.genome.common: Title: AbstractGraphModel
AbstractGraphModel() - Constructor for class gov.lbl.genome.common.AbstractGraphModel
action - Variable in class gov.lbl.genome.gui.action.VAbstractAction
action - Static variable in class gov.lbl.genome.gui.Debug
ActionDialog - Class in gov.lbl.genome.gui.dialog: Title: ActionDialog
ActionDialog(JApplet, String, boolean, int, Callback) - Constructor for class gov.lbl.genome.gui.dialog.ActionDialog: ActionDialog
ActionDialog(JApplet, String, boolean) - Constructor for class gov.lbl.genome.gui.dialog.ActionDialog: ActionDialog
ActionDialog(JApplet) - Constructor for class gov.lbl.genome.gui.dialog.ActionDialog: ActionDialog
actionIcon - Variable in class gov.lbl.genome.gui.action.VAbstractAction
actionPerformed(ActionEvent) - Method in class gnu.jpdf.PDFTest: Very basic action handler - a more robust app would use Action objects
actionPerformed(ActionEvent) - Method in class gov.lbl.genome.gui.action.BackAction: Show previous available position from history
actionPerformed(ActionEvent) - Method in class gov.lbl.genome.gui.action.ForwardAction: Show next available position from history
actionPerformed(ActionEvent) - Method in class gov.lbl.genome.gui.action.VAbstractAction: Usually you do not touch this method and use overriden run() But if you want to execute your action in the same thread, then override it.
actionThread - Variable in class gov.lbl.genome.gui.action.VAbstractAction
activeTracerPanel - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
ad - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
add(BoundingBox) - Method in class gnu.jpdf.BoundingBox: Make the specified box this box's child.
add(PDFObject) - Method in class gnu.jpdf.PDFDocument: This adds a top level object to the document.
add(String, PDFPage) - Method in class gnu.jpdf.PDFOutline: This method creates an outline, and attaches it to this one.
add(String, PDFPage, int, int, int, int) - Method in class gnu.jpdf.PDFOutline: This method creates an outline, and attaches it to this one.
add(PDFOutline) - Method in class gnu.jpdf.PDFOutline: This adds an already existing outline to this one.
add(PDFObject) - Method in class gnu.jpdf.PDFPage: This adds an object that describes some content to this page.
add(String) - Method in class gnu.jpdf.PDFPage.procset
add(PDFPage) - Method in class gnu.jpdf.PDFPageList: This adds a page to the document.
add(ChromSegment) - Method in class gov.lbl.genome.common.features.ChromSegment: Merges the specified chromosome segment with this segment
add(int, Object) - Method in class gov.lbl.genome.gui.panel.GraphViewList: add visible element
Add_ChromSegment(ChromSegment) - Method in class gov.lbl.genome.common.features.ChromSegments: Add ChromSegment
Add_ChromSegment(ChromSegment, long, long) - Method in class gov.lbl.genome.common.features.ChromSegments: Add ChromSegment
AddAction - Class in gov.lbl.genome.gui.action: Title: Add curve
AddAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.AddAction: AddAction
AddAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.AddAction: AddAction
addAnnotation(PDFObject) - Method in class gnu.jpdf.PDFPage: This adds an Annotation to the page.
addCurve(CurveModel) - Method in class gov.lbl.genome.common.GeneralGraphModel: add Curve
addCurve(CurveInfo) - Method in class gov.lbl.genome.common.GenomeInfo: add Curve
addCurve(CurveView) - Method in class gov.lbl.genome.gui.GeneralGraphView: add Curve
addCurves(Status) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: add Curves that are saved in status
addDefaultCurve(GenomeInfo) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: add Default Curves for the genome
addElement(Object) - Method in class gov.lbl.genome.gui.panel.GraphViewList: addElement.
addGraph(GeneralGraphView) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: add new Graph to the and
addImage(GifImage) - Method in class ranab.img.gif.GifImage: Add image - animation
addImageResource(String) - Method in class gnu.jpdf.PDFPage
addLayoutComponent(String, Component) - Method in class layout.TableLayout: Adds the specified component with the specified name to the layout.
addLayoutComponent(Component, Object) - Method in class layout.TableLayout: Adds the specified component with the specified name to the layout.
addLink(int, int, int, int, PDFObject) - Method in class gnu.jpdf.PDFPage: Adds a hyperlink to the document.
addLink(int, int, int, int, PDFObject, int, int, int, int) - Method in class gnu.jpdf.PDFPage: Adds a hyperlink to the document.
addNote(String, int, int, int, int) - Method in class gnu.jpdf.PDFJob: Convenience method: Adds a text note to the document.
addNote(String, int, int, int, int) - Method in class gnu.jpdf.PDFPage: This method adds a text note to the document.
addOutline(String) - Method in class gnu.jpdf.PDFJob: This method attaches an outline to the current page being generated.
addOutline(String, int, int, int, int) - Method in class gnu.jpdf.PDFJob: This method attaches an outline to the current page being generated.
addOutline(String) - Method in class gnu.jpdf.PDFPage: This method attaches an outline to the current page being generated.
addOutline(String, int, int, int, int) - Method in class gnu.jpdf.PDFPage: This method attaches an outline to the current page being generated.
addPoint(Point2D.Float) - Method in class gov.lbl.genome.common.AbstractCurveModel
addPoint(Point2D.Float) - Method in interface gov.lbl.genome.common.CurveModel: add Point
addPrintedGraph(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: add graph to a printedGraph list.
addResource(String) - Method in class gnu.jpdf.PDFPage: This adds a resource to the page.
addToProcset(String) - Method in class gnu.jpdf.PDFPage
addXObject(String) - Method in class gnu.jpdf.PDFPage: This adds an XObject resource to the page.
adjustedGraphHeight - Variable in class gov.lbl.genome.gui.AbstractCurveView
adjustedGraphWidth - Variable in class gov.lbl.genome.gui.AbstractCurveView
ANNOTATION_HEIGHT - Variable in class gov.lbl.genome.gui.panel.AnnotationPanel
ANNOTATION_HEIGHT - Variable in class gov.lbl.genome.gui.panel.AnnotationPanelPicture
ANNOTATION_PANEL_HEIGHT - Static variable in interface gov.lbl.genome.gui.UIConstants
annotationLegend(Graphics, Color, int, int, String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: draw annotation legend
AnnotationPanel - Class in gov.lbl.genome.gui.panel: Title: AnnotationPanel
AnnotationPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.AnnotationPanel: AnnotationPanel
AnnotationPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.AnnotationPanel: AnnotationPanel
AnnotationPanelPicture - Class in gov.lbl.genome.gui.panel: Title: AnnotationPanelPicture
AnnotationPanelPicture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.panel.AnnotationPanelPicture: AnnotationPanelPicture
annotations - Variable in class gnu.jpdf.PDFPage: This holds any Annotations contained within this page.
annotations - Variable in class gov.lbl.genome.common.AbstractCurveModel
arc(double, double, double, double, double, double, boolean) - Method in class gnu.jpdf.PDFGraphics: This produces an arc by breaking it down into one or more Bezier curves.
ArrowsPanel - Class in gov.lbl.genome.gui.panel: Title: ArrowsPanel
ArrowsPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.ArrowsPanel: small panel with UP and DOWN buttons
ASCII_ARRAY - Static variable in interface gov.lbl.genome.gui.UIConstants
Attribute - Class in sjg.xml: An xml attribute.
available() - Method in class gov.lbl.genome.common.StringInputStream
available - Variable in class gov.lbl.genome.gui.Parameter
AXIS_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
axisPanel - Variable in class gov.lbl.genome.gui.GeneralGraphView
AxisPanel - Class in gov.lbl.genome.gui.panel: Title: AxisPanel
AxisPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.AxisPanel: AxisPanel
AxisPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.AxisPanel: AxisPanel
axisPanel - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
AxisPanelPicture - Class in gov.lbl.genome.gui.panel: Title: AxisPanelPicture
AxisPanelPicture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.panel.AxisPanelPicture: AxisPanelPicture

B

BackAction - Class in gov.lbl.genome.gui.action: Title: Show last position
BackAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.BackAction: BackAction
BackAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.BackAction: BackAction
BadCoordinateTypeException - Exception in gov.lbl.genome.common: Title: BadCoordinateTypeException
BadCoordinateTypeException() - Constructor for exception gov.lbl.genome.common.BadCoordinateTypeException: Bad Type of Coordinate
BadCoordinateTypeException(String) - Constructor for exception gov.lbl.genome.common.BadCoordinateTypeException: Bad Type of Coordinate
baos - Variable in class gnu.jpdf.PDFOutput: This is the OutputStream used to write each object to.
barImage - Variable in class gov.lbl.genome.gui.panel.TracerPanel
base - Variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
base - Variable in class gov.lbl.genome.gui.panel.ChromPanel
base - Variable in class gov.lbl.genome.gui.panel.ChromPanelPicture
base - Variable in class gov.lbl.genome.gui.panel.XAxisPanel
BaseInfoPanel - Class in gov.lbl.genome.gui.panel: Title: BaseInfoPanel
BaseInfoPanel(VistaApp, String, String) - Constructor for class gov.lbl.genome.gui.panel.BaseInfoPanel: BaseInfoPanel
BEVELED - Static variable in class gnu.jpdf.PDFAnnot: The border is drawn in a beveled style (faux three-dimensional) such that it looks as if it is pushed out of the page (opposite of INSET)
bottom - Variable in class gov.lbl.genome.gui.panel.VistaPanel
BOTTOM - Static variable in interface layout.TableLayoutConstants: Indicates that the component is bottom justified in its cell
bottomSpace - Variable in class gov.lbl.genome.gui.panel.VistaPanel
BoundingBox - Class in gnu.jpdf: This class simplifies the placement of Strings within a canvas area where the placement of objects is absolute
BoundingBox(Point, Dimension) - Constructor for class gnu.jpdf.BoundingBox: Creates a new BoundingBox instance.
boxExists() - Method in class gnu.jpdf.BoundingBox: Returns false if for any reason this box has negative dimensions
BrowserInfo - Class in gov.lbl.genome.common: Title: BrowserInfo
BrowserInfo(String, String, String, int) - Constructor for class gov.lbl.genome.common.BrowserInfo: BrowserInfo
btnCancel - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
btnOK - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
buffer - Variable in class gov.lbl.genome.gui.Debug
ByteUtils - Class in ranab.util: Byte manipulation utility class.
ByteUtils() - Constructor for class ranab.util.ByteUtils

C

calculateSize(Container) - Method in class layout.TableLayout: Calculates the sizes of the rows and columns based on the absolute and relative sizes specified in rowSpec and columnSpec and the size of the container.
calcWindow - Variable in class gov.lbl.genome.common.VistaCurveModel
calcWindow - Variable in class gov.lbl.genome.gui.CurveParameters
callback - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
Callback - Interface in gov.lbl.genome.gui.dialog: Title: CallBack
cancelAction() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: close the dialog window, do nothing
canResize - Variable in class gov.lbl.genome.gui.VistaApp
CENTER - Static variable in interface layout.TableLayoutConstants: Indicates that the component is centered in its cell
centerDialog(JDialog) - Static method in class gov.lbl.genome.gui.dialog.VistaDialog: center Dialog window on the screen
changePanel(String, String) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: replace one visible Panel by enother
changeSequence(short) - Static method in class ranab.util.ByteUtils: Change LSB and MSB sequence.
checkCurves(Vector, String) - Method in class gov.lbl.genome.common.CommUnit: check Curves for visibility in the specified position
checkCurves(String) - Method in class gov.lbl.genome.gui.VistaApp: Method checkCurves starts separate thread, check curves for visibility and set visibility rules for displayed curves
checkVisible() - Method in class gov.lbl.genome.gui.GeneralGraphView: If graph vie contains invisible curve, then the graph view will be marked as invisible
children - Variable in class gov.lbl.genome.gui.GeneralGraphView
children - Variable in class gov.lbl.genome.gui.panel.TracerPanel
chkOrg - Variable in class gov.lbl.genome.gui.action.AddAction
CHROM_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
CHROM_INFO - Static variable in class gov.lbl.genome.common.CommUnit
ChromInfo - Class in gov.lbl.genome.common: Title: ChromInfo
ChromInfo(String, long, int) - Constructor for class gov.lbl.genome.common.ChromInfo: ChromInfo
ChromPanel - Class in gov.lbl.genome.gui.panel: Title: ChromPanel
ChromPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.ChromPanel: ChromPanel
ChromPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.ChromPanel: ChromPanel
ChromPanelPicture - Class in gov.lbl.genome.gui.panel: Title: ChromPanelPicture
ChromPanelPicture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.panel.ChromPanelPicture: ChromPanelPicture
ChromPosition - Class in gov.lbl.genome.common.features: ChromPosition represents a position in a DNA sequence.
ChromPosition(String, long) - Constructor for class gov.lbl.genome.common.features.ChromPosition: ChromPosition
ChromPosition(String, String, long) - Constructor for class gov.lbl.genome.common.features.ChromPosition: ChromPosition
ChromSegment - Class in gov.lbl.genome.common.features: ChromSegment represents a specific chromosome coordinate span.
ChromSegment(String, long, long, int) - Constructor for class gov.lbl.genome.common.features.ChromSegment: ChromSegment
ChromSegment(String, long, long) - Constructor for class gov.lbl.genome.common.features.ChromSegment: ChromSegment
ChromSegment(String, String, String) - Constructor for class gov.lbl.genome.common.features.ChromSegment: ChromSegment
ChromSegment(String, String, String, String) - Constructor for class gov.lbl.genome.common.features.ChromSegment: ChromSegment
ChromSegment(String, String, long, long) - Constructor for class gov.lbl.genome.common.features.ChromSegment: ChromSegment
ChromSegments - Class in gov.lbl.genome.common.features: Title: ChromSegments
ChromSegments() - Constructor for class gov.lbl.genome.common.features.ChromSegments: ChromSegments
ChromSegments(int) - Constructor for class gov.lbl.genome.common.features.ChromSegments: ChromSegments
clear() - Method in class gov.lbl.genome.gui.History: remove all saved information
clearAll() - Method in class gov.lbl.genome.gui.History: clear all available status (remove bulk information from status)
clearChildren() - Method in class gov.lbl.genome.gui.GeneralGraphView: remove Children
clearModel() - Method in class gov.lbl.genome.gui.CurveParameters: remove Model
clearRect(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This simply draws a White Rectangle to clear the area
clearStatus() - Method in class gov.lbl.genome.gui.Status: remove bulk information from the status
clearStatusBar() - Method in class gov.lbl.genome.gui.VistaApp: remove any text from the status bar
clipPolygon(Polygon) - Method in class gnu.jpdf.PDFGraphics: This extra method allows PDF users to clip to a Polygon.
clipRect(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Clips to a set of coordinates
clipRectangle - Variable in class gnu.jpdf.PDFGraphics: This holds the current clipRectangle
clone() - Method in class gov.lbl.genome.gui.AbstractCurveView: clone
clone() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: clone the panel
clone() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: clone
cloneCurve() - Method in class gov.lbl.genome.common.AbstractCurveModel: clone Curve
cloneCurve() - Method in class gov.lbl.genome.common.CurveInfo: clone Curve
cloneSegment() - Method in class gov.lbl.genome.common.features.ChromSegment: clone Segment
close() - Method in class gnu.jpdf.PDFOutput: This closes the Stream, writing the xref table
Cns - Class in gov.lbl.genome.common.features: Cns represents a conserved non-coding region
Cns(String, long, long) - Constructor for class gov.lbl.genome.common.features.Cns
codeBaseURL - Variable in class gov.lbl.genome.common.CommUnit
col1 - Variable in class layout.TableLayoutConstraints: Cell in which the upper left corner of the component lays
col2 - Variable in class layout.TableLayoutConstraints: Cell in which the lower right corner of the component lays
collectValues() - Method in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel: collect all values from the dialog window this method must be overriden for all dialog panels
collectValues() - Method in class gov.lbl.genome.gui.panel.ContigListPanel: collect Values
collectValues() - Method in class gov.lbl.genome.gui.panel.SaveAsPanel: collect values and put them in the Map
collectValues() - Method in class gov.lbl.genome.gui.panel.SearchResultsPanel: put "gene" information in the values Map
collectValues() - Method in class gov.lbl.genome.gui.panel.StatPanel: do nothing
colors - Static variable in class gov.lbl.genome.gui.Resource
columnOffset - Variable in class layout.TableLayout: Offsets of columns in pixels.
columnSize - Variable in class layout.TableLayout: Widths of columns in pixels
columnSpec - Variable in class layout.TableLayout: Widths of columns expressed in absolute and relative terms
comm - Static variable in class gov.lbl.genome.gui.Debug
Comment - Class in sjg.xml: Represent an XML-comment.
Comment(String) - Constructor for class sjg.xml.Comment: Constructs a new data comment containing the given data.
CommonConstants - Interface in gov.lbl.genome.common: Title:
commonParameters - Variable in class gov.lbl.genome.gui.panel.VGBPanel
CommUnit - Class in gov.lbl.genome.common: Title: CommUnit
CommUnit() - Constructor for class gov.lbl.genome.common.CommUnit: CommUnit
CommUnit(String, String) - Constructor for class gov.lbl.genome.common.CommUnit: CommUnit
CommUnit(String, String, boolean) - Constructor for class gov.lbl.genome.common.CommUnit: CommUnit
compareTo(Object) - Method in class gov.lbl.genome.common.features.ChromSegment: compare 2 segments
component - Variable in class gov.lbl.genome.gui.Picture
component - Variable in class layout.TableLayout.Entry: Component bound by the constraints
componentHidden(ComponentEvent) - Method in class gov.lbl.genome.gui.panel.DisplayPanel
componentMoved(ComponentEvent) - Method in class gov.lbl.genome.gui.panel.DisplayPanel
componentResized(ComponentEvent) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: Logic of this method is the following: If number of rows is fixed and only vertical size changed - do nothing.
componentShown(ComponentEvent) - Method in class gov.lbl.genome.gui.panel.DisplayPanel
condenseStrings(String[]) - Static method in class gov.lbl.genome.common.StringUtil: Merge a String array into a single String using a chosen delimiter that does not occur in any of the strings.
consIdentity - Variable in class gov.lbl.genome.common.VistaCurveModel
consIdentity - Variable in class gov.lbl.genome.gui.CurveParameters
contains(ChromSegment) - Method in class gov.lbl.genome.common.features.ChromSegment: Returns true if the specified chromosome segment overlaps at all with this segment.
contains(ChromPosition) - Method in class gov.lbl.genome.common.features.ChromSegment: Returns true if the specified Chromosome position falls within this segment.
contains(long) - Method in class gov.lbl.genome.common.features.ChromSegment: Returns true if the specified Chromosome position falls within this segment.
contents - Variable in class gnu.jpdf.PDFPage: This holds the contents of the page.
Contig - Class in gov.lbl.genome.common.features: A data set contig mapped onto a base genome.
Contig(String, long, long) - Constructor for class gov.lbl.genome.common.features.Contig: Contig
Contig(String, long, long, boolean, int, int, int, int, String, String, long, long, boolean) - Constructor for class gov.lbl.genome.common.features.Contig: Contig
contigLegend(Graphics, Color, int, int, String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: draw contig legend
ContigListDialog - Class in gov.lbl.genome.gui.dialog: Title: ContigListDialog
ContigListDialog(JApplet, String, boolean, int, Callback, String[]) - Constructor for class gov.lbl.genome.gui.dialog.ContigListDialog: ContigListDialog
ContigListDialog() - Constructor for class gov.lbl.genome.gui.dialog.ContigListDialog: ContigListDialog
ContigListPanel - Class in gov.lbl.genome.gui.panel: Title: ContigListPanel
ContigListPanel(ActionDialog, boolean, boolean, String[]) - Constructor for class gov.lbl.genome.gui.panel.ContigListPanel: Show Contig List
contigPanel - Variable in class gov.lbl.genome.gui.GeneralGraphView
ContigPanel - Class in gov.lbl.genome.gui.panel: Title: ContigPanel
ContigPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.ContigPanel: ContigPanel
ContigPanel(VistaApp, int) - Constructor for class gov.lbl.genome.gui.panel.ContigPanel: ContigPanel
ContigPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.ContigPanel: ContigPanel
ContigPanelPicture - Class in gov.lbl.genome.gui.panel: Title: ContigPanelPicture
ContigPanelPicture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.panel.ContigPanelPicture
convertX(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: convert graph coordinate into the screen coordinate
convertX(long) - Method in class gov.lbl.genome.gui.AbstractCurveView: convert graph coordinate into the screen coordinate
convertX(double) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: convert a chromosome coordinate into a screen coordinate
convertX(long) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: convert a chromosome coordinate into a screen coordinate
convertX(long) - Method in class gov.lbl.genome.gui.panel.VistaPanel: convert chromosome coordinates into screen (panel) coordinates
convertX(double) - Method in class gov.lbl.genome.gui.panel.VistaPanel: convert chromosome coordinates into screen (panel) coordinates
convertX(double) - Method in class gov.lbl.genome.gui.Picture: convert cromosome coordinate to the picture coordinate
convertX(long) - Method in class gov.lbl.genome.gui.Picture: convert cromosome coordinate to the picture coordinate
convertX(long, int, int, int) - Method in class gov.lbl.genome.gui.VistaApp: convert chromosome coordinate into screen coordinate,
convertX(double, int, int, int) - Method in class gov.lbl.genome.gui.VistaApp: convert chromosome coordinate into screen coordinate, according to the line number, offset and panel width
convertY(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: convert graph coordinate into the screen coordinate
COOR_DISPLAY_HEIGHT - Static variable in interface gov.lbl.genome.gui.UIConstants
copyArea(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This is unsupported - how do you do this with Vector graphics?
Count_Overlapped(ChromSegments) - Method in class gov.lbl.genome.common.features.ChromSegments
create() - Method in class gnu.jpdf.PDFGraphics: This returns a child instance of this Graphics object.
createBarImage() - Method in class gov.lbl.genome.gui.panel.TracerPanel: create a semi-transparent green bar image
createGraphic(PDFPage, PrintWriter) - Method in class gnu.jpdf.PDFGraphics: This method creates a new instance of the class based on the page and a print writer.
createImage() - Method in class gov.lbl.genome.gui.GeneralGraphComp: create Image
createImage() - Method in class gov.lbl.genome.gui.GeneralGraphView: create transparent Image if the graph view is not selected and semi-transparent gray bar if the graph view is selected
createImage() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: create annotation Image
createImage() - Method in class gov.lbl.genome.gui.panel.AxisPanel: create axis Image
createImage() - Method in class gov.lbl.genome.gui.panel.ChromPanel: createI cromosome ruler mage
createImage() - Method in class gov.lbl.genome.gui.panel.ContigPanel: createImage
createImage() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: createImage
createImage() - Method in class gov.lbl.genome.gui.panel.VistaPanel: create transparent bitmap image.
createImage() - Method in class gov.lbl.genome.gui.panel.XAxisPanel: createImage return null
createTracerImage() - Method in class gov.lbl.genome.gui.panel.TracerPanel: Create tracer image of correspondig size
crossMouseCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: show crosshair mouse cursor
cuready - Variable in class gov.lbl.genome.gui.VistaApp
currDisplayedPanel - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
currentPage - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
CursorInfoPanel - Class in gov.lbl.genome.gui.panel: Title: CursorInfoPanel
CursorInfoPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.CursorInfoPanel: CursorInfoPanel
curve - Variable in class gov.lbl.genome.gui.CurveParameters
CURVE_TYPES - Static variable in interface gov.lbl.genome.common.CommonConstants
curveColor - Variable in class gov.lbl.genome.gui.AbstractCurveView
curveInfo - Variable in class gov.lbl.genome.common.AbstractCurveModel
CurveInfo - Class in gov.lbl.genome.common: Title: CurveInfo
CurveInfo(String) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, boolean) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, boolean, boolean) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, String) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, String, String) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, String, String, boolean) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
CurveInfo(String, String, String, boolean, boolean, boolean, boolean) - Constructor for class gov.lbl.genome.common.CurveInfo: CurveInfo
curveInfo - Variable in class gov.lbl.genome.gui.CurveParameters
CurveModel - Interface in gov.lbl.genome.common: Title: CurveModel
CurveParameters - Class in gov.lbl.genome.gui: Title: Curve Parameters
CurveParameters(AbstractCurveModel) - Constructor for class gov.lbl.genome.gui.CurveParameters: Curve Parameters
curvesPerPage - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
curveto(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
curveto(double, double, double, double, double, double) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
curveto(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
curveto(double, double, double, double) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
curveto2(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
curveto2(double, double, double, double) - Method in class gnu.jpdf.PDFGraphics: This extension appends a Bezier curve to the path.
CurveView - Interface in gov.lbl.genome.gui: Title: CurveView
curveViews - Variable in class gov.lbl.genome.gui.GeneralGraphView
CUSTOM_CURVE_TYPE - Static variable in interface gov.lbl.genome.common.CommonConstants
CustomCurveModel - Class in gov.lbl.genome.common: Title: CustomCurveModel
CustomCurveModel(String, String, int, int) - Constructor for class gov.lbl.genome.common.CustomCurveModel
CustomCurveModel(TreeMap, String, String, int, int) - Constructor for class gov.lbl.genome.common.CustomCurveModel
CustomCurveModel(TreeMap, String, String, Vector, int, int) - Constructor for class gov.lbl.genome.common.CustomCurveModel
cx(int, int) - Method in class gnu.jpdf.PDFPage: This utility method converts the y coordinate from Java to User space within the page.
cxy(int, int) - Method in class gnu.jpdf.PDFPage: This utility method converts the Java coordinates to User space within the page.
cy(int, int) - Method in class gnu.jpdf.PDFPage: This utility method converts the y coordinate from Java to User space within the page.

D

D_CALC_WINDOW - Static variable in interface gov.lbl.genome.common.VistaModelConstants
D_CONS_IDENT - Static variable in interface gov.lbl.genome.common.VistaModelConstants
D_INTERVAL - Static variable in interface gov.lbl.genome.common.VistaModelConstants
D_MAX_CONS - Static variable in interface gov.lbl.genome.common.VistaModelConstants
D_MIN_CONS - Static variable in interface gov.lbl.genome.common.VistaModelConstants
D_MIN_CONS_WIDTH - Static variable in interface gov.lbl.genome.common.VistaModelConstants
DASHED - Static variable in class gnu.jpdf.PDFAnnot: The border is drawn with a dashed line.
data - Variable in class gov.lbl.genome.common.AbstractCurveModel
Data - Class in sjg.xml: Represent a data section of an XML-document.
Data(String) - Constructor for class sjg.xml.Data: Constructs a new data section containing the given data.
debug - Variable in class gov.lbl.genome.common.CommUnit
Debug - Class in gov.lbl.genome.gui: Title: Debug
Debug(String) - Constructor for class gov.lbl.genome.gui.Debug
debug(Object, String) - Method in class gov.lbl.genome.gui.Debug: Print a message to the standatd output
debug(Object) - Method in class gov.lbl.genome.gui.Debug: Print a message to the standatd output
debug - Static variable in class gov.lbl.genome.gui.panel.VGBPanel
Debug(String) - Method in class gov.lbl.genome.gui.panel.VGBPanel: Deprecated. Use Debug class
debug - Variable in class gov.lbl.genome.gui.Picture
debug(String) - Method in class gov.lbl.genome.gui.Picture: pring debuging output
debugAction - Static variable in class gov.lbl.genome.gui.VistaApp
debugComm - Static variable in class gov.lbl.genome.gui.VistaApp
debugException(Throwable) - Static method in class gov.lbl.genome.gui.Debug: Print an error's stackTrace.
debugException - Static variable in class gov.lbl.genome.gui.VistaApp
debugInit - Static variable in class gov.lbl.genome.gui.VistaApp
debugOff() - Method in class gov.lbl.genome.gui.Debug: Disable debug printing
debugOn() - Method in class gov.lbl.genome.gui.Debug: Enable debug printing
debugProgress - Static variable in class gov.lbl.genome.gui.VistaApp
decode(String) - Static method in class gov.lbl.genome.common.StringUtil: Decodes a x-www-form-urlencoded to a String.
decodeSpaces(String) - Static method in class gov.lbl.genome.common.StringUtil: replace "%20" by space
Decrement_All(int) - Method in class gov.lbl.genome.common.features.ChromSegments: shift all segments
DEF_REG_SIZE - Static variable in interface gov.lbl.genome.common.CommonConstants
DEFAULT_GRAPH_HEIGHT - Static variable in class gov.lbl.genome.gui.GeneralGraphComp
DEFAULT_GRAPH_VIEW_HEIGHT - Static variable in class gov.lbl.genome.gui.GeneralGraphView
DEFAULT_GRAPH_WIDTH - Static variable in class gov.lbl.genome.gui.GeneralGraphComp
DEFAULT_GRAPH_WIDTH - Static variable in class gov.lbl.genome.gui.GeneralGraphView
DEFAULT_GRAPH_WIDTH - Static variable in interface gov.lbl.genome.gui.UIConstants
DEFAULT_MAX_X - Static variable in interface gov.lbl.genome.gui.UIConstants
DEFAULT_MAX_Y - Static variable in interface gov.lbl.genome.gui.UIConstants
DEFAULT_MIN_X - Static variable in interface gov.lbl.genome.gui.UIConstants
DEFAULT_MIN_Y - Static variable in interface gov.lbl.genome.gui.UIConstants
defaultCursor - Variable in class gov.lbl.genome.gui.LinkLabel
defaultMouseCursor() - Method in class gov.lbl.genome.gui.panel.ChromPanel: set mouse cursor to the defaultMouseCursor
defaultMouseCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: show dafault mouse cursor
defaultOutlineBorder - Variable in class gnu.jpdf.PDFDocument: This holds a PDFObject describing the default border for annotations.
defaultSize - Static variable in class layout.TableLayout: Default row/column size
deleteColumn(int) - Method in class layout.TableLayout: Deletes a column in this layout.
deleteRow(int) - Method in class layout.TableLayout: Deletes a row in this layout.
descendants() - Method in class gnu.jpdf.PDFOutline: Returns the total number of descendants below this one.
DetailsAction - Class in gov.lbl.genome.gui.action: Title: Text Browser
DetailsAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.DetailsAction: DetailsAction
DetailsAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.DetailsAction: DetailsAction
df - Variable in class gov.lbl.genome.gui.panel.VistaPanel
df - Variable in class gov.lbl.genome.gui.Picture
Difference(ChromSegments) - Method in class gov.lbl.genome.common.features.ChromSegments: return Difference of two segment collections
dirty - Variable in class layout.TableLayout: Indicates whether or not the size of the cells are known for the last known size of the container.
disableCancelBtn() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: disable Cancel Button
disableGUI() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: call setEnabled(false) for all visible components
disableGUI() - Method in class gov.lbl.genome.gui.panel.GeneSearchPanel: Disable TextField and Button
disableGUI() - Method in class gov.lbl.genome.gui.VistaApp: call setEnabled(false) for all components joined with action
disableOKBtn() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: disable OK Button
dispatch(MouseEvent) - Method in class gov.lbl.genome.gui.panel.VGBPanel: dispatch event
dispatchEvent(MouseEvent) - Method in class gov.lbl.genome.gui.GeneralGraphComp: dispatchEvent
dispatchEvent(MouseEvent) - Method in class gov.lbl.genome.gui.panel.ContigPanel: return true in any case
dispatchEvent(MouseEvent) - Method in class gov.lbl.genome.gui.panel.VGBPanel: dispatch and push mouse event inside the panel structure
DisplayPanel - Class in gov.lbl.genome.gui.panel: Title: DisplayPanel
DisplayPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.DisplayPanel: DisplayPanel
dispose() - Method in class gnu.jpdf.PDFGraphics: This releases any resources used by this Graphics object.
DNA - Static variable in class gov.lbl.genome.common.features.Repeat
Document - Class in sjg.xml: Represents an XML-document.
Document(String, Element) - Constructor for class sjg.xml.Document: Constructs a new document with given header and document root.
Document(Element) - Constructor for class sjg.xml.Document: Constructs a new document with the given element as root and default header.
DOWN - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
dp - Variable in class gov.lbl.genome.gui.GeneralGraphView
dragged - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
draw3DRect(int, int, int, int, boolean) - Method in class gnu.jpdf.PDFGraphics: Not implemented
drawArc(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Draws an arc
drawbar - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
drawBytes(byte[], int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Not implemented
drawChoppedString(Graphics, FontMetrics, int, int) - Method in class gnu.jpdf.BoundingBox: Take the first line of the string (if it is wrapped, otherwise just take the whole string) and chop the end of it off to make it fit in the box.
drawContent(Graphics, PageFormat) - Method in class gov.lbl.genome.gui.GeneralGraphComp: draw Content
drawContent(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.GeneralGraphComp: draw Content
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: draw Content
drawContent(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: draw Content
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.AxisPanel: draw Content
drawContent(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.AxisPanel: draw Content
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.ChromPanel: draw chromosome ruler
drawContent(Graphics, PageFormat) - Method in class gov.lbl.genome.gui.panel.ChromPanel: draw chromosome ruler
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.ContigPanel: draw Content
drawContent(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.ContigPanel: draw Content
drawContent(Graphics, int, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: draw Content in area with specified size
drawContent(Graphics, PageFormat) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: print content on the page (printer, PDF or image)
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: drawContent
drawContent(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: drawContent
drawContent(Graphics) - Method in class gov.lbl.genome.gui.panel.XAxisPanel: Draw X axis
drawGene(Gene, Graphics) - Method in class gov.lbl.genome.gui.panel.AnnotationPanelPicture: draw gene name and arrow
drawGreenBar(long, long) - Method in class gov.lbl.genome.gui.panel.TracerPanel: draw semitransparent GreenBar
drawGrid(Container, Graphics) - Method in class layout.TableLayout: Draws a grid on the given container.
drawImage(Image, int, int, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draw's an image onto the page
drawImage(Image, int, int, int, int, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draws an image onto the page.
drawImage(Image, int, int, Color, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draw's an image onto the page, with a backing colour.
drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draw's an image onto the page, with a backing colour.
drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draw's an image onto the page, with scaling
drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class gnu.jpdf.PDFGraphics: Draw's an image onto the page, with scaling
drawLine(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Draws a line between two coordinates.
drawOval(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Draws an oval
drawPicture(Graphics, JComponent) - Method in class gov.lbl.genome.gui.panel.AnnotationPanelPicture: draw annotation Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.panel.AnnotationPanelPicture: draw annotation Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.panel.AxisPanelPicture: draw axis Picture
drawPicture(Graphics, JComponent, long, long) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: draw chromosome ruler Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: draw chromosome ruler Picture
drawPicture(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.ContigPanelPicture: drawPicture
drawPicture(Graphics, JComponent) - Method in class gov.lbl.genome.gui.panel.ContigPanelPicture: draw contig Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.panel.ContigPanelPicture: draw contig Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.panel.RepeatPanelPicture: Draw repeats
drawPicture(Graphics, JComponent, int) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPicture(Graphics, JComponent) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPicture(Graphics, PageFormat) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPicture(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPicture(Graphics, int, int) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPicture(Graphics) - Method in class gov.lbl.genome.gui.Picture: draw Picture
drawPolygon(int[], int[], int) - Method in class gnu.jpdf.PDFGraphics: Draws a polygon, linking the first and last coordinates.
drawPolyline(int[], int[], int) - Method in class gnu.jpdf.PDFGraphics: Draws a polyline.
drawRect(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: We override Graphics.drawRect as it doesn't join the 4 lines.
drawRoundRect(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This is not yet implemented
drawString(String, int, int) - Method in class gnu.jpdf.PDFGraphics: This draws a string.
drawString(AttributedCharacterIterator, int, int) - Method in class gnu.jpdf.PDFGraphics: Draws a string using a AttributedCharacterIterator.
drawWrappedString(Graphics, FontMetrics, int, int) - Method in class gnu.jpdf.BoundingBox: This method is called after getting the box by calling getStringBounds on the parent.
drawWrappedStringTruncate(Graphics, FontMetrics, int, int) - Method in class gnu.jpdf.BoundingBox: Draws lines from the wrapped string until there is no more room and then stops.

E

eastMouseCursor() - Method in class gov.lbl.genome.gui.panel.ChromPanel: set mouse cursor to the eastCursor
eh - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
eh - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
Element - Class in sjg.xml: Class that represents an XML element.
elementAt(int) - Method in class gov.lbl.genome.gui.panel.GraphViewList: return visible element
elements() - Method in class gnu.jpdf.PDFOutline: Returns all outlines directly below this one.
elements() - Method in class sjg.xml.Element: Returns an enumeration over the mixed contents of this element - of type String or Element.
elements(String) - Method in class sjg.xml.Element: Returns an enumeration over the subelements of this element that have the given name.
enableCancelBtn() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: enable Cancel Button
enableDialogButtons() - Method in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel: enable Dialog "OK" and "Cancel" Buttons remove it!
enableGUI() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: call setEnabled(true) for all visible components
enableGUI() - Method in class gov.lbl.genome.gui.panel.GeneSearchPanel: Enable TextField and Button
enableGUI() - Method in class gov.lbl.genome.gui.VistaApp: call setEnabled(true) for all components joined with action
enableOKBtn() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: enable OK Button
enablePrinting(boolean) - Method in class gov.lbl.genome.gui.VistaApp: enable or disable printing actions The only reason of using this method is bug in java 1.5
encode(OutputStream) - Method in class ranab.img.gif.GifImage: Encode GIF image
encodeSpaces(String) - Static method in class gov.lbl.genome.common.StringUtil: replace spaces by "%20"
end() - Method in class gnu.jpdf.PDFJob: This writes the PDF document to the OutputStream, finishing the document.
endTracerPanel - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
equals(String, String, int) - Method in class gnu.jpdf.PDFFont: This is used by the PDF and PDFPage classes to compare font names
equals(Object) - Method in class gov.lbl.genome.common.AbstractCurveModel: compare 2 corve models
equals(Object) - Method in class gov.lbl.genome.common.ViewSettings
equals(Object) - Method in class gov.lbl.genome.gui.CurveParameters: compare 2 parameter sets
equals(Object) - Method in class gov.lbl.genome.gui.Status: return true is 2 status objects are equal ignoring data
equals(Object) - Method in class layout.TableLayout.Entry: Determines whether or not two entries are equal.
equalsIgnoreData(Object) - Method in class gov.lbl.genome.gui.Status: compare 2 status objects ignoring data
error(Object, String) - Static method in class gov.lbl.genome.gui.Debug: Print a message to the standatd output
ErrorHandler - Class in gov.lbl.genome.gui: Title: ErrorHandler
ErrorHandler(VistaApp) - Constructor for class gov.lbl.genome.gui.ErrorHandler
Exon - Class in gov.lbl.genome.common.features: Exon represents a specific chromosome coordinate span.
Exon(String, long, long) - Constructor for class gov.lbl.genome.common.features.Exon

F

FILL - Static variable in interface layout.TableLayoutConstants: Indicates that the row/column should fill the available space
fill3DRect(int, int, int, int, boolean) - Method in class gnu.jpdf.PDFGraphics: Not implemented
fillAnnotations(Graphics) - Method in class gov.lbl.genome.gui.VistaCurveView: draw all annotations
fillArc(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Fills an arc, joining the start and end coordinates
fillOval(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Draws a filled oval
fillPolygon(int[], int[], int) - Method in class gnu.jpdf.PDFGraphics: Fills a polygon.
fillRect(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Fills a rectangle with the current colour
fillRoundRect(int, int, int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: This is not yet implemented
filterDigits(String) - Static method in class gov.lbl.genome.common.StringUtil: throw exception if string contains non-digit characters
findParentFrame() - Method in class gov.lbl.genome.gui.panel.VGBPanel: This method is important for applets.
first - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
firstElement() - Method in class gov.lbl.genome.gui.panel.GraphViewList: first visible Element
firstSet - Variable in class gov.lbl.genome.gui.panel.BaseInfoPanel
flipSelected() - Method in class gov.lbl.genome.gui.GeneralGraphView: reverse selection
FLOATING_POINT - Static variable in interface gov.lbl.genome.common.CommonConstants
FLOATING_POINT - Static variable in interface gov.lbl.genome.common.VistaModelConstants
fonts - Variable in class gnu.jpdf.PDFPage: The fonts associated with this page
ForwardAction - Class in gov.lbl.genome.gui.action: Title: Show next position
ForwardAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.ForwardAction: ForwardAction
ForwardAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.ForwardAction: ForwardAction
freezeCounters(boolean) - Method in class gov.lbl.genome.gui.VistaApp: Stop applet timer
fromString(String) - Static method in class gov.lbl.genome.common.features.ChromPosition: Restore a ChromPosition object from a one-line string.
fromString(String) - Static method in class gov.lbl.genome.common.features.Gap: Restore a Gap object from a one-line string.
FULL - Static variable in interface layout.TableLayoutConstants: Indicates that the component is full justified in its cell
FULLSCREEN - Static variable in class gnu.jpdf.PDFDocument: This page mode indicates that when the document is opened, it is displayed in full-screen-mode.

G

g - Variable in class gov.lbl.genome.gui.Picture
g2d - Variable in class gov.lbl.genome.gui.AbstractCurveView
g2d - Variable in class gov.lbl.genome.gui.panel.VistaPanel
g2d - Variable in class gov.lbl.genome.gui.Picture
G2D - Variable in class gov.lbl.genome.gui.Picture
Gap - Class in gov.lbl.genome.common.features: Gap represents a gap in a DNA sequence.
Gap(String, long) - Constructor for class gov.lbl.genome.common.features.Gap
Gap(String, String, long) - Constructor for class gov.lbl.genome.common.features.Gap
Gene - Class in gov.lbl.genome.common.features: Gene represents a specific chromosome coordinate span.
Gene(String, long, long) - Constructor for class gov.lbl.genome.common.features.Gene
Gene(long, long, String, String, boolean) - Constructor for class gov.lbl.genome.common.features.Gene: Gene
Gene(String, long, long, String, String, boolean) - Constructor for class gov.lbl.genome.common.features.Gene: Gene
GENE_NAME_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
GENE_NAME_OFFSET - Variable in class gov.lbl.genome.gui.panel.AnnotationPanel
GENE_NAME_OFFSET - Variable in class gov.lbl.genome.gui.panel.AnnotationPanelPicture
GENE_Y_POS - Variable in class gov.lbl.genome.gui.panel.AnnotationPanel
GENE_Y_POS - Variable in class gov.lbl.genome.gui.panel.AnnotationPanelPicture
GeneNotFoundException - Exception in gov.lbl.genome.common: Title: GeneNotFoundException
GeneNotFoundException() - Constructor for exception gov.lbl.genome.common.GeneNotFoundException: Gene Not Found Exception
GeneNotFoundException(String) - Constructor for exception gov.lbl.genome.common.GeneNotFoundException: Gene Not Found Exception
GeneralGraphComp - Class in gov.lbl.genome.gui: Title: GeneralGraphComponent
GeneralGraphComp(GeneralGraphView) - Constructor for class gov.lbl.genome.gui.GeneralGraphComp: GeneralGraphComp
GeneralGraphComp(GeneralGraphView, PageFormat) - Constructor for class gov.lbl.genome.gui.GeneralGraphComp: printable GeneralGraphComp
GeneralGraphModel - Class in gov.lbl.genome.common: Title: GeneralGraphModel
GeneralGraphModel(String) - Constructor for class gov.lbl.genome.common.GeneralGraphModel: GeneralGraphModel
GeneralGraphModel(String, double, double, double, double) - Constructor for class gov.lbl.genome.common.GeneralGraphModel: GeneralGraphModel
GeneralGraphModel(String, double, double) - Constructor for class gov.lbl.genome.common.GeneralGraphModel: GeneralGraphModel
GeneralGraphModel(String, String) - Constructor for class gov.lbl.genome.common.GeneralGraphModel: GeneralGraphModel
GeneralGraphModel(String, String, double, double) - Constructor for class gov.lbl.genome.common.GeneralGraphModel: GeneralGraphModel
GeneralGraphView - Class in gov.lbl.genome.gui: Title: GeneralGraphView
GeneralGraphView(VistaApp, GeneralGraphModel, NumberFormat) - Constructor for class gov.lbl.genome.gui.GeneralGraphView: create parent GeneralGraphView
GeneralGraphView(VistaApp, GeneralGraphModel, NumberFormat, int) - Constructor for class gov.lbl.genome.gui.GeneralGraphView: create child GeneralGraphView
generation - Variable in class gnu.jpdf.PDFXref: The generation of the object, usually 0
GeneSearchPanel - Class in gov.lbl.genome.gui.panel: Title: GeneSearchPanel
GeneSearchPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.GeneSearchPanel: GeneSearchPanel
geneSearchPanel - Variable in class gov.lbl.genome.gui.VistaApp
GenesInfo - Class in gov.lbl.genome.common: Title: GenesInfo
GenesInfo(String, String, String, String, String, String, String, String, boolean) - Constructor for class gov.lbl.genome.common.GenesInfo: GenesInfo
GenomeInfo - Class in gov.lbl.genome.common: Title: GenomeInfo
GenomeInfo(String, String, Vector, boolean) - Constructor for class gov.lbl.genome.common.GenomeInfo: GenomeInfo
GenomeInfo(String, String, String, Vector, GenesInfo[]) - Constructor for class gov.lbl.genome.common.GenomeInfo: GenomeInfo
GenomeInfo(int, String, String, String, Vector, GenesInfo[], String, boolean, String, Vector, int) - Constructor for class gov.lbl.genome.common.GenomeInfo: GenomeInfo
GET_ANNO - Static variable in class gov.lbl.genome.common.CommUnit
GET_AVAIL_CURVES - Static variable in class gov.lbl.genome.common.CommUnit
Get_ChromSegment(int) - Method in class gov.lbl.genome.common.features.ChromSegments: Get ChromSegment
GET_CURVE - Static variable in class gov.lbl.genome.common.CommUnit
GET_GENES - Static variable in class gov.lbl.genome.common.CommUnit
GET_INIT - Static variable in class gov.lbl.genome.common.CommUnit
getAbsoluteLocation() - Method in class gnu.jpdf.BoundingBox: Get the absolute upper left location point for this box
getAdb() - Method in class gov.lbl.genome.common.GenomeInfo: get Annotation db
getAddAction() - Method in class gov.lbl.genome.gui.VistaApp: return addAction3
getAlign() - Method in class gov.lbl.genome.common.features.Contig: get Align
getAllCurveInfos() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return vector with all CurveInfo
getAllCurves() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return all curves in all graphs
getAllGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return All Graphs
getAllPoints() - Method in class gov.lbl.genome.common.AbstractCurveModel
getAllPoints() - Method in interface gov.lbl.genome.common.CurveModel: Use this method to get all the points in this CurveModel.
getAllSelectedGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return list of All Selected Graphs
getAnno(String, String, String, String, String) - Method in class gov.lbl.genome.common.CommUnit: getAnno returns a Vector of ChromSegments (use getName() on each segment to find out the type) input: base (hg12, mm2, etc), src (refseq at the moment), position
getAnnotation() - Method in class gov.lbl.genome.gui.Status: return tAnnotation
getAnnotationColor(int) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: return Annotation Color
getAnnotationPanel() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return Annotation Panel
getAnnotations() - Method in class gov.lbl.genome.common.AbstractCurveModel: return Annotations
getAnnotations() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: return Annotations
getAnnotations() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: return annotations
getAttribute(String) - Method in class sjg.xml.Element: Returns the attribute given a name.
getAuthor() - Method in class gnu.jpdf.PDFInfo: Get the value of author.
getAutoStringList(String) - Static method in class gov.lbl.genome.common.StringUtil: Tokenize a String list using the first character of the string as the delimiter.
getAvailCurves() - Method in class gov.lbl.genome.common.CommUnit: getCurves Returns a list of curves available as an array [id] [name]
getAvailCurves(String) - Method in class gov.lbl.genome.common.CommUnit: getCurves returns a list of curves available at a given url as an array [id][name]
getBase() - Method in class gov.lbl.genome.common.CurveInfo: get Base
getBase() - Method in class gov.lbl.genome.common.features.Contig
getBase() - Method in class gov.lbl.genome.common.ViewSettings
getBaseFamily() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Base Family
getBaseGenome() - Method in class gov.lbl.genome.gui.VistaApp: get baseGenome
getBG() - Method in class gov.lbl.genome.gui.VistaApp: return base genome name
getBlockId() - Method in class ranab.img.gif.GifEx: Get the block identification block.
getBrowsers() - Method in class gov.lbl.genome.common.GenomeInfo: return all available Browsers
getCalcWindow() - Method in class gov.lbl.genome.common.ViewSettings
getCalcWindow() - Method in class gov.lbl.genome.common.VistaCurveModel: get Calc Window
getCalcWindow() - Method in class gov.lbl.genome.gui.VistaApp: return calc.
getCheckedCurves() - Method in class gov.lbl.genome.common.GenomeInfo: return list of Checked Curves
getChrom(String) - Method in class gov.lbl.genome.gui.VistaApp: try to extract chromosome name from the position string
getChrom() - Method in class gov.lbl.genome.gui.VistaApp: return current chromosome
getChromDX() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return number of selected points
getChromInfo(String, String) - Method in class gov.lbl.genome.common.CommUnit: get ChromInfo
getChromName() - Method in class gov.lbl.genome.common.features.ChromSegment: get Chromosome Name
getChromosome() - Method in class gov.lbl.genome.common.features.ChromPosition: get Chromosome
getChromosome() - Method in class gov.lbl.genome.common.features.ChromSegment: get Chromosome
getChromosome(boolean) - Method in class gov.lbl.genome.common.features.ChromSegment: get Chromosome
getChromosome() - Method in class gov.lbl.genome.common.ViewSettings
getChromSegment() - Method in class gov.lbl.genome.common.ViewSettings
getChromSize(String) - Method in class gov.lbl.genome.gui.VistaApp: Return chromosome size.
getChromSize() - Method in class gov.lbl.genome.gui.VistaApp: return size of current chromosome or contig
getChromX(int) - Method in class gov.lbl.genome.gui.panel.TracerPanel: convert screen coordinate into the chromosome coordinate
getChromX(int, int) - Method in class gov.lbl.genome.gui.panel.TracerPanel: convert screen coordinate into the chromosome coordinate
getClip() - Method in class gnu.jpdf.PDFGraphics: Returns the Shape of the clipping region As my JDK docs say, this may break with Java 2D.
getClipBounds() - Method in class gnu.jpdf.PDFGraphics: Returns the Rectangle that fits the current clipping region
getCnsUnderCurve() - Method in class gov.lbl.genome.common.ViewSettings
getCode() - Method in exception gov.lbl.genome.common.VGBException: get Exception Code
getColor() - Method in class gnu.jpdf.PDFGraphics: Returns the current pen Colour
getColor(String, Color) - Method in class gov.lbl.genome.gui.Parameter: try to return a Color object by name if fail return default Color
getColor(String) - Method in class gov.lbl.genome.gui.Parameter: return a color object by name
getColor() - Method in class ranab.img.gif.GifColor: Get color
getColorArray(String) - Method in class gov.lbl.genome.gui.Parameter: return an array of Color objects by name
getColumn() - Method in class layout.TableLayout: Gets the sizes of columns in this layout.
getColumn(int) - Method in class layout.TableLayout: Gets the width of a single column in this layout.
getComment() - Method in class gov.lbl.genome.common.GenesInfo: get Comment
getComment() - Method in class ranab.img.gif.GifCommentEx: Get the comment string.
getCommentBlock() - Method in class ranab.img.gif.GifImage: Get the gif comment block.
getCommUnit() - Method in class gov.lbl.genome.gui.VistaApp: return a CommUnit object
getComponent(String) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: return Component by name
getConnection() - Method in class gov.lbl.genome.gui.VistaApp: return connection field
getConsIdentity() - Method in class gov.lbl.genome.common.ViewSettings
getConsIdentity() - Method in class gov.lbl.genome.common.VistaCurveModel: get Cons Identity
getConsIdentity() - Method in class gov.lbl.genome.gui.VistaApp: return cons.
getConstraints(Component) - Method in class layout.TableLayout: Gets the constraints of a given component.
getConsWidth() - Method in class gov.lbl.genome.gui.VistaApp: return minConsWidth
getContents() - Method in class sjg.xml.Element: Returns a textual representation of the contents of this element.
getContig(String) - Method in class gov.lbl.genome.common.GenomeInfo: get Contig (Chromosome)
getContigName() - Method in class gov.lbl.genome.common.features.Contig: get Contig Name
getContigNum() - Method in class gov.lbl.genome.common.features.Contig: get Contig Number
getContigPanel() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Contig Panel
getContigs() - Method in class gov.lbl.genome.gui.panel.ContigPanel: return contigs
getContigs() - Method in class gov.lbl.genome.gui.VistaCurveView: return Contigs
getCoordinate() - Method in class gov.lbl.genome.common.features.ChromPosition: get Coordinate
getCreated() - Method in class gov.lbl.genome.common.GenesInfo: get Created
getCreator() - Method in class gnu.jpdf.PDFInfo: PDF has two values, a Creator and a Producer.
getCurrentPage() - Method in class gnu.jpdf.PDFJob: Returns the current PDFPage being worked on.
getCurrentPageNumber() - Method in class gnu.jpdf.PDFJob: Returns the current page number.
getCurrentPos() - Method in class gov.lbl.genome.common.GenomeInfo: get Current Position
getCurve(CurveInfo, String, CurveModel, VistaApp) - Method in class gov.lbl.genome.common.CommUnit: get Curve
getCurve(int) - Method in class gov.lbl.genome.common.GenomeInfo: get Curve Info
getCurve(String) - Method in class gov.lbl.genome.common.GenomeInfo
getCurveInfo() - Method in class gov.lbl.genome.common.AbstractCurveModel: get CurveInfo
getCurveModel() - Method in class gov.lbl.genome.gui.AbstractCurveView: return Curve Model
getCurveModel() - Method in interface gov.lbl.genome.gui.CurveView
getCurveModels() - Method in class gov.lbl.genome.common.GeneralGraphModel: get Curve Models Iterator
getCurveModels() - Method in interface gov.lbl.genome.common.GraphModel: Get all the CurveModels associated with this GraphModel.
getCurveModelsCollection() - Method in class gov.lbl.genome.common.GeneralGraphModel: get collection of Curve Models
getCurveParameters() - Method in class gov.lbl.genome.gui.Status: return Curve Parameters
getCurves() - Method in class gov.lbl.genome.common.GenomeInfo: get Curves
getCurveViews() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Curve Views
getData() - Method in class gov.lbl.genome.common.AbstractCurveModel: return Data points
getDataInterval() - Method in class gov.lbl.genome.gui.VistaApp: return interval between two pixils
getDataUrl() - Method in class gov.lbl.genome.common.GenomeInfo: get Data Url string
getDateString(Date) - Static method in class gov.lbl.genome.common.StringUtil: get Date String
getDecimalString(double, int) - Static method in class gov.lbl.genome.common.StringUtil: Parses a formatted string representation of a double value, with the specified number of decimal digits.
getDefaultBaseGenome() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: get Default Base Genome
getDefaultGenes() - Method in class gov.lbl.genome.gui.VistaApp: getDefaultGenes
getDefaultGenome() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: return Default Genome
getDeflate() - Method in class gnu.jpdf.PDFStream: Returs true if the stream will be compressed.
getDefPos() - Method in class gov.lbl.genome.common.GenomeInfo: ge tDefault Position
getDelayTime() - Method in class ranab.img.gif.GifGraphicEx: Get delay time
getDescr() - Method in class gov.lbl.genome.common.features.Gene: get Descriprion
getDetailsAction() - Method in class gov.lbl.genome.gui.VistaApp: return detailsAction2
getDialogElement(String) - Method in class gov.lbl.genome.gui.VistaApp: Retern Element from XML Document from dialogs.xml
getDimension() - Method in class gnu.jpdf.PDFPage
getDir() - Method in class gov.lbl.genome.common.features.Contig: get Dir
getDisplayPanel() - Method in class gov.lbl.genome.gui.VistaApp: getDisplayPanel
getDouble(String) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to a Double object.
getDouble(String, double) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to a double.
getDouble(TextField, double) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to a double.
getDouble(TextField, double, double, double) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to a double, constrained by min and max values.
getDouble(String, double) - Method in class gov.lbl.genome.gui.Parameter: try to return a double value by name, or return the default value
getDouble(String) - Method in class gov.lbl.genome.gui.Parameter: return double value by name
getDoubleArray(String) - Method in class gov.lbl.genome.gui.Parameter: get Array of double by name
getDrawingPoint() - Method in class gnu.jpdf.BoundingBox: Gets the drawing point to use in Graphics drawing methods.
getDs() - Method in class gov.lbl.genome.common.features.Contig: get DataSet
getDsChrom() - Method in class gov.lbl.genome.common.features.Contig: get DataSet Chromosome
getDsEnd() - Method in class gov.lbl.genome.common.features.Contig: get DataSet End
getDset() - Method in class gov.lbl.genome.common.ViewSettings
getDsStart() - Method in class gov.lbl.genome.common.features.Contig: get DataSet Start
getDsStrand() - Method in class gov.lbl.genome.common.features.Contig: get DataSet Strand
getDX() - Method in class gov.lbl.genome.gui.Picture: return maxX-minX
getEnabled() - Method in class gov.lbl.genome.gui.panel.TracerPanel: getEnabled
getEnd() - Method in class gov.lbl.genome.common.features.ChromSegment: get End
getEnd() - Method in class gov.lbl.genome.common.ViewSettings
getEndPoint() - Method in class gov.lbl.genome.common.AbstractCurveModel
getEndPoint() - Method in interface gov.lbl.genome.common.CurveModel: get End Point
getErrorHandler() - Method in class gov.lbl.genome.gui.VistaApp: return handler of the Error Message Box
getFamily() - Method in class gov.lbl.genome.common.BrowserInfo: get Family
getFirstSelectedIndex() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return index of the first (from top) selected graph
getFont(String, String, int) - Method in class gnu.jpdf.PDFDocument: This returns a font of the specified type and font.
getFont() - Method in class gnu.jpdf.PDFFont
getFont() - Method in class gnu.jpdf.PDFGraphics: Return's the current font.
getFont(String, String, int) - Method in class gnu.jpdf.PDFPage: Returns a PDFFont, creating it if not yet used.
getFont(String, Font) - Method in class gov.lbl.genome.gui.Parameter: try return a Font object by name if fail will return default Font Important: Font parser is not implemented
getFont(String) - Method in class gov.lbl.genome.gui.Parameter: return a Font object by name Important: Font parser is not implemented
getFontArray(String) - Method in class gov.lbl.genome.gui.Parameter: return array with Font object by name Important: Font parser is not implemented
getFontMetrics(Font) - Method in class gnu.jpdf.PDFGraphics: Returns the FontMetrics for a font.
getFormattedNumberString(double, int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: return formatted string
getFormattedNumberString(int, int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: return formattes string
getFormattedNumberString(double, int) - Method in class gov.lbl.genome.gui.Picture: return Formatted Number String
getFormattedNumberString(int, int) - Method in class gov.lbl.genome.gui.Picture: return Formatted Number String
getFormattedXDisplayString(int) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: format the cursor position string
getFormattedXDisplayString(int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: This method converts an x-coordinate on the data display panel to an x-coordinate on the graph and return formatted string.
getFormattedXDisplayString(int, int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: This method converts an x-coordinate on the data display panel to an x-coordinate on the graph and return formatted string.
getFormattedXDisplayString(int) - Method in class gov.lbl.genome.gui.Picture: return Formatted String converted to the chromosome coordinates
getFullString() - Method in class gnu.jpdf.BoundingBox: Returns the full string associated with a call to getStringBounds
getGeneName() - Method in class gov.lbl.genome.common.features.Gene: get Gene Name
getGeneralGraphView(int, int) - Method in class gov.lbl.genome.gui.GeneralGraphView: create child GeneralGraphView
getGenes(String, String, String, String) - Method in class gov.lbl.genome.common.CommUnit: getGenes returns an array of Genes whose names contain the given string
getGenesInfo() - Method in class gov.lbl.genome.gui.VistaApp: getGenesInfo
getGenesInfos() - Method in class gov.lbl.genome.common.GenomeInfo: return GenesInfos
getGenesName() - Method in class gov.lbl.genome.gui.panel.GeneSearchPanel: return names of found genes
getGenome() - Method in class gov.lbl.genome.gui.Status: return base genome
getGenomeId() - Method in class gov.lbl.genome.common.GenomeInfo: get Genome Id
getGenomes() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel
getGenomesIter() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: return Genomes Iterator
getGraph(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: get Graph
getGraphComp() - Method in class gov.lbl.genome.gui.GeneralGraphView: return GeneralGraphComp
getGraphHeight() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Graph Height
getGraphicBlock() - Method in class ranab.img.gif.GifImage: Get graphic extension block.
getGraphics(int) - Method in class gnu.jpdf.PDFJob: This returns a graphics object that can be used to draw on a page.
getGraphics() - Method in class gnu.jpdf.PDFJob: This returns a graphics object that can be used to draw on a page.
getGraphics() - Method in class gnu.jpdf.PDFPage: This returns a PDFGraphics object, which can then be used to render on to this page.
getGraphics() - Method in class ranab.img.gif.GifImage: Get graphics
getGraphModel() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Graph Model
getGraphModel() - Method in interface gov.lbl.genome.gui.GraphView
getGraphName() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Name
getGraphPanelSize() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return dimension of the graph panel
getGraphPos() - Method in class gov.lbl.genome.gui.GeneralGraphView: return position of the graph view in the display panel
getGraphView() - Method in class gov.lbl.genome.gui.AbstractCurveView: return Graph View
getGraphView() - Method in interface gov.lbl.genome.gui.CurveView: return GraphView
getGraphWidth() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Graph Width
getGraphWidth() - Method in class gov.lbl.genome.gui.VistaApp: return adjusted width of a curve panel
getHeader() - Method in class sjg.xml.Document: Returns the header of the document in unparsed textual form.
getHeight() - Method in class gnu.jpdf.PDFImage: Get the value of height.
getHeight() - Method in class gov.lbl.genome.gui.Picture: return picture Height
getHistory() - Method in class gov.lbl.genome.gui.VistaApp: Return history object
getHorizSize() - Method in class gov.lbl.genome.gui.panel.VistaPanel: return adjusted panel width
getID() - Method in class gov.lbl.genome.common.AbstractCurveModel: get ID
getID() - Method in class gov.lbl.genome.common.AbstractGraphModel: get ID
getId() - Method in class gov.lbl.genome.common.CurveInfo: get Id
getID() - Method in class gov.lbl.genome.common.CustomCurveModel
getId() - Method in class gov.lbl.genome.common.GenomeInfo: get Id
getImage() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: return pictures Image
getImage(int) - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: return pictures Image
getImage(int) - Method in class gov.lbl.genome.gui.panel.AxisPanel: return pictures Image
getImage() - Method in class gov.lbl.genome.gui.panel.AxisPanel: return pictires Image
getImage() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: return Image
getImage(int) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: return Image
getImage() - Method in class gov.lbl.genome.gui.Picture: return new Image with default size
getImage(JComponent, int) - Method in class gov.lbl.genome.gui.Picture: return new Image with the size equals to the componet size
getImage(JComponent) - Method in class gov.lbl.genome.gui.Picture: return new Image with the size equals to the componet size
getImage(PageFormat) - Method in class gov.lbl.genome.gui.Picture: return new Image with the size equals to the page size
getImage(int, int) - Method in class gov.lbl.genome.gui.Picture: return new Image with the size specified by parameters
getImage(String) - Method in class gov.lbl.genome.gui.VistaApp: download image from the server
getImageableHeight() - Method in class gov.lbl.genome.gui.Picture: return height of the Imageable rectangle
getImageableWidth() - Method in class gov.lbl.genome.gui.Picture: return width of the Imageable rectangle
getImageData() - Method in class ranab.img.gif.GifEx: Get image data.
getIndex(PDFOutline) - Method in class gnu.jpdf.PDFOutline: This is called by children to find their position in this outlines tree.
getInitInfo() - Method in class gov.lbl.genome.common.CommUnit: getInitInfo returns a hashmap genome id -> GenomeInfo
getInitInfo(String, String, String, String) - Method in class gov.lbl.genome.common.CommUnit: get Init Info
getInputStream() - Method in class gov.lbl.genome.gui.VistaApp: return InputStream from the connection
getInt(String, int) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to an int.
getInt(TextField, int) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to an int.
getInt(TextField, int, int, int) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to an int, constrained by min and max values.
getInt(String, int, int, int) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to an int, constrained by min and max values.
getInt(String, int) - Method in class gov.lbl.genome.gui.Parameter: try to return int value by name, or return the default value
getInt(String) - Method in class gov.lbl.genome.gui.Parameter: return int value by name
getIntArray(String, int) - Static method in class gov.lbl.genome.common.StringUtil: Returns an Array of int using the given delimiter.
getIntArray(String) - Method in class gov.lbl.genome.gui.Parameter: return array of int by name
getInteger(String) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to an Integer.
getInterval() - Method in class gov.lbl.genome.common.AbstractCurveModel
getInterval() - Method in interface gov.lbl.genome.common.CurveModel: return Interval between two points
getInterval() - Method in class gov.lbl.genome.common.ViewSettings
getIntValue() - Method in class sjg.xml.Attribute: Returns the value of this attribute as an integer - may throw an error if value is not an integer.
getInvisible() - Method in class gov.lbl.genome.gui.panel.GraphViewList: return Invisible elements
getIterationCount() - Method in class ranab.img.gif.GifNsAppEx: Get iteration count
getKeywords() - Method in class gnu.jpdf.PDFInfo: Get the value of keywords.
getLabel() - Method in class gov.lbl.genome.common.CurveInfo: return Label
getLast() - Method in class gnu.jpdf.PDFOutline: Returns the last index in this outline
getLastSelectedIndex() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return index of the last (from top) selected graph
getLayoutAlignmentX(Container) - Method in class layout.TableLayout: Returns the alignment along the x axis.
getLayoutAlignmentY(Container) - Method in class layout.TableLayout: Returns the alignment along the y axis.
getLong(String) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to a Long.
getLong(String, long) - Static method in class gov.lbl.genome.common.StringUtil: Converts a String to a long.
getLong(TextField, long) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to a long.
getLong(TextField, long, long, long) - Static method in class gov.lbl.genome.common.StringUtil: Converts the input in a TextField to a long, constrained by min and max values.
getLongArray(String, int) - Static method in class gov.lbl.genome.common.StringUtil: Returns an Array of long using the given delimiter.
getLongName() - Method in class gov.lbl.genome.common.AbstractCurveModel: get Long Name
getLongName() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Long Name
getLongName() - Method in class gov.lbl.genome.common.CurveInfo: return Long Name
getLongName() - Method in interface gov.lbl.genome.common.CurveModel: get Long Name
getLongName() - Method in class gov.lbl.genome.common.GeneralGraphModel
getLongName() - Method in class gov.lbl.genome.common.GenesInfo: get Long Name
getLongName() - Method in class gov.lbl.genome.common.VistaCurveInfo
getLongName() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Long Name
getMarginBottom() - Method in class gov.lbl.genome.gui.Picture: return bottom Margin
getMarginLeft() - Method in class gov.lbl.genome.gui.Picture: return left Margin
getMarginRight() - Method in class gov.lbl.genome.gui.Picture: return right Margin
getMarginTop() - Method in class gov.lbl.genome.gui.Picture: return top Margin
getMaxConservation() - Method in class gov.lbl.genome.common.ViewSettings
getMaxHeight() - Method in class gov.lbl.genome.gui.Picture: return Max drawable Height
getMaxWidth() - Method in class gov.lbl.genome.gui.Picture: return tMax drawable Width
getMaxX() - Method in class gov.lbl.genome.common.AbstractCurveModel: get Max X
getMaxX() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Max X
getMaxX() - Method in class gov.lbl.genome.gui.AbstractCurveView: get Max X
getMaxX(String) - Method in class gov.lbl.genome.gui.VistaApp: try to extract maxX from the position string
getMaxX() - Method in class gov.lbl.genome.gui.VistaApp: return maxX
getMaxX(int) - Method in class gov.lbl.genome.gui.VistaApp: return maxX for "i" line
getMaxY() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Max Y
getMaxY() - Method in class gov.lbl.genome.common.PCurveModel: get Max Y
getMaxY() - Method in class gov.lbl.genome.gui.AbstractCurveView: get Max Y
getMaxY() - Method in class gov.lbl.genome.gui.VistaApp: deturn default/actual maxY value
getMaxY(CurveInfo) - Method in class gov.lbl.genome.gui.VistaApp: rerurn maxY parameter for the curve.
getMedia() - Method in class gnu.jpdf.PDFPage: Returns the page's media.
getMessage() - Method in exception gnu.jpdf.StringTooLongException
getMethodResult(String, String) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: return object that is stored as a Method execution Result
getMimeType() - Method in class ranab.img.gif.GifImage: get mime type
getMinConservation() - Method in class gov.lbl.genome.common.ViewSettings
getMinConsWidth() - Method in class gov.lbl.genome.common.ViewSettings
getMinConsWidth() - Method in class gov.lbl.genome.common.VistaCurveModel: get Min Cons Width
getMinX() - Method in class gov.lbl.genome.common.AbstractCurveModel: get Min X
getMinX() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Min X
getMinX() - Method in class gov.lbl.genome.gui.AbstractCurveView: get Min X
getMinX(String) - Method in class gov.lbl.genome.gui.VistaApp: try to extract minX from the position string
getMinX() - Method in class gov.lbl.genome.gui.VistaApp: return minX
getMinX(int) - Method in class gov.lbl.genome.gui.VistaApp: return minX for "i" line
getMinY() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Min Y
getMinY() - Method in class gov.lbl.genome.common.PCurveModel: get Min Y
getMinY() - Method in class gov.lbl.genome.common.VistaCurveModel: get Min Y
getMinY() - Method in class gov.lbl.genome.gui.AbstractCurveView: get Min Y
getMinY() - Method in class gov.lbl.genome.gui.VistaApp: deturn default/actual minY value
getMinY(CurveInfo) - Method in class gov.lbl.genome.gui.VistaApp: rerurn minY parameter for the curve.
getMode() - Method in class gov.lbl.genome.common.VistaCurveModel: get Mode
getName() - Method in class gnu.jpdf.PDFFont: This is the most common method to use.
getName() - Method in class gnu.jpdf.PDFImage: Get the name
getName() - Method in class gov.lbl.genome.common.AbstractCurveModel: get Name
getName() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Name
getName() - Method in class gov.lbl.genome.common.BrowserInfo: get Name
getName() - Method in class gov.lbl.genome.common.ChromInfo: get Name
getName() - Method in class gov.lbl.genome.common.CurveInfo: return Name
getName() - Method in interface gov.lbl.genome.common.CurveModel: get Name
getName() - Method in class gov.lbl.genome.common.features.ChromSegment: get Name
getName() - Method in class gov.lbl.genome.common.GeneralGraphModel
getName() - Method in class gov.lbl.genome.common.GenesInfo: get Name
getName() - Method in class gov.lbl.genome.common.GenomeInfo: get Name
getName() - Method in class sjg.xml.Attribute: Returns the name of this attribute.
getName() - Method in class sjg.xml.Element: Returns the name of this element.
getNewHeight() - Method in class gov.lbl.genome.gui.VistaApp: return newHeight
getNewWidth() - Method in class gov.lbl.genome.gui.VistaApp: return newWidth
getNext() - Method in class gov.lbl.genome.gui.History: return next available status
getNode(int) - Method in class gnu.jpdf.PDFOutline: Returns the outline at a specified position.
getNsApplicationBlock() - Method in class ranab.img.gif.GifImage: Get Netscape application block.
getNumberOfCurves() - Method in class gov.lbl.genome.common.GenomeInfo: get Number Of Curves
getNumberOfGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return Number Of Graphs
getNumberOfPoints() - Method in class gov.lbl.genome.common.AbstractCurveModel
getNumberOfPoints() - Method in interface gov.lbl.genome.common.CurveModel: get Number Of Points
getNumberOfRows() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: return number of rows or 0
getNumColumn() - Method in class layout.TableLayout: Gets the number of columns in this layout.
getNumDataPoints() - Method in class gov.lbl.genome.common.ViewSettings
getNumDataPoints() - Method in class gov.lbl.genome.gui.VistaApp: return expected number of data points.
getNumRow() - Method in class layout.TableLayout: Gets the number of rows in this layout.
getObject(String, Object) - Method in class gov.lbl.genome.gui.Parameter: try to return an Object by name if fail, return the default Object
getObject(String) - Method in class gov.lbl.genome.gui.Parameter: return an Object by name
getObjectArray(String) - Method in class gov.lbl.genome.gui.Parameter: return an array of Objects by name
getOrganisms() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: return list of Organisms
getOrganisms() - Method in class gov.lbl.genome.gui.Status: return Organisms
getOrgId() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Organism Id
getOrgId() - Method in class gov.lbl.genome.common.VistaCurveModel: get Organism Id
getOrientation() - Method in class gnu.jpdf.PDFPage: Returns the pages orientation
getOS(String) - Static method in class gov.lbl.genome.common.StringUtil: Returns the Operating System being used, as defined in the specified string.
getOutline() - Method in class gnu.jpdf.PDFDocument
getOutputStream() - Method in class gnu.jpdf.PDFStream: Returns the OutputStream that will append to this stream.
getOutputStream(String) - Method in class gov.lbl.genome.gui.VistaApp: return OutputStream to "POST" data to the server ToDo This method should throw an exception instead of returning something
getPage(int) - Method in class gnu.jpdf.PDFDocument: This returns a specific page.
getPage() - Method in class gnu.jpdf.PDFGraphics: Returns the associated PDFPage for this graphic
getPage(int) - Method in class gnu.jpdf.PDFPageList: This returns a specific page.
getPageDimension() - Method in class gnu.jpdf.PDFJob: Returns the page dimension
getPageResolution() - Method in class gnu.jpdf.PDFJob: This returns the page resolution.
getPanel(String) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: return Panel by name
getPanelCapacity() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return number of rows that would be drawn in the panel
getParam(String, String) - Method in class gov.lbl.genome.gui.VistaApp: try to get String from Map parameters, then from applet getParameter(String) or return default value
getParam(String, int) - Method in class gov.lbl.genome.gui.VistaApp: try to get integer from Map parameters, then from applet getParameter(String) or return default value
getParameters() - Method in class gov.lbl.genome.common.AbstractCurveModel: return Curve Parameters
getParameters(Object) - Method in class gov.lbl.genome.gui.Resource: return Parameters associated with the object class
getParameterString(VistaApp) - Method in class gov.lbl.genome.common.AbstractCurveModel: return Parameter String
getParameterString(VistaApp) - Method in interface gov.lbl.genome.common.CurveModel: get Parameter String
getParameterString(VistaApp) - Method in class gov.lbl.genome.common.VistaCurveModel: this set of parameters will be passed to the server: &calcWindow=???&minConsWidth=???&minConsIdentity=???&numDataPoints=???&genes=???
getParent() - Method in class gnu.jpdf.BoundingBox: Get this box's parent box
getParent() - Method in class sjg.xml.Element: Returns the parent element of this element.
getPassword() - Method in class gov.lbl.genome.common.GenesInfo: get Password
getPDFDocument() - Method in class gnu.jpdf.PDFJob: Returns the PDFDocument object for this document.
getPDFDocument() - Method in class gnu.jpdf.PDFObject: Returns the PDF document this object belongs to.
getPDFInfo() - Method in class gnu.jpdf.PDFDocument: Get the PDFInfo object, which contains author, title, keywords, etc
getPicture() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: return annotation Picture
getPicture() - Method in class gov.lbl.genome.gui.panel.AxisPanel: return Picture
getPicture() - Method in class gov.lbl.genome.gui.panel.ChromPanel
getPicture() - Method in class gov.lbl.genome.gui.panel.ContigPanel: return picture
getPicture() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: getPicture
getPopup() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return Popup menu
getPos() - Method in class gov.lbl.genome.common.features.ChromSegment: get formatted Position string
getPos() - Method in class gov.lbl.genome.gui.VistaApp: return position as formated string
getPosition() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Position
getPosition() - Method in class gov.lbl.genome.gui.Status: return Position
getPositionString() - Method in class gov.lbl.genome.gui.VistaApp: return formated position string
getPostHeader() - Method in class gov.lbl.genome.gui.VistaApp: getPostHeader
getPrev() - Method in class gov.lbl.genome.gui.History: return previous available status
getPrintHeight(int, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return min height that is necessary to fit all the content
getProviderName() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Provider Name
getProviderUrl() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Provider Url
getPValue() - Method in class gov.lbl.genome.common.features.PValue: get P-Value
getRandomString(int) - Static method in class gov.lbl.genome.gui.VistaApp: return string of specified length with rndom content
getRealEnd() - Method in class gov.lbl.genome.common.features.ChromSegment: get Real Segment End
getRelX(long) - Method in class gov.lbl.genome.gui.Picture: return relative position from the begining
getRelX(double) - Method in class gov.lbl.genome.gui.Picture: eturn relative position from the begining
getRemoveAction() - Method in class gov.lbl.genome.gui.VistaApp: return removeAction2
getRepeatPanel() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return Repeat Panel
getRepeats() - Method in class gov.lbl.genome.gui.Status: return Repeats
getRoot() - Method in class sjg.xml.Document: Return the document root.
getRow() - Method in class layout.TableLayout: Gets the height of a single row in this layout.
getRow(int) - Method in class layout.TableLayout: Gets the sizes of a row in this layout.
getRowCount() - Method in class gov.lbl.genome.common.ViewSettings
GetRun() - Method in class gov.lbl.genome.common.GumbyCurveInfo: Get Run
getRun() - Method in class gov.lbl.genome.common.ViewSettings
getRun() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Run
getRunName() - Method in class gov.lbl.genome.common.ViewSettings
getRunOrg() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Run_ID and Org_ID in the form ready to pass to the server: _
getRunOrg() - Method in class gov.lbl.genome.common.VistaCurveModel: get Run_ID and Org_ID in the form ready to pass to the server: _
getRunOrg() - Method in class gov.lbl.genome.gui.VistaCurveView: return run_id and org_id in the form _
getRuns() - Method in class gov.lbl.genome.gui.VistaApp: return servlet-ready formated run list.
getScore() - Method in class gov.lbl.genome.common.features.PValue: get Score
getSecondFamily() - Method in class gov.lbl.genome.common.VistaCurveInfo: get Second Family
getSelectedIndices() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return numbers of selected lines in the bottom panel curve list
getSelectedOrg() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: return Selected Organism
getSelectedOrg() - Method in class gov.lbl.genome.gui.VistaApp: get selected organism
getSelectedRadio(String) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: return number of the selected radio button in the group
getSequence() - Method in class gov.lbl.genome.common.features.ChromPosition: get Sequence
getSerialID() - Method in class gnu.jpdf.PDFObject: Returns the unique serial number of this object.
getSettingsAction() - Method in class gov.lbl.genome.gui.VistaApp: return settingsAction2
getShow() - Method in class gov.lbl.genome.gui.VistaApp: return a servlet parameter "showdefaults"
getShowContigs() - Method in class gov.lbl.genome.common.ViewSettings
getShowGenes() - Method in class gov.lbl.genome.common.ViewSettings
getShowRepeats() - Method in class gov.lbl.genome.common.ViewSettings
getSize() - Method in class gov.lbl.genome.common.ChromInfo: return the minimum data coordinate available on disk
getSrcName() - Method in class gov.lbl.genome.common.GenesInfo: get Source Name
getSrcUrl() - Method in class gov.lbl.genome.common.GenesInfo: get Source Url
getStackTrace(Throwable) - Static method in class gov.lbl.genome.common.StringUtil
getStart() - Method in class gov.lbl.genome.common.features.ChromSegment: get Start
getStart() - Method in class gov.lbl.genome.common.ViewSettings
getStartPoint() - Method in class gov.lbl.genome.common.AbstractCurveModel
getStartPoint() - Method in interface gov.lbl.genome.common.CurveModel: get Start Point
getStatAction() - Method in class gov.lbl.genome.gui.VistaApp: return statAction2
getStatistics() - Method in class gov.lbl.genome.gui.GeneralGraphView: return Statistics
getStatistics() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return conservation Statistics for all curves
getStatistics() - Method in class gov.lbl.genome.gui.VistaCurveView: return Statistics about conserved regions for the curve
getStrand() - Method in class gov.lbl.genome.common.features.Contig: get Strand
getStream() - Method in class gnu.jpdf.PDFStream: This is for extenders, and provides access to the stream.
getString(String, String) - Method in class gov.lbl.genome.gui.Parameter: try to return a String by name if fail return the default one
getString(String) - Method in class gov.lbl.genome.gui.Parameter: return a String by name
getStringArray() - Method in class gnu.jpdf.BoundingBox: Get the wrapped strings if this box was from a call to getStringBounds, otherwise this method returns null
getStringArray(String) - Method in class gov.lbl.genome.gui.Parameter: return an array of Strings by name
getStringBounds(String, int, int, FontMetrics, int, boolean) - Method in class gnu.jpdf.BoundingBox: Gets the location of a String after it is adjusted for alignment within this box.
getStringBounds(String, int, int, FontMetrics, int) - Method in class gnu.jpdf.BoundingBox: Gets the location of a String after it is adjusted for alignment within this box.
getStrings(Enumeration) - Static method in class gov.lbl.genome.common.StringUtil: Returns an Array of strings from an Enumeration object.
getStrings(String, int, boolean) - Static method in class gov.lbl.genome.common.StringUtil: Tokenize a string using the given delimiter and return an array of the tokens found in the string.
getStrings(String, int, int, boolean) - Static method in class gov.lbl.genome.common.StringUtil: Tokenize a string starting at the specified index.
getStringWidth(String, Font) - Method in class gov.lbl.genome.gui.panel.VistaPanel: return width in pixels for the strind s and font f
getStringWidth(String, Font) - Method in class gov.lbl.genome.gui.Picture: return Width (in pixels) of the string
getStyle() - Method in class gnu.jpdf.PDFFont
getSubject() - Method in class gnu.jpdf.PDFInfo: Get the value of subject.
getSuperContigNum() - Method in class gov.lbl.genome.common.features.SuperContig: get SuperContig Number
getSwapCurvesAction() - Method in class gov.lbl.genome.gui.VistaApp
getTableName() - Method in class gov.lbl.genome.common.GenesInfo: get Table Name
getTestgpvParam() - Method in class gov.lbl.genome.gui.action.UCSCBrowserAction: form a parameter string to call UCSC browser
getText() - Method in class sjg.xml.Comment: Returns the text of this comment.
getText() - Method in class sjg.xml.ProcessingInstruction: Returns the text contents of this processing instruction.
getTextbrowserURL() - Method in class gov.lbl.genome.gui.VistaApp: return URL for the text browser
getTitle() - Method in class gnu.jpdf.PDFInfo: Get the value of title.
getTracerPanel() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return Tracer Panel
getType() - Method in class gnu.jpdf.PDFFont
getType() - Method in class gnu.jpdf.PDFObject: Returns the PDF Type of this object
getType() - Method in class gov.lbl.genome.common.BrowserInfo: get browser Type
getType() - Method in class gov.lbl.genome.common.ChromInfo: get chromosome Type
getType() - Method in class gov.lbl.genome.common.CurveInfo: get Type
getType() - Method in class gov.lbl.genome.common.features.PValue: get Type
getType() - Method in class gov.lbl.genome.common.features.Repeat: get Type
getType() - Method in class gov.lbl.genome.common.GenomeInfo: get Type
getUniqOrganisms() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return number uniq organisms
getUp2Date(String) - Method in class gov.lbl.genome.common.CommUnit: update init information
getUrl() - Method in class gov.lbl.genome.common.BrowserInfo: get Url string
getUrl(String) - Method in class gov.lbl.genome.common.BrowserInfo: get Url string with attached parameters
getURL() - Method in class gov.lbl.genome.common.CustomCurveModel
getValue() - Method in class sjg.xml.Attribute: Returns the value of this attribute.
getValues() - Method in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
getVersion() - Method in class gov.lbl.genome.common.CommUnit: getVersion returns current version
getVersion() - Method in class gov.lbl.genome.gui.VistaApp: getVersion
getVertSize() - Method in class gov.lbl.genome.gui.panel.VistaPanel: return adjusted panel height
getVisible() - Method in class gov.lbl.genome.gui.panel.GraphViewList: return Visible elements
getVisibleCurveNames() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: return names of visible Curves
getWidth() - Method in class gnu.jpdf.PDFImage: Get the value of width.
getWidth() - Method in class gov.lbl.genome.gui.AbstractCurveView: return adjusted graph width
getWidth() - Method in class gov.lbl.genome.gui.Picture: return picture Width
getWriter() - Method in class gnu.jpdf.PDFGraphics: Returns the PrintWriter handling the underlying stream
getWriter() - Method in class gnu.jpdf.PDFStream: Creates a PrintWriter that will append to this stream.
getXDisplay(int) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: convert screen coordinates into chromosome coordinates
getXDisplay(int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: convert screen coordinates into chromosome coordinates
getXDisplay(int, int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: convert screen coordinates into chromosome coordinates
getXDisplay(int) - Method in class gov.lbl.genome.gui.Picture: convert the parameter into chromosome coordinates
getXType() - Method in class gov.lbl.genome.common.AbstractCurveModel
getXType() - Method in interface gov.lbl.genome.common.CurveModel: return Type of the X axis
getXType() - Method in class gov.lbl.genome.common.GeneralGraphModel: get X Type
getXType() - Method in interface gov.lbl.genome.common.GraphModel
getXUnits() - Method in class gov.lbl.genome.common.AbstractGraphModel: get X Units
getXUnits() - Method in interface gov.lbl.genome.common.GraphModel
getYLabel() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Y Label
getYLabel() - Method in class gov.lbl.genome.common.PCurveModel: get Y Label Text
getYLabelOrientation() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Y Label Orientation
getYType() - Method in class gov.lbl.genome.common.AbstractCurveModel
getYType() - Method in interface gov.lbl.genome.common.CurveModel: return Type of the Y axis
getYType() - Method in class gov.lbl.genome.common.GeneralGraphModel: get Y Type
getYType() - Method in interface gov.lbl.genome.common.GraphModel
getYUnits() - Method in class gov.lbl.genome.common.AbstractGraphModel: get Y Units
getYUnits() - Method in interface gov.lbl.genome.common.GraphModel
GifAppEx - Class in ranab.img.gif: Gif application extension.
GifColor - Class in ranab.img.gif: Color data structure.
GifCommentEx - Class in ranab.img.gif: Comment extension block.
GifEx - Class in ranab.img.gif: Abstract base class of all the GIF extension blocks.
GifGraphicEx - Class in ranab.img.gif: Graphic extension block.
GifImage - Class in ranab.img.gif: GIF encoder class.
GifImage(int, int) - Constructor for class ranab.img.gif.GifImage: Constructor
GifImageDescriptor - Class in ranab.img.gif: GIF image descriptor data structure.
GifNsAppEx - Class in ranab.img.gif: Gif Netscape application extension.
GifScreenDescriptor - Class in ranab.img.gif: GIF screen descriptor data structure.
gifString - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
gnu.jpdf - package gnu.jpdf: PDF library
gov.lbl.genome.common - package gov.lbl.genome.common: This package contains data models, utils and comunication unit
gov.lbl.genome.common.features - package gov.lbl.genome.common.features: This package contains classes for various intervals on a genome.
gov.lbl.genome.gui - package gov.lbl.genome.gui: This is the main package
gov.lbl.genome.gui.action - package gov.lbl.genome.gui.action: This package contains classes for GUI actions.
gov.lbl.genome.gui.dialog - package gov.lbl.genome.gui.dialog: This package contains classes to show all dialog windows
gov.lbl.genome.gui.panel - package gov.lbl.genome.gui.panel: This package contains classes to draw various VGB panels.
graph - Variable in class gov.lbl.genome.gui.GeneralGraphView
GRAPH_BORDER - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_BORDER_WIDTH - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_COMP_HEIGHT - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_HEIGHT - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_INTERVAL - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_MIN_WIDTH - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_NAME_BOLD_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_OFFSET_WIDTH - Static variable in interface gov.lbl.genome.gui.UIConstants
GRAPH_SPACER_HEIGHT - Static variable in interface gov.lbl.genome.gui.UIConstants
GraphModel - Interface in gov.lbl.genome.common: Title: GraphModel
graphs - Variable in class gov.lbl.genome.gui.GeneralGraphView
graphView - Variable in class gov.lbl.genome.gui.AbstractCurveView
GraphView - Interface in gov.lbl.genome.gui: Title: GraphView
GraphViewList - Class in gov.lbl.genome.gui.panel: Title: GraphViewList
GraphViewList() - Constructor for class gov.lbl.genome.gui.panel.GraphViewList
GraphViewList(GraphViewList) - Constructor for class gov.lbl.genome.gui.panel.GraphViewList: GraphViewList
GumbyCurveInfo - Class in gov.lbl.genome.common: Title: GumbyCurveInfo
GumbyCurveInfo(String, String, String) - Constructor for class gov.lbl.genome.common.GumbyCurveInfo: GumbyCurveInfo

H

hAlign - Variable in class layout.TableLayoutConstraints: Horizontal justification if component occupies just one cell
handCursor - Variable in class gov.lbl.genome.gui.LinkLabel
handle(String, String, Exception) - Method in class gov.lbl.genome.gui.ErrorHandler: call this method to show error dialog window and print an exception if debugException is true
handleCallback(Map) - Method in interface gov.lbl.genome.gui.dialog.Callback
handlePixel(int, int, int) - Static method in class gnu.jpdf.PDFImage: Converts a pixel to a hex string
hasAttribute(String) - Method in class sjg.xml.Element: Returns whether an attribute of a given name exists.
hashCode() - Method in class gov.lbl.genome.common.features.ChromPosition
hashCode() - Method in class gov.lbl.genome.common.features.ChromSegment
hashCode() - Method in class gov.lbl.genome.common.features.Gap
hasImageB - Variable in class gnu.jpdf.PDFPage: These handle the procset for this page.
hasImageC - Variable in class gnu.jpdf.PDFPage: These handle the procset for this page.
hasImageI - Variable in class gnu.jpdf.PDFPage: These handle the procset for this page.
hasMoreElements() - Method in class sjg.xml.Tokenizer
hasParent() - Method in class gnu.jpdf.BoundingBox: Returns true if this box has a parent.
height - Variable in class gov.lbl.genome.gui.AbstractCurveView
height - Variable in class gov.lbl.genome.gui.panel.VistaPanel
height - Variable in class gov.lbl.genome.gui.Picture
HelpAction - Class in gov.lbl.genome.gui.action: Title: Help
HelpAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.HelpAction: HelpAction
HelpAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.HelpAction: HelpAction
hidden - Variable in class gov.lbl.genome.common.AbstractCurveModel
hidden() - Method in class layout.TableLayout: Determines whether or not there are any hidden components.
hide() - Method in class gov.lbl.genome.common.AbstractCurveModel: hidden = true
hideCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: hide tracer
hideGraph(String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: hide Graph
hideInvisibleElements() - Method in class gov.lbl.genome.gui.panel.GraphViewList: hideInvisibleElements
History - Class in gov.lbl.genome.gui: Title: History
History() - Constructor for class gov.lbl.genome.gui.History: History
HORIZ_ALIGN_CENTER - Static variable in class gnu.jpdf.BoundingBox: Used to align a String horizontally in the center of the box
HORIZ_ALIGN_LEFT - Static variable in class gnu.jpdf.BoundingBox: Used to align a String to the left in the box
HORIZ_ALIGN_RIGHT - Static variable in class gnu.jpdf.BoundingBox: Used to aling a String to the right in a box
horizSize - Variable in class gov.lbl.genome.gui.panel.VistaPanel

I

id - Variable in class gnu.jpdf.PDFXref: The id of a PDF Object
id - Variable in class gov.lbl.genome.common.AbstractCurveModel
ID - Variable in class gov.lbl.genome.common.AbstractGraphModel
image - Variable in class gov.lbl.genome.gui.GeneralGraphView
image - Variable in class gov.lbl.genome.gui.panel.VistaPanel
image - Variable in class gov.lbl.genome.gui.Picture
imageableHeight - Variable in class gov.lbl.genome.gui.Picture
imageableWidth - Variable in class gov.lbl.genome.gui.Picture
imageResources - Variable in class gnu.jpdf.PDFPage
imageUpdate(Image, int, int, int, int, int) - Method in class gnu.jpdf.PDFImage: Describe imageUpdate method here.
Increment_All(int) - Method in class gov.lbl.genome.common.features.ChromSegments: shift all segments
infoID - Variable in class gnu.jpdf.PDFOutput: This is used to track the /Info object (info)
init(PDFPage) - Method in class gnu.jpdf.PDFGraphics: This is called by PDFPage when creating a Graphcis instance.
init(PDFPage, PrintWriter) - Method in class gnu.jpdf.PDFGraphics: This method is used internally by create() and by the PDFJob class
init - Static variable in class gov.lbl.genome.gui.Debug
init() - Method in class gov.lbl.genome.gui.VistaApp: This is an important and big method.
INIT_CURR_POSITION - Static variable in interface gov.lbl.genome.gui.UIConstants
INPUT_COL_WIDTH - Static variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
insertColumn(int, double) - Method in class layout.TableLayout: Inserts a column in this layout.
insertRow(int, double) - Method in class layout.TableLayout: Inserts a row in this layout.
INSET - Static variable in class gnu.jpdf.PDFAnnot: The border is drawn in an inset style (faux three-dimensional) such that it looks as if it is inset into the page (opposite of BEVELED)
INTEGER - Static variable in interface gov.lbl.genome.common.CommonConstants
INTEGER - Static variable in interface gov.lbl.genome.common.VistaModelConstants
intersect(ChromSegment) - Method in class gov.lbl.genome.common.features.ChromSegment: Returns a new ChromSegment which is the intersection of this segment and the provided segment.
inTracerPanel - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
invalidateLayout(Container) - Method in class layout.TableLayout: Invalidates the layout, indicating that if the layout manager has cached information it should be discarded.
InvalidDataEntryException - Exception in gov.lbl.genome.gui: Title: InvalidDataEntryException
InvalidDataEntryException(String) - Constructor for exception gov.lbl.genome.gui.InvalidDataEntryException
INVERTEDPORTRAIT - Static variable in class gnu.jpdf.PDFPage: Specifies that the page is in INVERTEDPORTRAIT orientation.
invisibleElementAt(int) - Method in class gov.lbl.genome.gui.panel.GraphViewList: return invisibleElement or null
invisibleMouseCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: Hide mouse cursor
invisibleSize() - Method in class gov.lbl.genome.gui.panel.GraphViewList: return number of invisible elements
isCheckable() - Method in class gov.lbl.genome.common.CurveInfo: return true if curve is Checkable
isChrom() - Method in class gov.lbl.genome.gui.VistaApp: return true if current contig is real chromosome
isDangerous() - Method in class gov.lbl.genome.gui.VistaApp: return true if action can destroy the applet.
isDefault() - Method in class gov.lbl.genome.common.CurveInfo: return true if curve is Default
isDefault() - Method in class gov.lbl.genome.common.GenesInfo: return true if Default
isDefault() - Method in class gov.lbl.genome.common.GenomeInfo: return true if Default
isDefaultVisible() - Method in class gov.lbl.genome.gui.VistaApp: show or not to show default curves
isDelayed() - Method in class ranab.img.gif.GifGraphicEx: Is delayed
isDeleted() - Method in class gov.lbl.genome.common.AbstractCurveModel: return true if curve is deleted
isDeleted() - Method in class gov.lbl.genome.common.CurveInfo: return true if curve is Deleted
isDeleted() - Method in class gov.lbl.genome.common.GenomeInfo: return true if deleted
isDownEnabled() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: return true if Down button is Enabled
isForward() - Method in class gov.lbl.genome.common.features.Gene: return true if forward
isHidden() - Method in class gov.lbl.genome.common.AbstractCurveModel: return true if the curve is hidden
isIdle1() - Method in class gov.lbl.genome.gui.VistaApp: return true if idle more than 20 min
isIdle2() - Method in class gov.lbl.genome.gui.VistaApp: return true if idle more than 30 sec
isIdle3() - Method in class gov.lbl.genome.gui.VistaApp: return true if idle more than 0.5 sec
isInside(int) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: return true of mouse cursor is in the selected area
isInteger(String) - Static method in class gov.lbl.genome.common.StringUtil
isLoading - Variable in class gov.lbl.genome.gui.GeneralGraphComp
isNearEast(int) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: return true if mouse cursor is near the east edge of the selected area
isNearWest(int) - Method in class gov.lbl.genome.gui.panel.ChromPanelPicture: return true if mouse cursor is near the west edge of the selected area
isNextEmpty() - Method in class gov.lbl.genome.gui.History: return true if there are no next available status
isPopup() - Method in class gov.lbl.genome.gui.panel.TracerPanel: return true if ready to show a popup menu
isPrevEmpty() - Method in class gov.lbl.genome.gui.History: return true if there are no more saved status in the history
isReady() - Method in class gov.lbl.genome.gui.VistaApp
isRealChrom() - Method in class gov.lbl.genome.common.features.ChromSegment: return true if segment is a Real Chromosome
isSelected() - Method in class gov.lbl.genome.gui.GeneralGraphView: return true if selected
isTemp() - Method in class gov.lbl.genome.common.VistaCurveInfo: Ask Mitya
isTransparent() - Method in class ranab.img.gif.GifGraphicEx: Is transparent.
isUpEnabled() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: return true if Up button is Enabled
isVisible() - Method in class gov.lbl.genome.common.CurveInfo: return true if curve is Visible
isVisible() - Method in class gov.lbl.genome.gui.GeneralGraphView: return true if visible
iterator() - Method in class gov.lbl.genome.gui.panel.GraphViewList: visible iterator

J

jpgString - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel

K

kl - Variable in class gov.lbl.genome.gui.dialog.ActionDialog

L

l1 - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
l2 - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
l3 - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
LABEL_COL_WIDTH - Static variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
LANDSCAPE - Static variable in class gnu.jpdf.PDFPage: Specifies that the page is in LANDSCAPE orientation.
last - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
lastElement() - Method in class gov.lbl.genome.gui.panel.GraphViewList: last visible Element
lastPageFirst() - Method in class gnu.jpdf.PDFJob: In AWT's PrintJob, this would return true if the user requested that the file is printed in reverse order.
lastPosition() - Method in class gov.lbl.genome.gui.VistaApp: set status from previous position
layout - package layout: Table layout
layoutContainer(Container) - Method in class layout.TableLayout: To lay out the specified container using this layout.
lblMaxY - Variable in class gov.lbl.genome.gui.GeneralGraphView
lblMinY - Variable in class gov.lbl.genome.gui.GeneralGraphView
lblName - Variable in class gov.lbl.genome.gui.GeneralGraphView
LEFT - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
LEFT - Static variable in interface layout.TableLayoutConstants: Indicates that the component is left justified in its cell
leftSpace - Variable in class gov.lbl.genome.gui.panel.VistaPanel
legend - Static variable in class gov.lbl.genome.gui.VistaApp
LegendPanel - Class in gov.lbl.genome.gui.panel: Title: LegendPanel
LegendPanel() - Constructor for class gov.lbl.genome.gui.panel.LegendPanel: LegendPanel
LINE - Static variable in class gov.lbl.genome.common.features.Repeat
LINE_SPACING_PERCENTAGE - Static variable in class gnu.jpdf.BoundingBox: Percent f line height to space lines
lineNumber - Variable in class gov.lbl.genome.gui.AbstractCurveView
lineNumber - Variable in class gov.lbl.genome.gui.panel.VGBPanel
lineto(int, int) - Method in class gnu.jpdf.PDFGraphics: This adds a line segment to the current path
lineto(double, double) - Method in class gnu.jpdf.PDFGraphics: This adds a line segment to the current path
link - Variable in class gov.lbl.genome.gui.LinkLabel
LinkLabel - Class in gov.lbl.genome.gui: Title: LinkLabel
LinkLabel(VistaApp, String) - Constructor for class gov.lbl.genome.gui.LinkLabel: LinkLabel
LinkLabel(String, String) - Constructor for class gov.lbl.genome.gui.LinkLabel
LinkLabel(VistaApp, String, String) - Constructor for class gov.lbl.genome.gui.LinkLabel: LinkLabel
linkURL - Variable in class gov.lbl.genome.gui.LinkLabel
list - Variable in class layout.TableLayout: List of components and their sizes
listIterator() - Method in class gov.lbl.genome.gui.panel.GraphViewList: visible list iterator
ln10 - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
ln10 - Variable in class gov.lbl.genome.gui.panel.ChromPanelPicture
ln10 - Static variable in class gov.lbl.genome.gui.panel.XAxisPanel
loadURLContents(String) - Static method in class gov.lbl.genome.common.NetUtil: Returns the Html page contents of the given url.
lockDown() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: Disable Down Button
lockUp() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: Disable Up Button
longname - Variable in class gov.lbl.genome.common.AbstractGraphModel
LTR - Static variable in class gov.lbl.genome.common.features.Repeat

M

main(String[]) - Static method in class gnu.jpdf.BoundingBox: For testing
main(String[]) - Static method in class gnu.jpdf.PDFTest: The test is initiated through the main method.
makePDFString(String) - Static method in class gnu.jpdf.PDFStringHelper: This converts a string into PDF.
marginBottom - Variable in class gov.lbl.genome.gui.Picture
marginLeft - Variable in class gov.lbl.genome.gui.AbstractCurveView
marginLeft - Variable in class gov.lbl.genome.gui.GeneralGraphComp
marginLeft - Variable in class gov.lbl.genome.gui.Picture
marginRight - Variable in class gov.lbl.genome.gui.AbstractCurveView
marginRight - Variable in class gov.lbl.genome.gui.GeneralGraphComp
marginRight - Variable in class gov.lbl.genome.gui.Picture
marginTop - Variable in class gov.lbl.genome.gui.AbstractCurveView
marginTop - Variable in class gov.lbl.genome.gui.GeneralGraphComp
marginTop - Variable in class gov.lbl.genome.gui.Picture
markSupported() - Method in class gov.lbl.genome.common.StringInputStream
MAX_ALIGN - Static variable in interface layout.TableLayoutConstants: Maximum value for an alignment
MAX_REG_SIZE - Static variable in interface gov.lbl.genome.common.CommonConstants
maxHeight - Variable in class gov.lbl.genome.gui.Picture
maximumLayoutSize(Container) - Method in class layout.TableLayout: Returns the maximum dimensions for this layout given the components in the specified target container.
maxProc - Variable in class gov.lbl.genome.gui.GeneralGraphView
maxWidth - Variable in class gov.lbl.genome.gui.Picture
maxX - Variable in class gov.lbl.genome.common.AbstractCurveModel
maxX - Variable in class gov.lbl.genome.common.AbstractGraphModel
maxX - Variable in class gov.lbl.genome.gui.AbstractCurveView
maxX - Variable in class gov.lbl.genome.gui.panel.VistaPanel
maxX - Variable in class gov.lbl.genome.gui.Picture
maxY - Variable in class gov.lbl.genome.common.AbstractGraphModel
maxY - Variable in class gov.lbl.genome.gui.AbstractCurveView
maxY - Variable in class gov.lbl.genome.gui.CurveParameters
mbase - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
mbase - Variable in class gov.lbl.genome.gui.panel.ChromPanelPicture
mbase - Static variable in class gov.lbl.genome.gui.panel.XAxisPanel
mbyAppAuth - Variable in class ranab.img.gif.GifAppEx
mbyAppId - Variable in class ranab.img.gif.GifAppEx
mbyBlkSize - Static variable in class ranab.img.gif.GifAppEx
mbyBlkTerm - Static variable in class ranab.img.gif.GifEx
mbyByte - Variable in class ranab.img.gif.GifNsAppEx
mbyCtrlLab - Variable in class ranab.img.gif.GifEx
mbyExIntro - Static variable in class ranab.img.gif.GifEx
mbySubBlkSz - Variable in class ranab.img.gif.GifNsAppEx
media - Variable in class gnu.jpdf.PDFGraphics: This is the media we are working with
MEDIA_11x17 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in 11x17 format.
MEDIA_a0 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a0 format.
MEDIA_a1 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a1 format.
MEDIA_a10 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a10 format.
MEDIA_a2 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a2 format.
MEDIA_a3 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a3 format.
MEDIA_a4 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a4 format.
MEDIA_a5 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a5 format.
MEDIA_a6 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a6 format.
MEDIA_a7 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a7 format.
MEDIA_a8 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a8 format.
MEDIA_a9 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in a9 format.
MEDIA_archA - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in archA format.
MEDIA_archB - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in archB format.
MEDIA_archC - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in archC format.
MEDIA_archD - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in archD format.
MEDIA_archE - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in archE format.
MEDIA_b0 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b0 format.
MEDIA_b1 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b1 format.
MEDIA_b2 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b2 format.
MEDIA_b3 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b3 format.
MEDIA_b4 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b4 format.
MEDIA_b5 - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in b5 format.
MEDIA_flsa - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in flsa format.
MEDIA_flse - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in flse format.
MEDIA_halfletter - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in halfletter format.
MEDIA_ledger - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in ledger format.
MEDIA_legal - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in legal format.
MEDIA_letter - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in letter format.
MEDIA_note - Static variable in class gnu.jpdf.PDFPage: Rectangle defining a page in note format.
mediabox - Variable in class gnu.jpdf.PDFPage: This is this pages media box, ie the size of the page
MergeWith(ChromSegments) - Method in class gov.lbl.genome.common.features.ChromSegments: return new collection, combined from 2 collections
mImageData - Variable in class ranab.img.gif.GifEx
MIN_ALIGN - Static variable in interface layout.TableLayoutConstants: Minimum value for an alignment
minConsWidth - Variable in class gov.lbl.genome.common.VistaCurveModel
minConsWidth - Variable in class gov.lbl.genome.gui.CurveParameters
MINIMUM - Static variable in interface layout.TableLayoutConstants: Indicates that the row/column should be allocated just enough space to accomidate the minimum size of all components contained completely within this row/column.
minimumLayoutSize(Container) - Method in class layout.TableLayout: Determines the minimum size of the container argument using this layout.
minor - Variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
minor - Variable in class gov.lbl.genome.gui.panel.ChromPanel
minor - Variable in class gov.lbl.genome.gui.panel.ChromPanelPicture
minor - Variable in class gov.lbl.genome.gui.panel.XAxisPanel
minProc - Variable in class gov.lbl.genome.gui.GeneralGraphView
minX - Variable in class gov.lbl.genome.common.AbstractCurveModel
minX - Variable in class gov.lbl.genome.common.AbstractGraphModel
minX - Variable in class gov.lbl.genome.gui.AbstractCurveView
minX - Variable in class gov.lbl.genome.gui.panel.VistaPanel
minX - Variable in class gov.lbl.genome.gui.Picture
minY - Variable in class gov.lbl.genome.common.AbstractGraphModel
minY - Variable in class gov.lbl.genome.gui.AbstractCurveView
minY - Variable in class gov.lbl.genome.gui.CurveParameters
model - Variable in class gov.lbl.genome.gui.AbstractCurveView
model - Variable in class gov.lbl.genome.gui.GeneralGraphView
mouseClicked(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel: Open link in the new browser window
mouseClicked(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: Just do nothing
mouseDragged(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel
mouseDragged(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: draw selected area whem mouse is dragged
mouseEntered(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel: show link in the status bar, show hand cursor
mouseEntered(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: mouseEntered
mouseExited(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel: clear status bar, show default cursor
mouseExited(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: hide tracer
mouseMoved(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel
mouseMoved(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: show tracer coordinates
mousePressed(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel
mousePressed(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: Prepare to draw selection or to show a popup menu
mouseReleased(MouseEvent) - Method in class gov.lbl.genome.gui.LinkLabel
mouseReleased(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: process selected area and update position
moveMouseCursor() - Method in class gov.lbl.genome.gui.panel.ChromPanel: set mouse cursor to the moveMouseCursor
moveSelectedDown() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: move Selected Graphs Down
moveSelectedUp() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: move Selected Graphs Up
moveto(int, int) - Method in class gnu.jpdf.PDFGraphics: This moves the current drawing point.
moveto(double, double) - Method in class gnu.jpdf.PDFGraphics: This moves the current drawing point.
msItrCnt - Variable in class ranab.img.gif.GifNsAppEx
multiSelectGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: select more than one graph

N

name - Variable in class gov.lbl.genome.common.AbstractGraphModel
NAME - Static variable in class gov.lbl.genome.common.features.Repeat
name - Variable in class gov.lbl.genome.gui.CurveParameters
name - Variable in class gov.lbl.genome.gui.panel.VGBPanel
name - Variable in class gov.lbl.genome.gui.Picture
NetUtil - Class in gov.lbl.genome.common
NetUtil() - Constructor for class gov.lbl.genome.common.NetUtil
newGraphView - Variable in class gov.lbl.genome.gui.GeneralGraphView
nextElement() - Method in class sjg.xml.Tokenizer
nextPanel - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
nextPosition() - Method in class gov.lbl.genome.gui.VistaApp: set status from nextPosition
nomouse - Variable in class gov.lbl.genome.gui.panel.TracerPanel
NONE - Static variable in interface gov.lbl.genome.common.CommonConstants
nPoints - Variable in class gov.lbl.genome.gui.AbstractCurveView
numberOfActions - Variable in class gov.lbl.genome.gui.action.VAbstractAction

O

objects - Variable in class gnu.jpdf.PDFDocument: This vector contains each indirect object within the document.
objser - Variable in class gnu.jpdf.PDFDocument: This is used to allocate objects a unique serial number in the document.
objser - Variable in class gnu.jpdf.PDFObject: This is the unique serial number for this object.
offset - Variable in class gnu.jpdf.PDFOutput: This is the current position within the stream
offset - Variable in class gnu.jpdf.PDFXref: The offset within the PDF file
offsets - Variable in class gnu.jpdf.PDFOutput: This vector contains offsets of each object
offsetWidth - Variable in class gov.lbl.genome.gui.panel.VistaPanel
ok() - Method in class gov.lbl.genome.gui.dialog.SaveAsDialog
OK_CANCEL_OPTION - Static variable in class gov.lbl.genome.gui.dialog.ActionDialog
OK_OPTION - Static variable in class gov.lbl.genome.gui.dialog.ActionDialog
okAction() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: This method must be overriden to process OK action
okAction() - Method in class gov.lbl.genome.gui.dialog.ContigListDialog: process all data and close the window
okAction() - Method in class gov.lbl.genome.gui.dialog.SaveAsDialog: process all results and close the window
okAction() - Method in class gov.lbl.genome.gui.dialog.SearchResultsDialog: process results and close the window
okAction() - Method in class gov.lbl.genome.gui.dialog.StatDialog: Close dialog window
oldHeight - Variable in class layout.TableLayout: Previous known height of the container
oldWidth - Variable in class layout.TableLayout: Previous known width of the container
os - Variable in class gnu.jpdf.PDFJob: This is the OutputStream the PDF file will be written to when complete Note: This is transient, as it's not valid after being Serialized.
os - Variable in class gnu.jpdf.PDFOutput: This is the actual OutputStream used to write to.
OTHER - Static variable in class gov.lbl.genome.common.features.Repeat
Overlap(ChromSegments) - Method in class gov.lbl.genome.common.features.ChromSegments: return Overlap of two collections
Overlapped() - Method in class gov.lbl.genome.common.features.ChromSegments
overlapping() - Method in class layout.TableLayout: Determines whether or not there are any overlapping components.

P

page - Variable in class gnu.jpdf.PDFJob: This is the current page being constructed by the last getGraphics() call
pageFormat - Variable in class gov.lbl.genome.gui.VistaApp
pagenum - Variable in class gnu.jpdf.PDFJob: This is the page number of the current page
pages - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
PageSetupAction - Class in gov.lbl.genome.gui.action: Title: Page settings
PageSetupAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.PageSetupAction: PageSetupAction
PageSetupAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.PageSetupAction: PageSetupAction
pageSetupString - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
paintComponent(Graphics) - Method in class gov.lbl.genome.gui.GeneralGraphComp: paint Component
paintComponent(Graphics) - Method in class gov.lbl.genome.gui.GeneralGraphView: paint graph view
paintComponent(Graphics) - Method in class gov.lbl.genome.gui.panel.TracerPanel: draw tracer or green bar
paintComponent(Graphics) - Method in class gov.lbl.genome.gui.panel.VistaPanel: paintComponent overload JPanel paintComponent.
paintComponent(Graphics) - Method in class gov.lbl.genome.gui.VistaLabel: Add antialiasing to the standard JLabel
paper - Variable in class gov.lbl.genome.gui.VistaApp
param - Variable in class gov.lbl.genome.gui.AbstractCurveView
param - Variable in class gov.lbl.genome.gui.action.VAbstractAction
Parameter - Class in gov.lbl.genome.gui: Title: Parameter
Parameter(Hashtable) - Constructor for class gov.lbl.genome.gui.Parameter: Parameter
parameter - Static variable in class gov.lbl.genome.gui.Resource
parameters - Variable in class gov.lbl.genome.gui.panel.VGBPanel
parent - Variable in class gnu.jpdf.PDFOutline: For subentries, this points to it's parent outline
parent - Variable in class gov.lbl.genome.gui.GeneralGraphView
parent - Variable in class gov.lbl.genome.gui.panel.TracerPanel
parse(String) - Static method in class sjg.xml.Parser: Parses a text string.
parse(InputStream) - Static method in class sjg.xml.Parser: Parses an input stream.
parse(Applet, String) - Static method in class sjg.xml.Parser: Load a document from an applet jar
parseFormattedLong(String) - Static method in class gov.lbl.genome.common.StringUtil: Parses a formatted string representation of a chromosome coordinate.
parsePos(String) - Static method in class gov.lbl.genome.common.features.ChromSegment: build ChromSegment from the position string
Parser - Class in sjg.xml: An xml parser.
Parser() - Constructor for class sjg.xml.Parser
parseSpan(String) - Static method in class gov.lbl.genome.common.features.ChromSegment: return array with start and end
PCurveModel - Class in gov.lbl.genome.common: Title: PCurveModel
PCurveModel(Vector, String, GumbyCurveInfo, int, int) - Constructor for class gov.lbl.genome.common.PCurveModel: PCurveModel
PCurveModel(Vector, String, int, int) - Constructor for class gov.lbl.genome.common.PCurveModel: PCurveModel
PCurveModel(GumbyCurveInfo, int, int) - Constructor for class gov.lbl.genome.common.PCurveModel: PCurveModel
PCurveModel() - Constructor for class gov.lbl.genome.common.PCurveModel: PCurveModel
PDF_PAGE_MODES - Static variable in class gnu.jpdf.PDFDocument: These map the page modes just defined to the pagemodes setting of PDF.
PDFAnnot - Class in gnu.jpdf: This class defines an annotation (commonly known as a Bookmark).
PDFAnnot(String, int, int, int, int) - Constructor for class gnu.jpdf.PDFAnnot: This is used to create an annotation.
PDFAnnot(int, int, int, int, String) - Constructor for class gnu.jpdf.PDFAnnot: Creates a text annotation
PDFAnnot(int, int, int, int, PDFObject) - Constructor for class gnu.jpdf.PDFAnnot: Creates a link annotation
PDFAnnot(int, int, int, int, PDFObject, int, int, int, int) - Constructor for class gnu.jpdf.PDFAnnot: Creates a link annotation
PDFBorder - Class in gnu.jpdf: A border around an annotation
PDFBorder(short, double) - Constructor for class gnu.jpdf.PDFBorder: Creates a border using the predefined styles in PDFAnnot.
PDFBorder(double, double[]) - Constructor for class gnu.jpdf.PDFBorder: Creates a border of style PDFAnnot.DASHED
PDFCatalog - Class in gnu.jpdf: This class implements the PDF Catalog, also known as the root node
PDFCatalog(PDFPageList, int) - Constructor for class gnu.jpdf.PDFCatalog: This constructs a PDF Catalog object
PDFDocument - Class in gnu.jpdf: This class is the base of the PDF generator.
PDFDocument() - Constructor for class gnu.jpdf.PDFDocument: This creates a PDF document with the default pagemode
PDFDocument(int) - Constructor for class gnu.jpdf.PDFDocument: This creates a PDF document
pdfDocument - Variable in class gnu.jpdf.PDFJob: This is the PDF file being constructed
pdfDocument - Variable in class gnu.jpdf.PDFObject: This allows any PDF object to refer to the document being constructed.
PDFFont - Class in gnu.jpdf: This class defines a font within a PDF document.
PDFFont() - Constructor for class gnu.jpdf.PDFFont: This constructs a default PDFFont.
PDFFont(String, String, String, int) - Constructor for class gnu.jpdf.PDFFont: Constructs a PDFFont.
PDFGraphics - Class in gnu.jpdf: This class is our implementation of AWT's Graphics class.
PDFGraphics() - Constructor for class gnu.jpdf.PDFGraphics
PDFImage - Class in gnu.jpdf: This implements the Image XObject.
PDFImage() - Constructor for class gnu.jpdf.PDFImage: Creates a new PDFImage instance.
PDFImage(Image) - Constructor for class gnu.jpdf.PDFImage: Creates a new PDFImage instance.
PDFImage(Image, int, int, int, int, ImageObserver) - Constructor for class gnu.jpdf.PDFImage: Creates a new PDFImage instance.
PDFInfo - Class in gnu.jpdf: This class stores details of the author, the PDF generator etc.
PDFInfo() - Constructor for class gnu.jpdf.PDFInfo: This constructs a minimal info object
PDFInfo(String) - Constructor for class gnu.jpdf.PDFInfo
PDFJob - Class in gnu.jpdf: This class extends awt's PrintJob, to provide a simple method of writing PDF documents.
PDFJob() - Constructor for class gnu.jpdf.PDFJob: This constructs the job.
PDFJob(OutputStream) - Constructor for class gnu.jpdf.PDFJob: This constructs the job.
PDFJob(OutputStream, String) - Constructor for class gnu.jpdf.PDFJob: This constructs the job.
PDFObject - Class in gnu.jpdf: This is the base class for all Objects that form the PDF document.
PDFObject(String) - Constructor for class gnu.jpdf.PDFObject: This is usually called by extensors to this class, and sets the PDF Object Type
PDFOutline - Class in gnu.jpdf: This class manages the documents outlines (also known as bookmarks).
PDFOutline() - Constructor for class gnu.jpdf.PDFOutline: Constructs a PDF Outline object.
PDFOutline(String, PDFPage) - Constructor for class gnu.jpdf.PDFOutline: Constructs a PDF Outline object.
PDFOutline(String, PDFPage, int, int, int, int) - Constructor for class gnu.jpdf.PDFOutline: Constructs a PDF Outline object.
PDFOutput - Class in gnu.jpdf: This class is used to write a PDF document.
PDFOutput(OutputStream) - Constructor for class gnu.jpdf.PDFOutput: This creates a PDF OutputStream
PDFPage - Class in gnu.jpdf: This class defines a single page within a document.
PDFPage() - Constructor for class gnu.jpdf.PDFPage: This constructs a Page object, which will hold any contents for this page.
PDFPage(Rectangle) - Constructor for class gnu.jpdf.PDFPage: Constructs a page, using the supplied media size.
PDFPage(int) - Constructor for class gnu.jpdf.PDFPage: Constructs a page using A4 media, but using the supplied orientation.
PDFPage(Rectangle, int) - Constructor for class gnu.jpdf.PDFPage: Constructs a page using the supplied media size and orientation.
PDFPage.procset - Class in gnu.jpdf: This defines a procset
PDFPage.procset() - Constructor for class gnu.jpdf.PDFPage.procset
pdfPageList - Variable in class gnu.jpdf.PDFPage: This is the pages object id that this page belongs to.
PDFPageList - Class in gnu.jpdf: This object contains the document's pages.
PDFPageList() - Constructor for class gnu.jpdf.PDFPageList: This constructs a PDF Pages object.
PDFStream - Class in gnu.jpdf: This class implements a PDF stream object.
PDFStream() - Constructor for class gnu.jpdf.PDFStream: Constructs a plain stream.
PDFStream(String) - Constructor for class gnu.jpdf.PDFStream: Constructs a stream.
pdfString - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
PDFStringHelper - Class in gnu.jpdf: String manipulation methods
PDFStringHelper() - Constructor for class gnu.jpdf.PDFStringHelper
PDFTest - Class in gnu.jpdf: The purpose of this class is to test all functionality of the gnu.jpdf package and serve as a demonstration of how to use the library.
PDFTest(String, String, boolean) - Constructor for class gnu.jpdf.PDFTest
PDFXref - Class in gnu.jpdf: This class is used to hold the xref information in the PDF Trailer block.
PDFXref(int, int) - Constructor for class gnu.jpdf.PDFXref: Creates a crossreference for a PDF Object
PDFXref(int, int, int) - Constructor for class gnu.jpdf.PDFXref: Creates a crossreference for a PDF Object
PERCENTAGE - Static variable in interface gov.lbl.genome.common.CommonConstants
Picture - Class in gov.lbl.genome.gui: Title: Picture
Picture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.Picture: Picture
pixelWidth - Variable in class gov.lbl.genome.gui.panel.VistaPanel
pixelWidth - Variable in class gov.lbl.genome.gui.Picture
pnlContainer - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlContent - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
pnlContig - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlGraph - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlGraphs - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlName - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlNames - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlYAxis - Variable in class gov.lbl.genome.gui.GeneralGraphView
pnlYAxiss - Variable in class gov.lbl.genome.gui.GeneralGraphView
polygon(int[], int[], int) - Method in class gnu.jpdf.PDFGraphics: This is used to add a polygon to the current path.
popupOff() - Method in class gov.lbl.genome.gui.panel.TracerPanel: switch popup off
PORTRAIT - Static variable in class gnu.jpdf.PDFPage: Specifies that the page is in PORTRAIT orientation.
POS - Variable in class gov.lbl.genome.common.AbstractGraphModel
positionFormat(String) - Static method in class gov.lbl.genome.common.features.ChromSegment: return true if position is like chr9:10000-20000
PREFERRED - Static variable in interface layout.TableLayoutConstants: Indicates that the row/column should be allocated just enough space to accomidate the preferred size of all components contained completely within this row/column.
preferredLayoutSize(Container) - Method in class layout.TableLayout: Determines the preferred size of the container argument using this layout.
prevDisplayedPanelList - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
prevPage - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
print(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: print content
print(Graphics, PageFormat, int) - Method in class gov.lbl.genome.gui.panel.VGBPanel: print
PrintAction - Class in gov.lbl.genome.gui.action: Title: Print
PrintAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.PrintAction: PrintAction
PrintAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.PrintAction: PrintAction
printColor() - Method in class ranab.img.gif.GifImage: print the global color table (debug only)
PrinterSetupAction - Class in gov.lbl.genome.gui.action: Title: Printer settings
PrinterSetupAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.PrinterSetupAction: PrinterSetupAction
PrinterSetupAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.PrinterSetupAction: PrinterSetupAction
printInfo(Graphics, int, int) - Method in class gov.lbl.genome.gui.GeneralGraphComp: print summary info for all vista curves
printInfo(Graphics, int, int) - Method in class gov.lbl.genome.gui.VistaCurveView: print summary information on printer, PDF or bitmap image page
printJob - Variable in class gov.lbl.genome.gui.VistaApp
printStatusBar(String) - Method in class gov.lbl.genome.gui.VistaApp: show sring in the status bar
ProcessingInstruction - Class in sjg.xml: Represent an XML processing instruction.
ProcessingInstruction(String) - Constructor for class sjg.xml.ProcessingInstruction: Constructs a new data processing instruction with the given contents.
procset - Variable in class gnu.jpdf.PDFPage
push(Status) - Method in class gov.lbl.genome.gui.History: push status in the history
pushInHistory() - Method in class gov.lbl.genome.gui.VistaApp: push curent status in history
PValue - Class in gov.lbl.genome.common.features: Title: PValue
PValue(String, int, int, double) - Constructor for class gov.lbl.genome.common.features.PValue
PValue(String, int, int, double, double) - Constructor for class gov.lbl.genome.common.features.PValue: PValue
PValueCurveView - Class in gov.lbl.genome.gui: Title: PValueCurveView
PValueCurveView(PCurveModel, GeneralGraphView) - Constructor for class gov.lbl.genome.gui.PValueCurveView: PValueCurveView

Q

QSortAlgorithm - Class in gov.lbl.genome.gui: A quick sort demonstration algorithm SortAlgorithm.java
QSortAlgorithm() - Constructor for class gov.lbl.genome.gui.QSortAlgorithm
quote(String) - Static method in class gov.lbl.genome.common.StringUtil: escape quotations

R

ranab.img.gif - package ranab.img.gif: GIF library
ranab.util - package ranab.util
read() - Method in class gov.lbl.genome.common.StringInputStream
realGraphHeight - Variable in class gov.lbl.genome.gui.AbstractCurveView
realGraphWidth - Variable in class gov.lbl.genome.gui.AbstractCurveView
rebuildPanel() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: this method is responsible for positioning of all graphs, annotations, axis etc.
redispatchMouseEvent(MouseEvent) - Method in class gov.lbl.genome.gui.panel.TracerPanel: push mouse event inside the panel structure
refresh(VistaApp, long, long) - Method in interface gov.lbl.genome.common.CurveModel: request information from the server
refresh(VistaApp, long, long) - Method in class gov.lbl.genome.common.CustomCurveModel
refresh(VistaApp, long, long) - Method in class gov.lbl.genome.common.PCurveModel: request data from the server
refresh(VistaApp, long, long) - Method in class gov.lbl.genome.common.VistaCurveModel: request data from the server
refresh(long, long) - Method in class gov.lbl.genome.gui.AbstractCurveView: request new information from the server
refresh(long, long) - Method in interface gov.lbl.genome.gui.CurveView: request curve information from the server
refresh(long, long) - Method in class gov.lbl.genome.gui.GeneralGraphView: refresh all curves
refresh() - Method in interface gov.lbl.genome.gui.GraphView: refresh graph information
refreshAnnotations() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: request new information from the server for Annotations and repeats
refreshAnnotations(Status) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: set Annotations and repeats from Status.
refreshGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: request new data from the server for all graphs and repaint
refreshOrgList() - Method in class gov.lbl.genome.gui.VistaApp: refresh organism list in the pull-dawn menu
refreshThread - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
release() - Method in class gov.lbl.genome.gui.VistaApp: Do some work and refresh panels after slow operations, like data pulling
RELEASE_DATE - Static variable in class gov.lbl.genome.gui.VistaApp
RemoveAction - Class in gov.lbl.genome.gui.action: Title:
RemoveAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.RemoveAction: RemoveAction
RemoveAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.RemoveAction: RemoveAction
removeAll(Collection) - Method in class gov.lbl.genome.gui.panel.GraphViewList: remove collection of elements
removeAllElements() - Method in class gov.lbl.genome.gui.panel.GraphViewList: removeAllElements
removeAllGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: remove All Graphs
removeAllSelectedGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: remove All Selected Graphs
removeBarImage() - Method in class gov.lbl.genome.gui.panel.TracerPanel: set green bar image == null
removeChromSegment(int) - Method in class gov.lbl.genome.common.features.ChromSegments: remove ChromSegment in the position
removeCompImage() - Method in class gov.lbl.genome.gui.GeneralGraphView: remove Comp Image and contig Image
removeDataImages() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: remove images for all graphs, annotation panel, repeat panel and axis panel
removeElementAt(int) - Method in class gov.lbl.genome.gui.panel.GraphViewList: remove element from visible and total collections
removeGraph(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: remove Graph
removeGraph(String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: remove Graph
removeImage() - Method in class gov.lbl.genome.gui.GeneralGraphComp: remove Image
removeImage() - Method in class gov.lbl.genome.gui.GeneralGraphView: remove Images
removeImage() - Method in class gov.lbl.genome.gui.panel.TracerPanel: remove tracer image
removeImage() - Method in class gov.lbl.genome.gui.panel.VistaPanel: remove image.
removeLayoutComponent(Component) - Method in class layout.TableLayout: Removes the specified component from the layout.
render(Graphics) - Method in interface gov.lbl.genome.gui.CurveView: draw everything
render(Graphics) - Method in class gov.lbl.genome.gui.PValueCurveView: Draw Rank Vista
render(Graphics) - Method in class gov.lbl.genome.gui.VistaCurveView: draw curve and annotation
renderInitialize() - Method in class gov.lbl.genome.gui.AbstractCurveView: Initialize rendered This should be called every time the curve is rendered.
repaint() - Method in class gov.lbl.genome.gui.panel.ChromPanel: override VistaPanel repaint
repaintTracerPanels() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: repaint all TracerPanels
Repeat - Class in gov.lbl.genome.common.features: Repeat represents a segment of a DNA sequence that is a repeated portion.
Repeat(String, long, long, String) - Constructor for class gov.lbl.genome.common.features.Repeat: Repeat
REPEAT_HEIGHT - Variable in class gov.lbl.genome.gui.panel.ContigPanel
REPEAT_HEIGHT - Variable in class gov.lbl.genome.gui.panel.ContigPanelPicture
REPEAT_HEIGHT - Variable in class gov.lbl.genome.gui.panel.RepeatPanel
REPEAT_HEIGHT - Variable in class gov.lbl.genome.gui.panel.RepeatPanelPicture
REPEAT_OFFSET - Variable in class gov.lbl.genome.gui.panel.ContigPanel
REPEAT_OFFSET - Variable in class gov.lbl.genome.gui.panel.ContigPanelPicture
REPEAT_OFFSET - Variable in class gov.lbl.genome.gui.panel.RepeatPanel
REPEAT_OFFSET - Variable in class gov.lbl.genome.gui.panel.RepeatPanelPicture
repeatLegend(Graphics, Color, int, int, String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: draw repeat legend
RepeatPanel - Class in gov.lbl.genome.gui.panel: Title: RepeatPanel
RepeatPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.RepeatPanel
RepeatPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.RepeatPanel: RepeatPanel
RepeatPanelPicture - Class in gov.lbl.genome.gui.panel: Title: RepeatPanelPicture
RepeatPanelPicture(VistaApp, String) - Constructor for class gov.lbl.genome.gui.panel.RepeatPanelPicture: RepeatPanelPicture
replaceChar(String, char, char) - Static method in class gov.lbl.genome.common.StringUtil: Replace all occurrences of one specified character with the other specified character.
replaceGraph(GeneralGraphView, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: replace Graph at the "i" position by another graph
requestAnnotations(String, long, long) - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: request Annotations from the server
requestAnnotations(String, long, long) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: request Annotations from server
rereadInitInfo(HashMap) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: reread Init Info
reRenderOff() - Method in class gov.lbl.genome.gui.AbstractCurveView: switch reRender Off
reRenderOn() - Method in class gov.lbl.genome.gui.AbstractCurveView: switch reRender On
reset() - Method in class gov.lbl.genome.gui.panel.TracerPanel: reset some variables and repaint
resetBaseGenome(String) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: reset Base Genome
resetConnection() - Method in class gov.lbl.genome.gui.VistaApp: set connection to null
resetCounter1() - Method in class gov.lbl.genome.gui.VistaApp: start 20 min counter
resetCounter2() - Method in class gov.lbl.genome.gui.VistaApp: start 30 sec counter
resetCounter3() - Method in class gov.lbl.genome.gui.VistaApp: start 0.5 sec min counter
resetDefaultBaseGenome() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: reset Default Base Genome
resetDelay() - Method in class ranab.img.gif.GifGraphicEx: Reset delay
resetDelay() - Method in class ranab.img.gif.GifImage: Reset delay.
resetOrgList() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: reset Org List
resetPicture() - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: reset annotation Picture
resetPicture() - Method in class gov.lbl.genome.gui.panel.ContigPanel: reset Picture parameters
resetPicture() - Method in class gov.lbl.genome.gui.panel.RepeatPanel: reset picture size and margins
resetPrintedGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: clear list of printed graphs
resetTransparency() - Method in class ranab.img.gif.GifImage: Reset transparency
resetXBorders() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: resetXBorders
Resource - Class in gov.lbl.genome.gui: Title: Resource
Resource(InputStream) - Constructor for class gov.lbl.genome.gui.Resource: Resource
resource - Variable in class gov.lbl.genome.gui.VistaApp: This public parameter provides access to the default section of the resource file.
resources - Variable in class gnu.jpdf.PDFPage: This holds any resources for this page
RETRIES - Static variable in class gov.lbl.genome.common.CommUnit
retrieveInitInfo() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: retrieve Init Info
retrieveInitInfoDone - Variable in class gov.lbl.genome.gui.panel.BaseInfoPanel
RIGHT - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
RIGHT - Static variable in interface layout.TableLayoutConstants: Indicates that the component is right justified in its cell
rightSpace - Variable in class gov.lbl.genome.gui.panel.VistaPanel
RNA - Static variable in class gov.lbl.genome.common.features.Repeat
rootID - Variable in class gnu.jpdf.PDFOutput: This is used to track the /Root object (catalog)
rotate - Variable in class gnu.jpdf.PDFPage: Specifies the number of degrees the page should be rotated clockwise when it is displayed.
row1 - Variable in class layout.TableLayoutConstraints: Cell in which the upper left corner of the component lays
row2 - Variable in class layout.TableLayoutConstraints: Cell in which the lower right corner of the component lays
ROW_HEIGHT - Static variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
rowOffset - Variable in class layout.TableLayout: Offsets of rows in pixels.
rowSize - Variable in class layout.TableLayout: Heights of rows in pixels
rowSpec - Variable in class layout.TableLayout: Heights of rows expressed in absolute and relative terms
run() - Method in class gov.lbl.genome.gui.action.AboutAction: Just open an "about" window
run() - Method in class gov.lbl.genome.gui.action.AddAction: Open dialog window with a list of available curves and parameters for them
run() - Method in class gov.lbl.genome.gui.action.BackAction
run() - Method in class gov.lbl.genome.gui.action.DetailsAction: Open text browser window
run() - Method in class gov.lbl.genome.gui.action.ForwardAction: just empty method
run() - Method in class gov.lbl.genome.gui.action.HelpAction: Open new internet browser window with a link to our help pages
run() - Method in class gov.lbl.genome.gui.action.PageSetupAction: Show a standatd dialog window with paper settings There are some problems with printing from an applet in java 1.5
run() - Method in class gov.lbl.genome.gui.action.PrintAction: Show standatd dialogs window with printer and paper settings This must be done to initialise properly printJob There are some problems with printing from an applet in java 1.5
run() - Method in class gov.lbl.genome.gui.action.PrinterSetupAction: Show standatd dialog window with printer settings There are some problems with printing from an applet in java 1.5
run() - Method in class gov.lbl.genome.gui.action.RemoveAction: Remove selected curves from the browser window
run() - Method in class gov.lbl.genome.gui.action.SaveAsAction: Open dialog window in which you can select one of three available data formats, then send file to the server and open internet browser with a link on this file.
run() - Method in class gov.lbl.genome.gui.action.ScrollBackwardAction: Try to show new data interval shfted to the left.
run() - Method in class gov.lbl.genome.gui.action.ScrollForwardAction: Try to show new data interval shfted to the right.
run() - Method in class gov.lbl.genome.gui.action.SettingsAction: Open a dialog window with all curve settings.
run() - Method in class gov.lbl.genome.gui.action.StatAction: Open a dialog window with some conservation statistics for each curve
run() - Method in class gov.lbl.genome.gui.action.SwapCurvesAction: Try to set genome of the socond organism as a primary genome
run() - Method in class gov.lbl.genome.gui.action.UCSCBrowserAction: If more than one alternative browsers available, show popup menu and finish its work.
run() - Method in class gov.lbl.genome.gui.action.VAbstractAction: Override run method if you want to execute action in a separate thread.
run() - Method in class gov.lbl.genome.gui.action.ZoomInAction: Try to decrease data interval.
run() - Method in class gov.lbl.genome.gui.action.ZoomOutAction: Try to increase data interval.
run() - Method in class gov.lbl.genome.gui.panel.GeneSearchPanel: do all work to find gene or other named sequence
run() - Method in class gov.lbl.genome.gui.VistaApp: Main thread of the applet.

S

SaveAsAction - Class in gov.lbl.genome.gui.action: Title: Save Your Data
SaveAsAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.SaveAsAction: SaveAsAction
SaveAsAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.SaveAsAction: SaveAsAction
SaveAsDialog - Class in gov.lbl.genome.gui.dialog: Title: SaveAsDialog
SaveAsDialog(JApplet, String, boolean, int, Callback) - Constructor for class gov.lbl.genome.gui.dialog.SaveAsDialog: SaveAsDialog
SaveAsDialog() - Constructor for class gov.lbl.genome.gui.dialog.SaveAsDialog: SaveAsDialog
SaveAsPanel - Class in gov.lbl.genome.gui.panel: This panel must be raplaced by dialogs.xml description and removed! That's why parameters are not included in VistaApp.rc
SaveAsPanel(ActionDialog, boolean, boolean) - Constructor for class gov.lbl.genome.gui.panel.SaveAsPanel: SaveAsPanel
saveData(OutputStream, ByteArrayOutputStream) - Method in class gov.lbl.genome.gui.action.SaveAsAction: send bytes to the output stream
ScrollBackwardAction - Class in gov.lbl.genome.gui.action: Title:
ScrollBackwardAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.ScrollBackwardAction: ScrollBackwardAction
ScrollBackwardAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.ScrollBackwardAction: ScrollBackwardAction
scrollbar - Variable in class gov.lbl.genome.gui.VistaApp
ScrollForwardAction - Class in gov.lbl.genome.gui.action: Title: Scroll Forward
ScrollForwardAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.ScrollForwardAction: ScrollForwardAction
ScrollForwardAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.ScrollForwardAction: ScrollForwardAction
SearchResultsDialog - Class in gov.lbl.genome.gui.dialog: Title: SearchResultsDialog
SearchResultsDialog(JApplet, String, boolean, int, Callback) - Constructor for class gov.lbl.genome.gui.dialog.SearchResultsDialog: SearchResultsDialog
SearchResultsDialog() - Constructor for class gov.lbl.genome.gui.dialog.SearchResultsDialog: SearchResultsDialog
SearchResultsPanel - Class in gov.lbl.genome.gui.panel: Title:
SearchResultsPanel(ActionDialog, boolean, boolean) - Constructor for class gov.lbl.genome.gui.panel.SearchResultsPanel: SearchResultsPanel
SEASCAPE - Static variable in class gnu.jpdf.PDFPage: Specifies that the page is in SEASCAPE orientation.
select() - Method in class gov.lbl.genome.gui.GeneralGraphView: select the graph view
selectChildren() - Method in class gov.lbl.genome.gui.GeneralGraphView: select all Children
selected - Variable in class gov.lbl.genome.gui.GeneralGraphView
selectGraph(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: select Graph in index position
sendRequest(String) - Method in class gov.lbl.genome.common.CommUnit: send Request
servletURL - Variable in class gov.lbl.genome.common.CommUnit
Set_ChromSegment(ChromSegment, int) - Method in class gov.lbl.genome.common.features.ChromSegments: Set ChromSegment
setAbsoluteLocation(Point) - Method in class gnu.jpdf.BoundingBox: Set the absolute upper left world location point for this box
setAnnotations(Vector) - Method in class gov.lbl.genome.common.AbstractCurveModel: set Annotations
setAnnotations(Vector) - Method in class gov.lbl.genome.gui.panel.AnnotationPanel: set Annotations
setAnnotations(Vector) - Method in class gov.lbl.genome.gui.panel.RepeatPanel: set annotations
setApplet(VistaApp) - Method in class gov.lbl.genome.gui.LinkLabel: set the Applet
setArrows() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: set buttons with Arrows in the bottom panel
setAsDefault(boolean) - Method in class gov.lbl.genome.common.CurveInfo: set curve as Default
setAuthor(String) - Method in class gnu.jpdf.PDFInfo: Set the value of author.
setBackground(byte) - Method in class ranab.img.gif.GifScreenDescriptor: Set background
setBaseGenome(CurveInfo, Vector) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set Base Genome
setBaseGenome(Status) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set Base Genome from status
setBaseGenome(String) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set Base Genome
setBaseGenome(GenomeInfo) - Method in class gov.lbl.genome.gui.VistaApp: set baseGenome
setBorder(short, double) - Method in class gnu.jpdf.PDFAnnot: Sets the border for the annotation.
setBorder(double, double[]) - Method in class gnu.jpdf.PDFAnnot: Sets the border for the annotation.
setCheckable(boolean) - Method in class gov.lbl.genome.common.CurveInfo: set curve Checkable mode
setCheckedCurves(Vector) - Method in class gov.lbl.genome.common.GenomeInfo: set list of Checked Curves
setChrom(String) - Method in class gov.lbl.genome.gui.VistaApp: set current chromosome
setChromosome(int) - Method in class gov.lbl.genome.common.features.ChromSegment: set Chromosome
setChromosome(String) - Method in class gov.lbl.genome.common.features.ChromSegment: set Chromosome
setClip(int, int, int, int) - Method in class gnu.jpdf.PDFGraphics: Clips to a set of coordinates
setClip(Shape) - Method in class gnu.jpdf.PDFGraphics: As my JDK docs say, this may break with Java 2D.
setCodeBaseURL(String) - Method in class gov.lbl.genome.common.CommUnit: set CodeBase URL
setColor(Color) - Method in class gnu.jpdf.PDFGraphics: Sets the colour for drawing
setColumn(double[]) - Method in class layout.TableLayout: Adjusts the number and sizes of rows in this layout.
setColumn(int, double) - Method in class layout.TableLayout: Adjusts the width of a single column in this layout.
setComment(String) - Method in class ranab.img.gif.GifCommentEx: Set the comment.
setComponent(JComponent) - Method in class gov.lbl.genome.gui.Picture: set Component
setComponentsAction(String, AbstractAction) - Method in class gov.lbl.genome.gui.dialog.VistaDialog: set Components Action
setCompSize(int, int, int, int) - Method in class gov.lbl.genome.gui.GeneralGraphComp: set GeneralGraphComp Size
setConstraints(Component, TableLayoutConstraints) - Method in class layout.TableLayout: Sets the constraints of a given component.
setContig(String, ChromInfo) - Method in class gov.lbl.genome.common.GenomeInfo: setContig (Chromosome)
setContig(String) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: setText (contig name) for current contig label
setContig(String) - Method in class gov.lbl.genome.gui.panel.CursorInfoPanel: set Contig name in the contig Label
setContigs(Vector) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Contigs
setContigs(Vector) - Method in class gov.lbl.genome.gui.panel.ContigPanel: set Contigs
setCreator(String) - Method in class gnu.jpdf.PDFInfo: Set the value of creator.
setCurrentPos(String) - Method in class gov.lbl.genome.common.GenomeInfo: set Current Position
setCurveInfo(CurveInfo) - Method in class gov.lbl.genome.common.AbstractCurveModel: set CurveInfo
setCurveModel(CurveModel) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Curve Model
setCurveModel(CurveModel) - Method in interface gov.lbl.genome.gui.CurveView: set Curve Model
setCurveModels(Collection) - Method in class gov.lbl.genome.common.GeneralGraphModel: set collection of Curve Models
setDangerous(boolean) - Method in class gov.lbl.genome.gui.VistaApp: Some actions set dangerous field in true in order to disable other actions.
setData(TreeMap) - Method in class gov.lbl.genome.common.AbstractCurveModel: set Data points
setDebug(boolean) - Method in class gov.lbl.genome.gui.Picture: set Debuging mode
setDebug(boolean) - Method in class gov.lbl.genome.gui.Resource: set Debug mode of the parser
setDebugExceptions(boolean) - Static method in class gov.lbl.genome.gui.Debug: enable or disable printing of exceptions
setDebugLevel(String) - Static method in class gov.lbl.genome.gui.VistaApp: debugInit = "1" or "init" debugProgress = "2" or "progress" debugComm = "4" or "comm" debugAction = "8" or "action" debugException = "16" or "exception" debug All = 1|2|4|8|16 or "all"
setDebugMode(boolean) - Method in class gov.lbl.genome.gui.Debug: Set debug mode
setDefault(boolean) - Method in class gov.lbl.genome.common.GenesInfo
setDefaultBaseGenome() - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set Default Base Genome
setDefaultLineWidth() - Method in class gnu.jpdf.PDFGraphics: This extension sets the line width to the default of 1mm which is what Java uses when drawing to a PrintJob.
setDeflate(boolean) - Method in class gnu.jpdf.PDFStream
setDelay(int) - Method in class ranab.img.gif.GifGraphicEx: Set delay timing
setDelay(int) - Method in class ranab.img.gif.GifImage: Set delay.
setDeleted(boolean) - Method in class gov.lbl.genome.common.CurveInfo: mark curve as Deleted
setDeleted(boolean) - Method in class gov.lbl.genome.common.GenomeInfo: set genome as Deleted
setDetails() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: Enable or disable detailsAction
setDetailsActionEnabled(boolean) - Method in class gov.lbl.genome.gui.VistaApp: call setEnabled(boolean) for detailsAction and detailsAction2
setDragged(boolean) - Method in class gov.lbl.genome.gui.panel.TracerPanel: Is called when mouse button is pressed and mouse moved
setDsEnd(long) - Method in class gov.lbl.genome.common.features.Contig: set DataSet End
setDsStart(long) - Method in class gov.lbl.genome.common.features.Contig: set DataSet Start
setElementAt(Object, int) - Method in class gov.lbl.genome.gui.panel.GraphViewList: set visible element in pos
setEnd(long) - Method in class gov.lbl.genome.common.features.ChromSegment: set End
setFixedRows(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: set number of rows to show in the Display Panel
setFont(Font) - Method in class gnu.jpdf.PDFGraphics: This sets the font.
setForwardBackBtns() - Method in class gov.lbl.genome.gui.VistaApp: Enable od disable >> or/ond << button
setFullString(String) - Method in class gnu.jpdf.BoundingBox: Sets the full string associated with getStringBounds
setGenomes(HashMap) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel
setGraphModel(GeneralGraphModel) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Graph Model
setGraphPos(int) - Method in class gov.lbl.genome.gui.GeneralGraphView: set position of the graph view in the display panel
setGraphView(GeneralGraphView) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Graph View
setGraphView(GeneralGraphView) - Method in interface gov.lbl.genome.gui.CurveView: set GraphView
setHeight(int) - Method in class gnu.jpdf.PDFImage: Set the value of height.
setImage(Image, int, int, int, int, ImageObserver) - Method in class gnu.jpdf.PDFImage: Set the image
setImage(BufferedImage) - Method in class gov.lbl.genome.gui.panel.VistaPanel: set new image created by somebody else.
setImageableArea(PageFormat) - Method in class gov.lbl.genome.gui.Picture: setI mageable Area from the pages Imageable area
setImageableArea(int, int, int, int) - Method in class gov.lbl.genome.gui.Picture: set Imageable Area from the parameters
setImageName(PDFImage) - Method in class gnu.jpdf.PDFDocument: Sets a unique name to a PDFImage
setInterval(int) - Method in class gov.lbl.genome.common.ViewSettings
setIterationCount(int) - Method in class ranab.img.gif.GifImage: set iteration count
setIterationCount(int) - Method in class ranab.img.gif.GifNsAppEx: Set iteration count.
setKeywords(String) - Method in class gnu.jpdf.PDFInfo: Set the value of keywords.
setLineNumber(int) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Line Number
setLineWidth(double) - Method in class gnu.jpdf.PDFGraphics: This extension allows the width of the drawn line to be set
setLink(String) - Method in class gov.lbl.genome.gui.LinkLabel: set Link
setLocation() - Method in class gov.lbl.genome.gui.dialog.ActionDialog: center dialog window
setLocation() - Method in class gov.lbl.genome.gui.dialog.VistaDialog: center dialog window
setLocation() - Method in class gov.lbl.genome.gui.SplashWindow: center the window on the screen
setLongName(String) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Long Name
setLongName(String) - Method in class gov.lbl.genome.common.GeneralGraphModel
setMarginLeft(int) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Left Margin
setMarginRight(int) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Right Margin
setMarginRight(int) - Method in class gov.lbl.genome.gui.Picture: set right Margin
setMargins(PageFormat) - Method in class gov.lbl.genome.gui.Picture: set Margins from the page margins
setMargins(int, int, int, int) - Method in class gov.lbl.genome.gui.Picture: set Margins from the parameters
setMarginTop(int) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Top Margin
setMaxX(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Max X
setMaxX(long) - Method in class gov.lbl.genome.gui.Picture: set Max X
setMaxX(int) - Method in class gov.lbl.genome.gui.Picture: set Max X
setMaxY(double) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Max Y
setMaxY(double) - Method in class gov.lbl.genome.common.PCurveModel: set Max Y
setMaxY(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Max Y
setMedia(Rectangle) - Method in class gnu.jpdf.PDFPage: Sets the media size for this page.
setMinMaxX(long, long) - Method in class gov.lbl.genome.gui.Picture: set Min and Max X
setMinMaxX(int) - Method in class gov.lbl.genome.gui.Picture: set Min and Max X
setMinX(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Min X
setMinX(long) - Method in class gov.lbl.genome.gui.Picture: set Min X
setMinX(int) - Method in class gov.lbl.genome.gui.Picture: set Min X
setMinY(double) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Min Y
setMinY(double) - Method in class gov.lbl.genome.common.PCurveModel: set Min Y
setMinY(int) - Method in class gov.lbl.genome.common.VistaCurveModel: set Min Y
setMinY(double) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Min Y
setName(String) - Method in class gnu.jpdf.PDFImage: Set the name
setName(String) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Name
setName(String) - Method in class gov.lbl.genome.common.GeneralGraphModel
setName(String) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Name
setNewHeight(int) - Method in class gov.lbl.genome.gui.VistaApp: setNewHeight
setNewSize(int, int) - Method in class gov.lbl.genome.gui.VistaApp: This method is called from JavaScript and sets new applet size.
setNewWidth(int) - Method in class gov.lbl.genome.gui.VistaApp: setNewWidth
setNumDataPoints(int) - Method in class gov.lbl.genome.common.ViewSettings
setOrgLabel(int) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set OrgLabel text: number of available organisms
setOrgLabel(int) - Method in class gov.lbl.genome.gui.VistaApp: set orgLabel
setOrgList(Vector, Vector) - Method in class gov.lbl.genome.gui.panel.BaseInfoPanel: set List of Organisms
setOrientation() - Method in class gnu.jpdf.PDFGraphics: This sets the media Orientation (0=Portrait, 90=Landscape, 180=Inverse, 270=Seascape).
setOrientation(int) - Method in class gnu.jpdf.PDFPage: Sets the page's orientation.
setOutline(PDFOutline) - Method in class gnu.jpdf.PDFCatalog: This sets the root outline object
setPage(PageFormat) - Method in class gov.lbl.genome.gui.Picture: set Page
setPaintMode() - Method in class gnu.jpdf.PDFGraphics: Not implemented, as this is not supported in the PDF specification.
setParam(String, Object) - Method in class gov.lbl.genome.gui.VistaApp: replace an object in the parameters Map
setParent(BoundingBox) - Method in class gnu.jpdf.BoundingBox: Make the specified box this box's parent
setParent(GeneralGraphView) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Parent
setPDFInfo(PDFInfo) - Method in class gnu.jpdf.PDFDocument: Set the PDFInfo object, which contains author, title, keywords, etc
setPosition(int) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Position of the model among other models
setPosition(String) - Method in class gov.lbl.genome.gui.panel.CursorInfoPanel: set position string in the position Label
setPositionString(String, String, String) - Method in class gov.lbl.genome.gui.VistaApp: set position from parameters
setPositionString(String) - Method in class gov.lbl.genome.gui.VistaApp: set position (chromosome, start, end) from formated string
setPrintCapacity(int, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: Set number of graphs and lines to be printed
setReady(boolean) - Method in class gov.lbl.genome.gui.VistaApp
setRealChrom(boolean) - Method in class gov.lbl.genome.common.features.ChromSegment: set Real Chromosome mode
setRegion(String) - Method in class gov.lbl.genome.gui.panel.GeneSearchPanel: set string in the TextField
setRow(double[]) - Method in class layout.TableLayout: Adjusts the number and sizes of rows in this layout.
setRow(int, double) - Method in class layout.TableLayout: Adjusts the height of a single row in this layout.
setRowCount(int) - Method in class gov.lbl.genome.common.ViewSettings
setRun(Integer) - Method in class gov.lbl.genome.common.ViewSettings
setSelected(boolean) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Selected
setSelectedIndices(int[]) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: select lines in the bottom panel curve list
setServletURL(String) - Method in class gov.lbl.genome.common.CommUnit: set Servlet URL
setSettings() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: SettingsAction can be enabled only if all curves are of the same type
setSettingsVisible(boolean) - Method in class gov.lbl.genome.gui.VistaApp: Enable or disable settings actions
setSize(double, double) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Size
setSize() - Method in class gov.lbl.genome.gui.Picture: set size from the default component
setSize(JComponent) - Method in class gov.lbl.genome.gui.Picture: set size from the component
setSize(PageFormat) - Method in class gov.lbl.genome.gui.Picture: set Size from the page
setSize(int, int) - Method in class gov.lbl.genome.gui.Picture: set Size from the parameters
setStart(long) - Method in class gov.lbl.genome.common.features.ChromSegment: set Start
setStringArray(String[]) - Method in class gnu.jpdf.BoundingBox: Set the value of the string array
setStroke(Stroke) - Method in class gov.lbl.genome.gui.AbstractCurveView: set Stroke
setSubject(String) - Method in class gnu.jpdf.PDFInfo: Set the value of subject.
setText(String) - Method in class gov.lbl.genome.gui.LinkLabel: add some html decoration to the text
setThumbnail(PDFObject) - Method in class gnu.jpdf.PDFPage: This adds an object that describes a thumbnail for this page.
SettingsAction - Class in gov.lbl.genome.gui.action: Title: Curve Settings Action
SettingsAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.SettingsAction: SettingsAction
SettingsAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.SettingsAction: SettingsAction
setTip(String) - Method in class gov.lbl.genome.gui.action.UCSCBrowserAction: set action toolTip according to an alternative browser type
setTitle(String) - Method in class gnu.jpdf.PDFInfo: Set the value of title.
setTracerPanel(TracerPanel) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: set Tracer Panel
setTransparency(Color) - Method in class ranab.img.gif.GifGraphicEx: Set transparency.
setTransparency(Color) - Method in class ranab.img.gif.GifImage: Set transparency.
setUCSCActionTip(String) - Method in class gov.lbl.genome.gui.VistaApp: Set ToolTip for UCSC action button and menu.
setVisible(boolean) - Method in class gov.lbl.genome.common.CurveInfo: set curve Visible
setVisible(boolean) - Method in class gov.lbl.genome.gui.GeneralGraphView: set Visible mode
setWidth(int) - Method in class gnu.jpdf.PDFImage: Set the value of width.
setXBorders(int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: set Borders of the selected region
setXORMode(Color) - Method in class gnu.jpdf.PDFGraphics: Not implemented, as this is not supported in the PDF specification.
setYLabel(String) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Y Label Text
setYLabelOrientation(int) - Method in class gov.lbl.genome.common.AbstractGraphModel: set Y Label Orientation
setZ(int) - Method in class gov.lbl.genome.gui.Picture: this parameter can be 0 or 1.
shortenString(String, Font, int) - Method in class gov.lbl.genome.gui.panel.VistaPanel: shorten string is useful if string is long and does not fit in width.
shortenString(String, Font, int) - Method in class gov.lbl.genome.gui.Picture: remove last characters from the string until its width is less or equal the maximum parameter
show() - Method in class gov.lbl.genome.common.AbstractCurveModel: hidden = false
showCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: show tracer
showGraph(String) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: show Graph
SINE - Static variable in class gov.lbl.genome.common.features.Repeat
singleCell - Variable in class layout.TableLayout.Entry: Does the component occupy a single cell
size() - Method in class gov.lbl.genome.gui.panel.GraphViewList: return number of visible elements
sjg.xml - package sjg.xml: Simple XML parser
SOLID - Static variable in class gnu.jpdf.PDFAnnot: Solid border.
SOLID_STROKE - Static variable in interface gov.lbl.genome.gui.UIConstants
Sort() - Method in class gov.lbl.genome.common.features.ChromSegments
sort(long[]) - Method in class gov.lbl.genome.gui.QSortAlgorithm: return sorted array
SplashWindow - Class in gov.lbl.genome.gui: Title: SplashWindow
SplashWindow(JApplet) - Constructor for class gov.lbl.genome.gui.SplashWindow: SplashWindow
split(String, String) - Static method in class gov.lbl.genome.common.StringUtil: split the string using token.
split(String, String, boolean) - Static method in class gov.lbl.genome.common.StringUtil: split the string using token.
STANDARD_BOLD_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
STANDARD_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
STANDARD_FONT11 - Static variable in interface gov.lbl.genome.gui.UIConstants
started - Variable in class gov.lbl.genome.gui.VistaApp
startProgress(String) - Method in class gov.lbl.genome.gui.VistaApp: Start RIGHT-TOP DNA Icon rotation set ready(false), stop timers, disable GUI, write comment in the status bar
startsWithIgnoreCase(String, String) - Static method in class gov.lbl.genome.common.StringUtil: return true if firts strings start with the same letters, ignoring letter case
startTracerPanel - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
StatAction - Class in gov.lbl.genome.gui.action: Title: Statistics Action
StatAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.StatAction: StatAction
StatAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.StatAction: StatAction
StatDialog - Class in gov.lbl.genome.gui.dialog: Title: StatDialog
StatDialog(JApplet, String, boolean, int, Callback) - Constructor for class gov.lbl.genome.gui.dialog.StatDialog: StatDialog
StatDialog() - Constructor for class gov.lbl.genome.gui.dialog.StatDialog: StatDialog
StatPanel - Class in gov.lbl.genome.gui.panel: Title:
StatPanel(ActionDialog, boolean, boolean) - Constructor for class gov.lbl.genome.gui.panel.StatPanel: StatPanel
Status - Class in gov.lbl.genome.gui: Title: Status
Status(GenomeInfo, String, Vector, Vector, Vector, Vector) - Constructor for class gov.lbl.genome.gui.Status: Status
stopProgress() - Method in class gov.lbl.genome.gui.VistaApp: Stop RIGHT-TOP DNA Icon rotation start timers, enable GUI, remove comment from the status bar
STR_CANCEL - Static variable in class gov.lbl.genome.gui.dialog.ActionDialog
STR_OK - Static variable in class gov.lbl.genome.gui.dialog.ActionDialog
StringInputStream - Class in gov.lbl.genome.common: Title:
StringInputStream(Reader) - Constructor for class gov.lbl.genome.common.StringInputStream: StringInputStream
StringTooLongException - Exception in gnu.jpdf: This exception is thrown from BoundingBox if the string won't fit into the box
StringTooLongException(String) - Constructor for exception gnu.jpdf.StringTooLongException: Normally this exception is constructed with a message containing information about the sizes of the parent and child box, and maybe the string that caused the overflow.
StringUtil - Class in gov.lbl.genome.common
StringUtil() - Constructor for class gov.lbl.genome.common.StringUtil
stroke - Variable in class gov.lbl.genome.gui.AbstractCurveView
subtract(BoundingBox, int) - Method in class gnu.jpdf.BoundingBox: Removes the child box from this parent box.
SUBTRACT_FROM_BOTTOM - Static variable in class gnu.jpdf.BoundingBox: Used to subtract a child from a box, *leaving* the bottom portion
SUBTRACT_FROM_LEFT - Static variable in class gnu.jpdf.BoundingBox: Used to subtract a child from a box, *leaving* the left portion
SUBTRACT_FROM_RIGHT - Static variable in class gnu.jpdf.BoundingBox: Used to subtract a child from a box, *leaving" the right portion
SUBTRACT_FROM_TOP - Static variable in class gnu.jpdf.BoundingBox: Used to subtract a child from a box, *leaving* the top portion
SuperContig - Class in gov.lbl.genome.common.features: SuperContig is a row of data retrieved from one of the chr%_short tables.
SuperContig(int, String, long, long) - Constructor for class gov.lbl.genome.common.features.SuperContig: SuperContig
swapCurves() - Method in class gov.lbl.genome.gui.VistaApp: Switch base genome.
SwapCurvesAction - Class in gov.lbl.genome.gui.action: Title: Swap Curves
SwapCurvesAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.SwapCurvesAction: SwapCurvesAction
SwapCurvesAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.SwapCurvesAction: SwapCurvesAction
swapElements(int, int) - Method in class gov.lbl.genome.gui.panel.GraphViewList: swap 2 graphViews.
swapGraphs(int, int) - Method in class gov.lbl.genome.gui.panel.DisplayPanel: swap 2 selected Graphs graph1<=>graph2

T

TableLayout - Class in layout: TableLayout is a layout manager that arranges components in rows and columns like a spreadsheet.
TableLayout() - Constructor for class layout.TableLayout: Constructs an instance of TableLayout.
TableLayout(double[][]) - Constructor for class layout.TableLayout: Constructs an instance of TableLayout.
TableLayout.Entry - Class in layout
TableLayout.Entry(Component, TableLayoutConstraints) - Constructor for class layout.TableLayout.Entry: Constructs an Entry that binds a component to a set of constraints.
TableLayoutConstants - Interface in layout: Constants used by TableLayout.
TableLayoutConstraints - Class in layout: The following inner class is used to bind components to their constraints.
TableLayoutConstraints() - Constructor for class layout.TableLayoutConstraints: Constructs an TableLayoutConstraints with the default settings.
TableLayoutConstraints(String) - Constructor for class layout.TableLayoutConstraints: Constructs an TableLayoutConstraints from a string.
TableLayoutConstraints(int, int, int, int, int, int) - Constructor for class layout.TableLayoutConstraints: Constructs an TableLayoutConstraints a set of constraints.
testPosition(int, int) - Method in class gov.lbl.genome.gui.VistaApp: testPosition
thumbnail - Variable in class gnu.jpdf.PDFPage: Object ID that contains a thumbnail sketch of the page.
TITLE_BORDER_FONT - Static variable in interface gov.lbl.genome.gui.UIConstants
toArray(Vector) - Static method in class gnu.jpdf.PDFObject: This utility method returns a String containing an array definition based on a Vector containing PDFObjects
Tokenizer - Class in sjg.xml: Tokenizer for the parser.
Tokenizer(String) - Constructor for class sjg.xml.Tokenizer
tooSmall - Variable in class gov.lbl.genome.gui.Picture
top - Variable in class gov.lbl.genome.gui.panel.VistaPanel
TOP - Static variable in interface layout.TableLayoutConstants: Indicates that the component is top justified in its cell
topSpace - Variable in class gov.lbl.genome.gui.panel.VistaPanel
toString() - Method in class gnu.jpdf.PDFObject: Returns the unique serial number in PDF format
toString() - Method in class gnu.jpdf.PDFXref
toString() - Method in exception gnu.jpdf.StringTooLongException
toString() - Method in class gov.lbl.genome.common.BrowserInfo: return formated XML string
toString() - Method in class gov.lbl.genome.common.ChromInfo: return XML formatted summary
toString() - Method in class gov.lbl.genome.common.CurveInfo: return summary string
toString() - Method in class gov.lbl.genome.common.CustomCurveModel
toString() - Method in class gov.lbl.genome.common.features.ChromPosition
toString() - Method in class gov.lbl.genome.common.features.ChromSegment: return XML formatted summary string
toString(long) - Method in class gov.lbl.genome.common.features.ChromSegment: return XML formatted summary string
toString() - Method in class gov.lbl.genome.common.features.ChromSegments
toString() - Method in class gov.lbl.genome.common.features.Contig: return XML formatted string
toString(long) - Method in class gov.lbl.genome.common.features.Contig: return XML formatted string
toString() - Method in class gov.lbl.genome.common.features.Gap
toString() - Method in class gov.lbl.genome.common.features.Gene: return XML formatted string
toString(long) - Method in class gov.lbl.genome.common.features.Gene: return XML formatted string
toString() - Method in class gov.lbl.genome.common.features.PValue: return XML formatted string
toString() - Method in class gov.lbl.genome.common.features.Repeat: return XML formatted string
toString(long) - Method in class gov.lbl.genome.common.features.Repeat: return XML formatted string
toString() - Method in class gov.lbl.genome.common.features.SuperContig: return XML formatted string
toString(long) - Method in class gov.lbl.genome.common.features.SuperContig: return XML formatted string
toString() - Method in class gov.lbl.genome.common.GenesInfo: return XML formatted summary
toString() - Method in class gov.lbl.genome.common.GenomeInfo: return XML formatted summary string
toString() - Method in class gov.lbl.genome.common.ViewSettings
toString() - Method in class gov.lbl.genome.common.VistaCurveInfo: return summary string
toString() - Method in class gov.lbl.genome.gui.AbstractCurveView: return text column with all points
toString() - Method in class gov.lbl.genome.gui.CurveParameters: return parameters summary
toString() - Method in class gov.lbl.genome.gui.GeneralGraphComp: return component model name
toString() - Method in class gov.lbl.genome.gui.GeneralGraphView: return graph name
toString() - Method in class gov.lbl.genome.gui.Picture: return summary string
toString() - Method in class gov.lbl.genome.gui.Status: return string with the status summary
toString() - Method in class layout.TableLayout: Converts this TableLayout to a string.
toString() - Method in class layout.TableLayoutConstraints: Gets a string representation of this TableLayoutConstraints.
toString() - Method in class sjg.xml.Comment: Returns the data of this data section.
toString() - Method in class sjg.xml.Data: Returns the data of this data section.
toString() - Method in class sjg.xml.Document: Returns the textual representation of this document.
toString() - Method in class sjg.xml.Element: Returns a textual representation of this element.
toString() - Method in class sjg.xml.ProcessingInstruction: Returns the textual representation of this pi.
touches(ChromSegment) - Method in class gov.lbl.genome.common.features.ChromSegment: Returns true if the specified Chromosome segment either intersects or is adjacent to this Segment.
toURLString() - Method in class gov.lbl.genome.common.ViewSettings
tracerImage - Variable in class gov.lbl.genome.gui.panel.TracerPanel
TracerPanel - Class in gov.lbl.genome.gui.panel: Title: TracerPanel
TracerPanel(VGBPanel, DisplayPanel, int) - Constructor for class gov.lbl.genome.gui.panel.TracerPanel: TracerPanel
translate(int, int) - Method in class gnu.jpdf.PDFGraphics: Translate the origin.
translate(int, int) - Method in class gov.lbl.genome.gui.Picture: translate imageable area
translate(int, int, int, int) - Method in class gov.lbl.genome.gui.Picture: change size and position of the imageable area
trax - Variable in class gnu.jpdf.PDFGraphics: This is used to translate coordinates
tray - Variable in class gnu.jpdf.PDFGraphics: This is used to translate coordinates
type - Variable in class gov.lbl.genome.common.CurveInfo
TYPES - Static variable in class gov.lbl.genome.common.features.Repeat

U

UCSCBrowserAction - Class in gov.lbl.genome.gui.action: Title: Alternative Browser action
UCSCBrowserAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.UCSCBrowserAction: UCSCBrowserAction
UCSCBrowserAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.UCSCBrowserAction: UCSCBrowserAction
UIConstants - Interface in gov.lbl.genome.gui: Title: User Interface Constants
uiInit() - Method in class gov.lbl.genome.gui.GeneralGraphView: build graph view
UNDERLINED - Static variable in class gnu.jpdf.PDFAnnot: The border is drawn as a line on the bottom of the annotation rectangle
Union(ChromSegments) - Method in class gov.lbl.genome.common.features.ChromSegments: return Union of two segment collections
unlockDown() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: Enable Down Button
unlockUp() - Method in class gov.lbl.genome.gui.panel.ArrowsPanel: Enable Up Button
unselect() - Method in class gov.lbl.genome.gui.GeneralGraphView: unselect the graph view
unselectAllGraphs() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: unselect all Graphs
unselectChildren() - Method in class gov.lbl.genome.gui.GeneralGraphView: unselect all Children
UP - Static variable in class gov.lbl.genome.gui.panel.AxisPanelPicture
UP2DATE - Static variable in class gov.lbl.genome.common.CommUnit
upDate() - Method in class gov.lbl.genome.gui.VistaApp: currently Not used Check server for new and deleted curves and new versions since start time.
updateColor(Color) - Method in class ranab.img.gif.GifColor: Update color entry
updateColorTable(Color) - Method in class ranab.img.gif.GifImage: Update color table
updateContig(String) - Method in class gov.lbl.genome.gui.VistaApp
updateCurrPosition(String) - Method in class gov.lbl.genome.gui.VistaApp
updatePosition() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: update Position
updatePosition() - Method in class gov.lbl.genome.gui.VistaApp: updatePosition is a key method for geting curves.
updatePosition(long, long) - Method in class gov.lbl.genome.gui.VistaApp: updatePosition is a key method for geting curves.
updatePosition(String) - Method in class gov.lbl.genome.gui.VistaApp: updatePosition is a key method for geting curves.
updatePosition(String, long, long) - Method in class gov.lbl.genome.gui.VistaApp: updatePosition is a key method for geting curves.
updateSelectList() - Method in class gov.lbl.genome.gui.panel.DisplayPanel: update Select List in the bottom panel curve list
USENONE - Static variable in class gnu.jpdf.PDFDocument: This page mode indicates that the document should be opened just with the page visible.
USEOUTLINES - Static variable in class gnu.jpdf.PDFDocument: This page mode indicates that the Outlines should also be displayed when the document is opened.
useParameters - Variable in class gov.lbl.genome.gui.VistaApp
USETHUMBS - Static variable in class gnu.jpdf.PDFDocument: This page mode indicates that the Thumbnails should be visible when the document first opens.
Utr - Class in gov.lbl.genome.common.features: Utr represents a specific chromosome coordinate span.
Utr(String, long, long) - Constructor for class gov.lbl.genome.common.features.Utr

V

va - Variable in class gov.lbl.genome.gui.AbstractCurveView
va - Variable in class gov.lbl.genome.gui.action.VAbstractAction
va - Variable in class gov.lbl.genome.gui.dialog.ActionDialog
va - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
va - Variable in class gov.lbl.genome.gui.panel.VGBPanel
va - Variable in class gov.lbl.genome.gui.Picture
VAbstractAction - Class in gov.lbl.genome.gui.action: Title: VAbstractAction
VAbstractAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.VAbstractAction: VAbstractAction
VAbstractAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.VAbstractAction: VAbstractAction
vAlign - Variable in class layout.TableLayoutConstraints: Verical justification if component occupies just one cell
values - Variable in class gov.lbl.genome.gui.panel.AbstractActionDialogPanel
VERSION - Static variable in class gov.lbl.genome.common.CommUnit
VERT_ALIGN_BOTTOM - Static variable in class gnu.jpdf.BoundingBox: Used to align a String at the bottom of the box
VERT_ALIGN_CENTER - Static variable in class gnu.jpdf.BoundingBox: Used to a align a String centered vertically
VERT_ALIGN_TOP - Static variable in class gnu.jpdf.BoundingBox: Used to align a String at the top of the box
vertSize - Variable in class gov.lbl.genome.gui.panel.VistaPanel
VGBException - Exception in gov.lbl.genome.common: Title: VGBException
VGBException() - Constructor for exception gov.lbl.genome.common.VGBException: VGBException
VGBException(String) - Constructor for exception gov.lbl.genome.common.VGBException: VGBException
VGBException(String, int) - Constructor for exception gov.lbl.genome.common.VGBException: VGBException
VGBPanel - Class in gov.lbl.genome.gui.panel: Title: VGBPanel
VGBPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.VGBPanel
VGBPanel(VistaApp, int) - Constructor for class gov.lbl.genome.gui.panel.VGBPanel: VGBPanel requires VistaApp parameter because all applets use one and the same JVM and we can not use static reference.
view - Variable in class gov.lbl.genome.gui.GeneralGraphComp
ViewSettings - Class in gov.lbl.genome.common
ViewSettings(Integer, int, int, String, ChromSegment, int, int, double, int, int, int, boolean, boolean, boolean, boolean, int, int) - Constructor for class gov.lbl.genome.common.ViewSettings
visible() - Method in class gov.lbl.genome.gui.panel.TracerPanel: visible
VISTA_CURVE_TYPE - Static variable in interface gov.lbl.genome.common.CommonConstants
VistaApp - Class in gov.lbl.genome.gui: Title: VistaApp
VistaApp() - Constructor for class gov.lbl.genome.gui.VistaApp: VistaApp is the main class of the applet
VistaCurveInfo - Class in gov.lbl.genome.common: Title: VistaCurveInfo
VistaCurveInfo(String, boolean) - Constructor for class gov.lbl.genome.common.VistaCurveInfo: VistaCurveInfo
VistaCurveInfo(String, String) - Constructor for class gov.lbl.genome.common.VistaCurveInfo: VistaCurveInfo
VistaCurveInfo(String, String, String) - Constructor for class gov.lbl.genome.common.VistaCurveInfo: VistaCurveInfo
VistaCurveInfo(String, String, String, int, boolean) - Constructor for class gov.lbl.genome.common.VistaCurveInfo: VistaCurveInfo
VistaCurveInfo(String, String, String, String, String, String, String, int, boolean, boolean, boolean) - Constructor for class gov.lbl.genome.common.VistaCurveInfo: VistaCurveInfo
VistaCurveModel - Class in gov.lbl.genome.common: Title: VistaCurveModel
VistaCurveModel(String, int, int, int, int, int) - Constructor for class gov.lbl.genome.common.VistaCurveModel
VistaCurveModel(TreeMap, String, int, int, int, int, int) - Constructor for class gov.lbl.genome.common.VistaCurveModel: VistaCurveModel
VistaCurveModel(TreeMap, String, int, int, int, Vector, int, int) - Constructor for class gov.lbl.genome.common.VistaCurveModel: VistaCurveModel
VistaCurveView - Class in gov.lbl.genome.gui: Title: VistaCurveView
VistaCurveView(VistaCurveModel, GeneralGraphView, Color) - Constructor for class gov.lbl.genome.gui.VistaCurveView: VistaCurveView
VistaDialog - Class in gov.lbl.genome.gui.dialog: Title: Standard dialog slass
VistaDialog(Frame, Element, HashMap, Callback) - Constructor for class gov.lbl.genome.gui.dialog.VistaDialog: VistaDialog
VistaLabel - Class in gov.lbl.genome.gui: Title: VistaLabel
VistaLabel() - Constructor for class gov.lbl.genome.gui.VistaLabel: VistaLabel
VistaLabel(String) - Constructor for class gov.lbl.genome.gui.VistaLabel: VistaLabel
VistaModelConstants - Interface in gov.lbl.genome.common: Title:
VistaPanel - Class in gov.lbl.genome.gui.panel: Title: VistaPanel
VistaPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.VistaPanel: VistaPanel
VistaPanel(VistaApp, int) - Constructor for class gov.lbl.genome.gui.panel.VistaPanel
VistaPanel(VistaApp, PageFormat, int) - Constructor for class gov.lbl.genome.gui.panel.VistaPanel
VistaPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.VistaPanel

W

wait_cursor - Variable in class gov.lbl.genome.gui.panel.VistaPanel
waitCursor - Variable in class gov.lbl.genome.gui.panel.VistaPanel
waitMouseCursor() - Method in class gov.lbl.genome.gui.panel.TracerPanel: show wait mouse cursos
westMouseCursor() - Method in class gov.lbl.genome.gui.panel.ChromPanel: set mouse cursor to the westCursor
width - Variable in class gov.lbl.genome.gui.AbstractCurveView
width - Variable in class gov.lbl.genome.gui.GeneralGraphComp
width - Variable in class gov.lbl.genome.gui.Picture
widthString - Static variable in class gov.lbl.genome.gui.panel.SaveAsPanel
windowActivated(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
windowClosed(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
windowClosing(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp: Stop dataPuller thread when closing
windowDeactivated(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
windowDeiconified(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
windowIconified(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
windowOpened(WindowEvent) - Method in class gov.lbl.genome.gui.VistaApp
write(OutputStream) - Method in class gnu.jpdf.PDFAnnot: Should this be public??
write(OutputStream) - Method in class gnu.jpdf.PDFBorder
write(OutputStream) - Method in class gnu.jpdf.PDFCatalog
write(OutputStream) - Method in class gnu.jpdf.PDFDocument: This writes the document to an OutputStream.
write(OutputStream) - Method in class gnu.jpdf.PDFFont
write(OutputStream) - Method in class gnu.jpdf.PDFImage: Compression needs to be improved here
write(OutputStream) - Method in class gnu.jpdf.PDFInfo
write(OutputStream) - Method in class gnu.jpdf.PDFObject: Writes the object to the output stream.
write(OutputStream) - Method in class gnu.jpdf.PDFOutline
write(PDFObject) - Method in class gnu.jpdf.PDFOutput: This method writes a PDFObject to the stream.
write(OutputStream) - Method in class gnu.jpdf.PDFPage.procset
write(OutputStream) - Method in class gnu.jpdf.PDFPage
write(OutputStream) - Method in class gnu.jpdf.PDFPageList
write(OutputStream) - Method in class gnu.jpdf.PDFStream
write(DataOutputStream) - Method in class ranab.img.gif.GifColor: Write gif color
write(DataOutputStream) - Method in class ranab.img.gif.GifCommentEx: Write comment this block.
write(DataOutputStream) - Method in class ranab.img.gif.GifGraphicEx: Write this block
write(DataOutputStream) - Method in class ranab.img.gif.GifImageDescriptor: Write image descriptor
write(DataOutputStream) - Method in class ranab.img.gif.GifNsAppEx: Write the block
write(DataOutputStream) - Method in class ranab.img.gif.GifScreenDescriptor: write screen descriptor
writeblock(int, Vector) - Method in class gnu.jpdf.PDFOutput: Writes a block of references to the PDF file
writeEnd(OutputStream) - Method in class gnu.jpdf.PDFObject: The write method should call this after writing anything to the OutputStream.
writeStart(OutputStream) - Method in class gnu.jpdf.PDFObject: The write method should call this before writing anything to the OutputStream.
writeStream(OutputStream) - Method in class gnu.jpdf.PDFImage: Writes the image to the stream
writeStream(OutputStream) - Method in class gnu.jpdf.PDFStream: This inserts the Streams length, then the actual stream, finally the end of stream/object markers.

X

X(int) - Method in class gov.lbl.genome.gui.Picture: correct x coordinates
X_TYPE - Static variable in class gov.lbl.genome.common.AbstractCurveModel
XAxisPanel - Class in gov.lbl.genome.gui.panel: Title: XAxisPanel
XAxisPanel(VistaApp) - Constructor for class gov.lbl.genome.gui.panel.XAxisPanel: XAxisPanel
XAxisPanel(VistaApp, PageFormat) - Constructor for class gov.lbl.genome.gui.panel.XAxisPanel: XAxisPanel
xDifference - Variable in class gov.lbl.genome.gui.AbstractCurveView
xDisplay(int) - Method in class gov.lbl.genome.gui.AbstractCurveView: convert screen coordinate into the graph coordinate
xend - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
xPoints - Variable in class gov.lbl.genome.gui.AbstractCurveView
xstart - Variable in class gov.lbl.genome.gui.panel.DisplayPanel
xUnits - Variable in class gov.lbl.genome.common.AbstractGraphModel

Y

Y(int) - Method in class gov.lbl.genome.gui.Picture: correct y coordinates
Y_AXIS_OFFSET_WIDTH - Static variable in interface gov.lbl.genome.gui.UIConstants
Y_TYPE - Static variable in class gov.lbl.genome.common.AbstractCurveModel
yDifference - Variable in class gov.lbl.genome.gui.AbstractCurveView
yLabel - Variable in class gov.lbl.genome.common.AbstractGraphModel
yLabelOrientation - Variable in class gov.lbl.genome.common.AbstractGraphModel
yPoints - Variable in class gov.lbl.genome.gui.AbstractCurveView
yUnits - Variable in class gov.lbl.genome.common.AbstractGraphModel
yUnitsFormat - Variable in class gov.lbl.genome.gui.GeneralGraphView

Z

z - Variable in class gov.lbl.genome.gui.Picture
ZoomInAction - Class in gov.lbl.genome.gui.action: Title:
ZoomInAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.ZoomInAction: ZoomInAction
ZoomInAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.ZoomInAction: ZoomInAction
ZoomOutAction - Class in gov.lbl.genome.gui.action: Title:
ZoomOutAction(VistaApp) - Constructor for class gov.lbl.genome.gui.action.ZoomOutAction: ZoomOutAction
ZoomOutAction(VistaApp, String) - Constructor for class gov.lbl.genome.gui.action.ZoomOutAction: ZoomOutAction

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