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P

paint(Graphics2D, float, float, IconLabelFormats, float) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIcon

paint(Graphics2D, float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.ShapeLabelIcon

Paints the shape of the implementing class depending on the specified formats and restores the current Stroke after the operation.

paint(Graphics2D, float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.UnknownIcon

Displays a questionmark.

paint(Graphics) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPreviewPanel

paint(Graphics) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorPreviewPanel

PaintableElement - Interface in info.bioinfweb.treegraph.document

paintBranch(Branch) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintComponent(Graphics) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler

paintComponent(Graphics) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRulerUnitField

paintComponent(Graphics) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

paintDimensions - Variable in class info.bioinfweb.treegraph.document.Tree

painters - Variable in class info.bioinfweb.treegraph.document.Document

painterType - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

paintIcon(Component, Graphics, int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorIcon

paintIconPreview() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel

paintInternalNode(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

Paints the given node.

paintLabelBlock(Labels, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintLeaf(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintLegend(Legend) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintPointNode(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintPreview(Graphics2D, double) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

paintScaleBar(ScaleBar) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintSelection(ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintStart - Variable in class info.bioinfweb.treegraph.document.Tree

paintSubtree(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintText(String, TextFormats, float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintTree(Graphics2D, Document, TreeSelection, float, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintTree(Graphics2D, Rectangle, Document, TreeSelection, float, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

paintTree(Graphics2D, Document, TreeSelection, float, boolean) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.TreePainter

Paints the whole specified document.

paintTree(Graphics2D, Rectangle, Document, TreeSelection, float, boolean) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.TreePainter

Paints the specified rectangle of the specified document.

panels - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory

parent - Variable in class info.bioinfweb.treegraph.document.Node

parent - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertRemoveSubtreeEdit

parent - Variable in class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit

parse(String) - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickScanner

parse(String) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

parseName(String) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

parseNumericValues - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit

parseNumericValuesCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

parser - Variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

PasteAction - Class in info.bioinfweb.treegraph.gui.actions.edit

PasteAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.PasteAction

PasteAllLabelsEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteAllLabelsEdit(Document, Branch, Label[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteAllLabelsEdit

PasteLabelEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteLabelEdit(Document, Branch, Label) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteLabelEdit

PasteLegendEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteLegendEdit(Document, Node, Node, Legend) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteLegendEdit

pasteLegends() - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster

PasteRootEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteRootEdit(Document, Node, Legend[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteRootEdit

PasteSiblingEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteSiblingEdit(Document, Node, Node, Legend[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteSiblingEdit

PasteSubtreeEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PasteSubtreeEdit(Document, Node, Node, Legend[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit

path - Variable in class info.bioinfweb.treegraph.document.TreePath

pattern - Variable in class info.bioinfweb.treegraph.gui.actions.edit.SearchTextAction

PDFFactory - Class in info.bioinfweb.treegraph.graphics.export.pdf

PDFFactory() - Constructor for class info.bioinfweb.treegraph.graphics.export.pdf.PDFFactory

PDFFilter - Class in info.bioinfweb.treegraph.graphics.export.pdf

PDFFilter() - Constructor for class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter

PDFWriter - Class in info.bioinfweb.treegraph.graphics.export.pdf

PDFWriter() - Constructor for class info.bioinfweb.treegraph.graphics.export.pdf.PDFWriter

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.edit.LadderizeEdit

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.edit.RescaleNodeDataEdit

performRedo() - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.AbstractSelectionAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.InvertSelectionAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectAllAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsInSubtreeAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLabelsWithIDAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInDocumentAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLeafsInSubtreeAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsInSubtreeAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectLegendsWithPosIndexAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectSubtreeAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInDocumentAction

performSelection(ActionEvent, TreeInternalFrame, TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.select.SelectTypeInSubtreeAction

phylogenies - Variable in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader

PHYLOGRAM_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.ImageGenerator

PhylogramFactory - Class in info.bioinfweb.treegraph.graphics.positionpaint

The factory class for the phylogram/chronogram view.

PhylogramFactory() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory

PhylogramPainter - Class in info.bioinfweb.treegraph.graphics.positionpaint

PhylogramPainter() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPainter

PhylogramPositioner - Class in info.bioinfweb.treegraph.graphics.positionpaint

PhylogramPositioner() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner

PhyloXMLConstants - Interface in info.bioinfweb.treegraph.document.io.phyloxml

Provides XML constants for the phyloXML format.

PhyloXMLFactory - Class in info.bioinfweb.treegraph.document.io.phyloxml

PhyloXMLFactory() - Constructor for class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFactory

PhyloXMLFilter - Class in info.bioinfweb.treegraph.document.io.phyloxml

PhyloXMLFilter() - Constructor for class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFilter

PhyloXMLReader - Class in info.bioinfweb.treegraph.document.io.phyloxml

Reads a phyloXML document.

PhyloXMLReader() - Constructor for class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader

PieChartLabel - Class in info.bioinfweb.treegraph.document

Represents a pie chart label.

PieChartLabel(Labels) - Constructor for class info.bioinfweb.treegraph.document.PieChartLabel

PieChartLabelFormats - Class in info.bioinfweb.treegraph.document.format

Stores the formats of pie chart label.

PieChartLabelFormats(Label, boolean, int, int) - Constructor for class info.bioinfweb.treegraph.document.format.PieChartLabelFormats

PieChartLabelFormats(Label) - Constructor for class info.bioinfweb.treegraph.document.format.PieChartLabelFormats

PieChartLabelIDsEdit - Class in info.bioinfweb.treegraph.document.undo.edit

PieChartLabelIDsEdit(Document, PieChartLabel[], String[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.PieChartLabelIDsEdit

pieChartPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel

PieColorCellRenderer - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor

Renders a cell in the pie color table of the IconPieChartLabelPanel.

PieColorCellRenderer() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorCellRenderer

pieColorCount() - Method in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats

PieColorIcon - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor

Icon used in the pie color list of the IconPieChartLabelPanel.

PieColorIcon() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorIcon

PieColorListEntry - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor

Represents an entry in the pie color list of the IconPieChartLabelPanel.

PieColorListEntry(String, Color) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.piecolor.PieColorListEntry

PieColorManager - Class in info.bioinfweb.treegraph.document

Defines the default colors for the pies in pie chart labels.

PieColorManager() - Constructor for class info.bioinfweb.treegraph.document.PieColorManager

pieColorMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel

PieColorOperator - Class in info.bioinfweb.treegraph.document.format.operate

PieColorOperator(Color[]) - Constructor for class info.bioinfweb.treegraph.document.format.operate.PieColorOperator

pieColors - Variable in class info.bioinfweb.treegraph.document.format.PieChartLabelFormats

PIXELS_PER_MM_100 - Static variable in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

pixelsPerMillimeter - Variable in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

pixelsPerMillimeter() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

pixelsToMillimeters(float, float) - Static method in class info.bioinfweb.treegraph.document.format.DistanceValue

pixelsToMillimeters(float) - Method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput

PLAIN - Static variable in interface info.bioinfweb.treegraph.document.format.TextFormats

PNGFactory - Class in info.bioinfweb.treegraph.graphics.export.png

PNGFactory() - Constructor for class info.bioinfweb.treegraph.graphics.export.png.PNGFactory

PNGFilter - Class in info.bioinfweb.treegraph.graphics.export.png

PNGFilter() - Constructor for class info.bioinfweb.treegraph.graphics.export.png.PNGFilter

PNGWriter - Class in info.bioinfweb.treegraph.graphics.export.png

PNGWriter() - Constructor for class info.bioinfweb.treegraph.graphics.export.png.PNGWriter

POINTS_PER_MM - Static variable in class info.bioinfweb.treegraph.document.format.DistanceValue

pointsToMillimeters(float) - Static method in class info.bioinfweb.treegraph.document.format.DistanceValue

pointsToUnits(float, float) - Static method in class info.bioinfweb.treegraph.document.format.ScaleValue

popupActions - Variable in class info.bioinfweb.treegraph.gui.actions.ActionManagement

popupMenu - Variable in class info.bioinfweb.treegraph.gui.actions.ActionManagement

position - Variable in class info.bioinfweb.treegraph.document.format.LegendFormats

position - Variable in class info.bioinfweb.treegraph.document.format.operate.LegendPositionOperator

position - Variable in exception info.bioinfweb.treegraph.document.io.newick.NewickException

position - Variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

position - Variable in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit

position(Branch, String[]) - Static method in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit

position(Node) - Static method in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit

positionAll(Document, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

positionAll(Document, float) - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.TreePositioner

positionArrowLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog

positionContentLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog

PositionData - Class in info.bioinfweb.treegraph.document.position

PositionData() - Constructor for class info.bioinfweb.treegraph.document.position.PositionData

positionElements(Node, float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

Positions the subtree under root.

positioners - Variable in class info.bioinfweb.treegraph.document.Document

positionLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog

positionLabelBlockX(Branch, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

positionLabelBlockY(Branch) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

positionLabelsToLeft - Variable in class info.bioinfweb.treegraph.document.format.GlobalFormats

positionLegends(float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

Positions all legends rigths if startX.

PositionPaintFactory - Class in info.bioinfweb.treegraph.graphics.positionpaint

PositionPaintFactory() - Constructor for class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

PositionPaintType - Enum in info.bioinfweb.treegraph.graphics.positionpaint

PositionPaintType() - Constructor for enum info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintType

positionPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

positions - Variable in class info.bioinfweb.treegraph.document.ConcretePaintableElement

positionScaleBar(float, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

Positions the scale bar.

positiveExampleLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

ppiToPPM(float) - Static method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput

ppmmToPPI(float) - Static method in class info.bioinfweb.treegraph.gui.dialogs.ResolutionInput

PRE_LEGEND_ANCHOR - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants

predifinedTable - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

preferencesPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

PreferencesPanel - Interface in info.bioinfweb.treegraph.gui.dialogs.io.exporttographic

This interface should be implemented by all panels that are used to edit format specific preferences in the ExportToGraphics-dialog.

PreferencesPanelFactory - Class in info.bioinfweb.treegraph.gui.dialogs.io.exporttographic

This class provides instances of the accordant preferences panels to the different graphic formats TreeGraph can export data to.

PreferencesPanelFactory() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory

prefixLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

preview() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

PREVIEW_SIZE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel

previewLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

previewLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel

previewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

previewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

previewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

previewScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

previewTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontFormatsPanel

PreviousDocumentAction - Class in info.bioinfweb.treegraph.gui.actions.window

PreviousDocumentAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.window.PreviousDocumentAction

previousUnit - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput

printRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

process(CommandLineReader) - Method in class info.bioinfweb.treegraph.cmd.CmdProcessor

processRooted - Variable in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit

processSubtree(Node) - Method in class info.bioinfweb.treegraph.document.undo.file.AddSupportValuesEdit

Finds the support or conflict values in the source document.

put(String, TextElementData) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap

put(String, Object) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints

put(LabelIcon) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap

putAll(Map<? extends String, ? extends TextElementData>) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap