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

G

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

generalEditorPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

generalPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

generalScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

generate(CommandLineReader) - Static method in class info.bioinfweb.treegraph.cmd.ImageGenerator

generatePattern(String, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit

get(Object) - Method in class info.bioinfweb.treegraph.document.HiddenDataMap

get(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable

get(String) - Method in class info.bioinfweb.treegraph.document.io.nexus.TranslTable

get(int) - Method in class info.bioinfweb.treegraph.document.LabelLine

get(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels

Returns the label at the specified position

get(String) - Method in class info.bioinfweb.treegraph.document.Labels

get(int) - Method in class info.bioinfweb.treegraph.document.Legends

get(String) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints

get(String) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap

get(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

get(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

GET_VALUE_FUNC - Static variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

getAbove() - Method in class info.bioinfweb.treegraph.document.Label

getAbove(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels

getAboveBelowGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

getAboveBelowPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes labelAboveBelowPanel

getAboveRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes aboveRadioButton

getActionManagement() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

getActionManagement() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel

getActiveTreeFrame() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

Returns the currently avctive Frame where a tree is displayed.

getAdapter() - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit

getAdapter(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getAdapterComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes adapterComboBox

getAdapterComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes nodeDataComboBox

getAddButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes addButton

getAdditionalCount() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo

getAfferentBranch() - Method in class info.bioinfweb.treegraph.document.Node

getAlignGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

getAlignLegendsToSubtree() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getAlignment() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

getAlignmentPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes anchorPanel

getAlignToSubtreeCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes alignLegendsToSubtreeCheckBox

getAllFilters() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

getAnchor(int) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getAnchorName(int) - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getApachePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes apachePanel

getApacheScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes apacheScrollPane

getApacheTextArea() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes apacheTextArea

getAssignImportColumnsDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction

getAttributeMap() - Method in class info.bioinfweb.treegraph.document.Node

The attribute map can store data that is specific to special tasks like ladderizing or tree merging.

getBackgroundColor() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getBeginningRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes beginningRadioButton

getBelow() - Method in class info.bioinfweb.treegraph.document.Label

getBelow(boolean, int, int) - Method in class info.bioinfweb.treegraph.document.Labels

getBelowRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes belowRadioButton

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

This method initializes boldCheckBox

getBoolean(String, boolean) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints

getBothRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes bothRadioButton

getBottom() - Method in class info.bioinfweb.treegraph.document.format.Margin

getBottom() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput

getBottomInMillimeters() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getBottomInPixels(float) - Method in class info.bioinfweb.treegraph.document.position.PositionData

getBraceRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes braceRadioButton

getBracketRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes bracketRadioButton

getBranchDataRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes branchDataRadioButton

getBranches(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getBranchLengthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

This method initializes branchLengthCheckBox

getBranchLengthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

getBranchLengthScale() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getBranchLengthScale() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput

getBranchLengthsDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

getBranchLengthsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes branchLengthsPanel

getBranchLengthsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes branchLengthsRadioButton

getButtonPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes buttonPanel

getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes caseSensitiveCheckBox

getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes caseSensitiveCheckBox

getCaseSensitiveCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes caseSensitiveCheckBox

getChangeUndefinedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes hCheckBox

getChangeUndefinedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

This method initializes changeUndefinedCheckBox

getChildren() - Method in class info.bioinfweb.treegraph.document.Node

getClearButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes clearButton

getClipboard() - Method in class info.bioinfweb.treegraph.Main

getCloseButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes closeButton

getCmdProcessor() - Method in class info.bioinfweb.treegraph.Main

getColor(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.BranchLineColorAdapter

getColor(Node) - Method in interface info.bioinfweb.treegraph.document.format.adapters.color.ColorAdapter

getColor(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.LabelLineColorAdapter

getColor(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.LabelTextColorAdapter

getColor(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.NodeLineColorAdapter

getColor(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.color.NodeTextColorAdapter

getColorChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

This method initializes lineColorChooser

getColorChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

getColorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes colorPanel

getColorPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes colorPreviewPanel

getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getColumnClass(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

getColumnCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getColumnCount() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getColumnInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getColumnName(int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getColumnPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes columnPanel

getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput

getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput

getComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput

getCommandGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

getCommandPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes commandPanel

getComment() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken

Returns the comment which was located behind this element in the Newick string (if there was any).

getCompressionMethodComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TIFFPrefPanel

This method initializes compressionMethodComboBox

getConstantWidthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel

This method initializes constantWidthCheckBox

getContentsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes contentsTabbedPane

getContentType() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

getCopyPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

This method initializes copyPanel

getCornerRadius() - Method in interface info.bioinfweb.treegraph.document.format.CornerRadiusFormats

getCornerRadius() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getCornerRadius() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats

The line wich is dasplayed for an node can be rounded at ist top and bottom end The inner radius (without the line width) of the quater of a circle at the ends of this line is specified by the corner radius.

getCurrentValue(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

Returns the value of the specified column in the current line (specified by CalculateColumnEdit.position).

getData() - Method in class info.bioinfweb.treegraph.document.AbstractTextElement

getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter

getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter

getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter

getData(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter

getData() - Method in interface info.bioinfweb.treegraph.document.TextElement

getData() - Method in class info.bioinfweb.treegraph.document.TextLabel

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenBranchDataAdapter

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenNodeDataAdapter

getDataElement(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter

This method should return the tree element which contains the data which is edited with the implementation of the respective adapter.

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter

getDataElement(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter

getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenBranchDataAdapter

getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter

getDataMap(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenNodeDataAdapter

getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter

getDecimal(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter

getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter

getDecimal(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter

getDecimal() - Method in class info.bioinfweb.treegraph.document.TextElementData

Return the stored decimal value or Double.NaN is no decimal is stored.

getDecimalCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

This method initializes decimalCheckBox

getDecimalFormat() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getDecimalFormat() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getDecimalFormat() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.HiddenDataAdapter

getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter

getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter

getDecimalFormat(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextLabelAdapter

getDecimalFormat() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

getDecimalFormatterFactory() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

getDecimalInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog

getDecRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes decRadioButton

getDefaultExtension() - Method in interface info.bioinfweb.treegraph.document.io.DocumentFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.SupportedFormatsFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter

getDefaultExtension() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter

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

getDefaultType() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getDescent() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getDescent() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getDescent() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getDescription() - Method in interface info.bioinfweb.treegraph.document.io.DocumentFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.SupportedFormatsFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFilter

getDescription() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter

getDescription() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter

getDesktopPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes desktopPane

getDestAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

getDestInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

getDialog() - Method in class info.bioinfweb.treegraph.gui.actions.EditDialogAction

getDialog() - Method in class info.bioinfweb.treegraph.gui.actions.help.AboutAction

getDifAbove() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData

getDifBelow() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData

getDimensionsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes widthPanel

getDimensionsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes pngPanel

getDirectionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes directionPanel

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractDistanceValueAdapter

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLabelDistanceAdapter

Returns the distance value of the label with the specified ID in millimeters.

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLegendAdapter

This method always returns Float.NaN.

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchLineWidthAdapter

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchMinLengthAdapter

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchSpaceAboveAdapter

getDistance(Node) - Method in interface info.bioinfweb.treegraph.document.format.adapters.distance.DistanceAdapter

Returns the distance value in millimeters

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.NodeLineWidthAdapter

getDistance(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.NodeTextHeightAdapter

getDistancesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

This method initializes distancesPanel

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractDistanceValueAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractIconLabelDistanceAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLabelDistanceAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractLegendAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.BranchSpaceBelowAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.CornerRadiusAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LabelMarginBottomAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LabelMarginLeftAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LabelMarginRightAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LabelMarginTopAdapter

getDistanceValue(LabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LabelTextHeightAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LeafMarginBottomAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LeafMarginLeftAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LeafMarginRightAdapter

getDistanceValue(Node) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LeafMarginTopAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendLineWidthAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendMarginBottomAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendMarginLeftAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendMarginRightAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendMarginTopAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendSpacingAdapter

getDistanceValue(LegendFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.LegendTextHeightAdapter

getDocument() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog

getDocument() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog

getDocument() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getDocument() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

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

Returns the currently associated document.

getDocumentMargin() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getDocumentPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

getDocumentRect() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

getDocumentSplitPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes documentSplitPane

getDownButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes downButton

getDownRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes downRadioButton

getDownwards() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo

getEditMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes editMenu

getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel

getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel

getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel

getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel

getElementAt(int) - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel

getElementByPosition(MouseEvent) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener

getElements(Node, T[], boolean, boolean, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getElementsOfType(Node, PaintableElement, T[], boolean) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getEndRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes endRadioButton

getError() - Method in exception info.bioinfweb.treegraph.document.io.nexus.NexusException

getErrorReporter() - Method in class info.bioinfweb.treegraph.Main

getErrors() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

Returns a description of the errors that occured during the last call of CalculateColumnEdit.redo() or CalculateColumnEdit.evaluate().

getExamplePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes examplePanel

getExpressionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes expressionPanel

getExpressionTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes expressionTextField

getFileButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes fileButton

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes fileChooser

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes fileChooser

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes fileChooser.

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

This method initializes fileChooser

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

getFileChooser() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes fileChooser

getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes fileChooserPanel

getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes fileChooserPanel

getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes fileChooserPanel

getFileChooserPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes fileChooserPanel

getFileMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes fileMenu

getFileName() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel

getFilePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes filePanel

getFilePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

This method initializes filePanel

getFileTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes fileTextField

getFilter() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory

getFilter() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory

getFilter() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFactory

getFilter(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

getFilter() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory

getFilter() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory

getFilter() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory

getFilter() - Method in interface info.bioinfweb.treegraph.graphics.export.GraphicsFactory

getFilter(GraphicFormat) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

getFilter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory

getFindTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes findTextField

getFirstBranch() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstEdgeRadiusElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstIconLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager

getFirstIconLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager

getFirstLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstLeaf() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstLegend() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstLineElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstNode() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstTextElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstTextLabel(Node, String) - Static method in class info.bioinfweb.treegraph.document.IDManager

getFirstTextLabel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFirstTreeElement() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getFloat(String, float) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterHints

getFont(float) - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getFont(float) - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getFont(float) - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

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

This method initializes fontFamilyList

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

This method initializes fontFamilyPanel

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

This method initializes fontFamilyTextField

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

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

This method initializes fontHeightPanel

getFontName() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getFontName() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getFontName() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

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

This method initializes fontStylePanel

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.GraphicFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFilter

getFormat() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFilter

getFormat() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

Returns the graphic format the user selected.

getFormatMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes formatMenu

getFormatPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes formatPanel

getFormats() - Method in class info.bioinfweb.treegraph.document.AbstractTextElement

getFormats() - Method in class info.bioinfweb.treegraph.document.Branch

getFormats() - Method in interface info.bioinfweb.treegraph.document.CornerRadiusElement

getFormats() - Method in class info.bioinfweb.treegraph.document.IconLabel

getFormats() - Method in class info.bioinfweb.treegraph.document.Label

getFormats() - Method in class info.bioinfweb.treegraph.document.Legend

getFormats() - Method in interface info.bioinfweb.treegraph.document.LineElement

getFormats() - Method in class info.bioinfweb.treegraph.document.Node

getFormats() - Method in interface info.bioinfweb.treegraph.document.PaintableElement

getFormats() - Method in class info.bioinfweb.treegraph.document.ScaleBar

getFormats() - Method in interface info.bioinfweb.treegraph.document.TextElement

getFormats() - Method in class info.bioinfweb.treegraph.document.TextLabel

getFormats() - Method in class info.bioinfweb.treegraph.document.Tree

getFormatsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog

This method initializes formatsTabbedPane

getFormatsTabbedPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes formatsTabbedPane

getFormatTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes formatTextField

getFrame() - Method in class info.bioinfweb.treegraph.document.Document

getGeneralEditorPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes generalEditorPane

getGeneralPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes generalPanel

getGeneralScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes generalScrollPane

getGplEditorPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes gplTextArea

getGPLPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes gplPanel

getGplScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes gplScrollPane

getHasLengthCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog

This method initializes hasLengthCheckBox

getHeight() - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension

getHeight() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

Defines the height of the long dashes (the height of the text below is not included.)

getHeight() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

getHeight() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getHeightAbove() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData

getHeightBelow() - Method in class info.bioinfweb.treegraph.document.position.NodePositionData

getHeightTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes heightTextField

getHelpMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes helpMenu

getHelpTopic() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

getHiddenBranchDataIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

Searches for all the IDs of hidden data that is assigned to a branch present in the subtree under root.

getHiddenBranchDataIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getHiddenDataAdded() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader

Returns whether hidden data has been read from commetns in the newick string (e.g. from BEAST) during the last call of NewickStringReader.read(String, NodeBranchDataAdapter, NodeBranchDataAdapter, TranslTable, boolean) or one of its convenience methods.

getHiddenDataMap() - Method in class info.bioinfweb.treegraph.document.Branch

getHiddenDataMap() - Method in interface info.bioinfweb.treegraph.document.HiddenDataElement

getHiddenDataMap() - Method in class info.bioinfweb.treegraph.document.Node

getHiddenNodeDataIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

Searches for all the IDs of hidden data that is assigned to a node present in the subtree under root.

getHiddenNodeDataIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getHighestChild() - Method in class info.bioinfweb.treegraph.document.Node

Returns the upper most subnode of this node (e.g. needed for legend positioning).

getHints() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

Returns the graphic writer hints that have been specified by the user.

getHoldingBranch() - Method in class info.bioinfweb.treegraph.document.Label

getHoldingBranch() - Method in class info.bioinfweb.treegraph.document.Labels

getHorizontalRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes horizontalRadioButton

getIcon() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

getIconComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

This method initializes iconComboBox

getIconComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.AbstractIconLabelDistanceAdapter

getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.IconHeightAdapter

getIconDistanceValue(IconLabelFormats) - Method in class info.bioinfweb.treegraph.document.format.adapters.distance.IconWidthAdapter

getIconFilled() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

getIconFilledCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

This method initializes iconFilledCheckBox

getIconFormatsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog

getIconHeight() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

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

getIconHeightInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

getIconLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getIconPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

This method initializes iconPanel

getIconPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

This method initializes iconPreviewPanel

getIconWidth() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

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

getIconWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

getID() - Method in class info.bioinfweb.treegraph.document.Label

getID() - Method in class info.bioinfweb.treegraph.document.nodebranchdata.AbstractIDElementAdapter

getID() - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.IDElementAdapter

getID() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.AbstractLabelAdapter

getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog

This method initializes idComboBox

getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog

This method initializes idComboBox

getIDComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog

This method initializes idComboBox

getIdList() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog

This method initializes idList

getIdNamePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes idNamePanel

getIDNameTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes idNameTextField

getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog

This method initializes idPanel

getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog

This method initializes idPanel

getIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog

This method initializes idPanel

getIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

Searches for all IDs (hidden data and label IDs) present in the subtree under root.

getIDValue(String) - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

Returns the value of the current line in the column specified the passed id present.

getIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

Searches for all IDs present in the subtree under root.

getImageHeight() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

Return the height entered by the user in pixels or millimeters.

getImageWidth() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

Returns the width entered by the user in pixels or millimeters.

getImportButtonGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

getImportPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes importPanel

getImportPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog

This method initializes importPanel

getImportTableDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ImportTableAction

getIncludeHiddenCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes includeHiddenCheckBox

getIncludeLeafs() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

getIncludeLeafsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

This method initializes includeLeafsCheckBox

getIncRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes incRadioButton

getIncreaseGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

getInheritToTerminalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes inheritToTerminalsCheckBox

getInheritToTerminalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

This method initializes inheritToTerminalsCheckBox

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

getInMillimeters() - Method in class info.bioinfweb.treegraph.document.format.DistanceValue

getInMillimeters(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

getInPixels(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue

getInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

getInPoints() - Method in class info.bioinfweb.treegraph.document.format.DistanceValue

Returns the value in DTP-Points (1 pt = 0.3527777 mm).

getInPoints(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

getInputPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog

This method initializes InputPanel

getInstance() - Static method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.LabelIconMap

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPainter

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPainter

getInstance() - Static method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

getInstance() - Static method in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel

getInstance() - Static method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory

getInstance() - Static method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

getInstance() - Static method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

getInstance() - Static method in class info.bioinfweb.treegraph.Main

getInstanceWithBranch() - Static method in class info.bioinfweb.treegraph.document.Node

getInternalFrameByFile(File) - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

getInternalFrameListener() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

getInternalInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

getInternalNodesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes internalNodesPanel

getInternalsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes InternalsRadioButton

getIntervalPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes decimalPanel

getIntervalPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

This method initializes intervalPanel

getInUnits(float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

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

This method initializes italicCheckBox

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditBranchLengthDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.EditTextElementDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AssignImportColumnsDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup

This method initializes jContentPane

getJContentPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes jContentPane

getLabel() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

Returns a deep copy of the label in the clipboard.

getLabelIDPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog

This method initializes labelIDPanel

getLabelIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

Searches for all label IDs present in the subtree under root.

getLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getLabelingPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes labelingPanel

getLabelList() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

Returns a deep copy of the label list in the clipboard.

getLabelNumbersPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes labelNumbersPanel

getLabelRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes labelRadioButton

getLabels() - Method in class info.bioinfweb.treegraph.document.Branch

getLabels() - Method in class info.bioinfweb.treegraph.document.Label

getLabels(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

Returns all labels in the subtree under root.

getLabels(Labels) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

Returns all labels of this labels-object.

getLabelsToLeftCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes labelsToLeftCheckBox

getLabelsWithID(Node, String) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getLabelsWithIDInBlock(Vector<Label>, Labels, boolean, String) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

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

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

getLeafInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

getLeafMargin() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats

getLeafNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getLeafNodesBetween(Node, Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getLeafsRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes LeafsRadioButton

getLeft() - Method in class info.bioinfweb.treegraph.document.format.Margin

getLeft() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

getLeft() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getLeft() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput

getLeftRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes leftRadioButton

getLegend() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

Returns a deep copy of the legend in the clipboard.

getLegendBottom(LegendFormats) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

getLegendNumbersPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes legendNumbersPanel

getLegendOrientationPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes legendOrientationPanel

getLegendPositionTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes positionTextField

getLegends() - Method in class info.bioinfweb.treegraph.document.Legend

getLegends() - Method in class info.bioinfweb.treegraph.document.Tree

getLegends() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesBackup

getLegendsInSubtree(Tree, Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

Returns an array of all legends which are completely anchored inside the subtree under root.

getLegendsReanchored() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit

getLegendsReanchored() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

getLegendsRemoved() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit

getLegendsRemoved() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

getLegendsSave() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

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

getLegendStyle() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getLegendStylePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes legendStylePanel

getLegendTop(LegendFormats) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

getLength() - Method in class info.bioinfweb.treegraph.document.Branch

getLength() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken

getLengthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog

Returns the length input and creates it if necessary.

getLengthPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ScaleBranchLengthsDialog

This method initializes lengthPanel

getLineColor() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats

getLineColor(Document) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils

Returns the default line color or its inversion depending in the backgound color of the specified document.

getLineColor() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

getLineColor() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getLineColor() - Method in interface info.bioinfweb.treegraph.document.format.LineFormats

getLineColor() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats

getLineColor() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

getLineColorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

This method initializes lineColorPanel

getLineElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getLineFormats() - Method in class info.bioinfweb.treegraph.document.Branch

getLineIndex() - Method in class info.bioinfweb.treegraph.document.Label

Returns the line index of the label or -1 if it is not linked to a Labels-object.

getLineIndex(Label) - Method in class info.bioinfweb.treegraph.document.Labels

getLineIndex(boolean, Label) - Method in class info.bioinfweb.treegraph.document.Labels

Returns the index of the specified label in its line.

getLineIndex(boolean, int, Label) - Method in class info.bioinfweb.treegraph.document.Labels

Returns the index of the specified label in its line.

getLineNo() - Method in class info.bioinfweb.treegraph.document.Label

Returns the line number of this label or -1 if it is not linked to a Labels-object.

getLineNo(boolean, Label) - Method in class info.bioinfweb.treegraph.document.Labels

Returns the line number this label is located in.

getLineNoTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes lineNoTextField

getLineNumber() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats

The number of the line in which this label shall be displayed.

getLinePos() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

The position if the icon (for labels) or the bracket (for legends).

getLinePosition() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats

If more than one element is located in the same line the line position is used to determine the order of the elements.

getLinePosTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes linePosTextField

getLines(boolean) - Method in class info.bioinfweb.treegraph.document.Labels

getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats

getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.IconLabelFormats

getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getLineWidth() - Method in interface info.bioinfweb.treegraph.document.format.LineFormats

getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.NodeFormats

getLineWidth() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Branch

getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Label

getLinkedNode() - Method in class info.bioinfweb.treegraph.document.Node

getLinkedNode(PaintableElement) - Static method in class info.bioinfweb.treegraph.document.Tree

Returns the linked node to the given element.

getLinkedNode() - Method in interface info.bioinfweb.treegraph.document.TreeElement

getLocale() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getLocale() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

Return the local object used in the decimal formats.

getLocale() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getLocaleComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes localeComboBox

getLocaleValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

getLongInterval() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

The long interval specifies how often the scale bar is labeles with a value.

getLowerBorder() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

getLowerToolBar() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel

This method initializes editFormatToolBar

getLowestChild() - Method in class info.bioinfweb.treegraph.document.Node

Returns the lowest subnode of this node (e.g. needed for legend positioning).

getMainFrame() - Method in class info.bioinfweb.treegraph.gui.actions.DocumentAction

getMainMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes mainMenu

getMargin() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats

getMargin() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

getMarginInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel

getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelPanel

This method initializes marginPanel

getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes marginPanel

getMarginPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel

This method initializes marginPanel

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

getMaxColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes maxColorButton

getMaxWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

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

getMinColorButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes minColorButton

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

getMinLength() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats

getMinMaxPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

This method initializes minMaxPanel

getMinSpaceAbove() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats

getMinSpaceBelow() - Method in class info.bioinfweb.treegraph.document.format.BranchFormats

getMinTreeDistance() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getMinWidthInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

getModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput

getName() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusCommand

getName(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument

getName(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getNameManager() - Method in class info.bioinfweb.treegraph.Main

getNegativeExampleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

getNewMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes newMenu

getNewNameTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog

This method initializes newNameTextField

getNext() - Method in class info.bioinfweb.treegraph.document.Label

getNext(List<LabelLine>, int, int, int) - Method in class info.bioinfweb.treegraph.document.Labels

getNext() - Method in class info.bioinfweb.treegraph.document.Node

getNextLeaf() - Method in class info.bioinfweb.treegraph.document.Node

getNode() - Method in class info.bioinfweb.treegraph.document.NodeLadderizeComparable

getNode() - Method in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo

getNodeBranchDataMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes nodeBranchDataMenu

getNodeByUniqueName(String) - Method in class info.bioinfweb.treegraph.document.Tree

Searches for a node with the given unique name in this tree.

getNodeByUniqueName(Node, String) - Static method in class info.bioinfweb.treegraph.document.Tree

Searches for a node with the given unique name in the subtree under root.

getNodeDataButtonsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes nodeDataButtonsPanel

getNodeDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes nodeDataPanel

getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes nodeDataPanel

getNodeDataPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

This method initializes nodeDataPanel

getNodeDataRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes nodeDataRadioButton

getNodeNamesDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

getNodeNamesRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes nodeNamesRadioButton

getNodes(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getNodesGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

getNodesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes NodesPanel

getNoneRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes noneRadioButton

getNumberOfParameters() - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction

getOpenRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes openRadioButton

getOrientation() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getOrientation() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel

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

getOrientationGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

getOtherLineFormatsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

This method initializes otherLineFormatsPanel

getOuterPreferencesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes preferencesPanel

getOwner() - Method in class info.bioinfweb.treegraph.document.format.LabelFormats

getOwner() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

getPaintableElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getPaintDimension(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Tree

Returnes the stored paint dimension (the size of the document) for the given painter ID.

getPainter() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory

getPainter(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getPainter() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory

getPainter() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory

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

getPaintStart() - Method in class info.bioinfweb.treegraph.document.Tree

getPanel(GraphicFormat) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.PreferencesPanelFactory

getParent() - Method in class info.bioinfweb.treegraph.document.Node

getParseNumericValuesCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes parseNumericValuesCheckBox

getPixelsPerMillimeter() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

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

getPopupMenu(PaintableElement) - Method in class info.bioinfweb.treegraph.gui.actions.ActionManagement

getPosBeforeLinePos(int) - Method in class info.bioinfweb.treegraph.document.LabelLine

Returns the index of the label at the given line position.

getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.ConcretePaintableElement

getPosition() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

The position of a legend defined in which order vertically overlapping legends are positioned.

getPosition() - Method in exception info.bioinfweb.treegraph.document.io.newick.NewickException

getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Legend

getPosition(PositionPaintType) - Method in class info.bioinfweb.treegraph.document.Node

getPosition(PositionPaintType) - Method in interface info.bioinfweb.treegraph.document.PaintableElement

Returns the stored DataPosition-object of an for an positioner- identifier.

getPosition(int) - Method in class info.bioinfweb.treegraph.document.TreePath

Returns the position in this path on the specified level.

getPositioner() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory

getPositioner(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getPositioner() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory

getPositioner() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory

getPositionLabelsToLeft() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getPositionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes positionPanel

getPositiveExampleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

getPredifinedTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes predifinedTable

getPreferences() - Method in class info.bioinfweb.treegraph.Main

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

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

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.BranchLengthEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.ChangeLabelIDEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CopyColumnEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.CutEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteColumnEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteOutsideIntervalEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteSubelementsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.EditNodeBranchDataEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLabelsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertLegendEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.InsertSubtreeEdit

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

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.MoveSubtreeEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteAllLabelsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLabelEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteLegendEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteRootEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSiblingEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.PasteSubtreeEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLabelEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveLegendEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.RenameDataIDEdit

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

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

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

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.SetColumnTypeEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.edit.TextElementEdit

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

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.file.ImportTableEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.AutoPositionLabelsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ReanchorLegendEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ScaleDistanceValuesEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ShowHideScaleBarEdit

getPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.format.ShowRootedEdit

getPreviewLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

This method initializes previewPanel

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

This method initializes previewPanel

getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconLabelPanel

This method initializes previewPanel

getPreviewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes previewPanel

getPreviewScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes previewScrollPane

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

This method initializes previewTextField

getPrevious() - Method in class info.bioinfweb.treegraph.document.Label

getPrevious() - Method in class info.bioinfweb.treegraph.document.Node

getPreviousLeaf() - Method in class info.bioinfweb.treegraph.document.Node

getPrintRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes printRadioButton

getQualitySlider() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.JPEGPrefPanel

This method initializes qualitySlider

getReader() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory

getReader() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory

getReader() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFactory

getReader(File) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

getReader(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

getReader() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory

getReader() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory

getReader() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory

getRecentlyUsedList() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes recentlyUsedList

getRecentlyUsedListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

getRecentlyUsedPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes recentlyUsedPanel

getRecentlyUsedScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CalculateColumnDialog

This method initializes recentlyUsedScrollPane

getRedoMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes redoMenu

getRedoPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit

getRemoveButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes removeButton

getRenameButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog

This method initializes renameButton

getReplaceButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes replaceButton

getReplacePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes replacePanel

getReplaceRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes replaceRadioButton

getReplaceTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes replaceTextField

getResourcePath(String) - Static method in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

getRight() - Method in class info.bioinfweb.treegraph.document.format.Margin

getRight() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput

getRightInMillimeters() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getRightInPixels(float) - Method in class info.bioinfweb.treegraph.document.position.PositionData

getRightRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes leafsRadioButton

getRoundedInPixels(float) - Method in class info.bioinfweb.treegraph.document.format.DistanceValue

Gives the uprounded value in pixels

getRoundedInPixels(float, float) - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

getRow(Node) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

getRowCount() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getRowCount() - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getScaleBar() - Method in class info.bioinfweb.treegraph.document.Tree

getScaleBar() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

getScaleInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog

getScalePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog

This method initializes rescalePanel

getScrollableBlockIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler

getScrollableBlockIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

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

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

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

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

getScrollableUnitIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.ruler.TreeViewRuler

getScrollableUnitIncrement(Rectangle, int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeViewPanel

getSearchPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes searchPanel

getSearchTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes searchTextField

getSelctedIndex() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog

getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput

getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput

Returns the currently selected adapter.

getSelectedAdapter() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

Returns the selected adapter in the node/branch data table.

getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

Returns the selected file with a valid extension.

getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.FileDialog

Override this method if you e.g. want to add a default extension.

getSelectedFile() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

getSelectedItem() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel

getSelectedItem() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel

getSelectedNode(TreeSelection) - Method in class info.bioinfweb.treegraph.gui.actions.edit.MoveSubtreeAction

Returns the node that should be moved if the selection contains this node or its afferent branch as the first element.

getSelection() - Method in class info.bioinfweb.treegraph.gui.dialogs.EditDialog

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

getSelectionPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes selectionPanel

getSelectMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes selectMenu

getSeparator() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

getSeparator() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel

getSeparatorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes separatorPanel

getSeparatorPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ImportTableDialog

This method initializes separatorPanel

getSeparatorTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel

This method initializes separatorTextField

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.CrossIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.EllipseIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.HexagonIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.OctagonIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RectangleIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.RoundRectangleIcon

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

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.StarIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedCrossIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TitedHexagonIcon

getShape(float, float, IconLabelFormats, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.labelicons.TriangleIcon

getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler

getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader

getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter

getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter

getSharedInstance() - Static method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter

getShowRooted() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getShowRootedCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes showRootedCheckBox

getShowScaleBar() - Method in class info.bioinfweb.treegraph.document.format.GlobalFormats

getShowScaleBarCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

This method initializes showScaleBarCheckBox

getShowWarnings() - Method in class info.bioinfweb.treegraph.document.undo.edit.DeleteEdit

getShowWarnings() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

getShowWarnings() - Method in interface info.bioinfweb.treegraph.document.undo.WarningEdit

getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LabelIconComboBoxModel

getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RecentlyUsedExpressionsListModel

getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel

getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorAdapterListModel

getSize() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceAdapterListModel

getSlider() - Method in class info.bioinfweb.treegraph.gui.mainframe.tools.DistanceValuePopup

This method initializes slider

getSmallInterval() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

The small interval speccifies the distance between the small dashes of the branch length scale bar in branch length units.

getSourceComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

This method initializes sourceComboBox

getSourceComboBoxModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

getSourceInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

Creates the source input if necessary.

getSourcePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

This method initializes sourcePanel

getSourcePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.FormatsByNodeBranchDataDialog

This method initializes sourcePanel

getSpacing() - Method in class info.bioinfweb.treegraph.document.format.LegendFormats

The legend spacing is the distance between the bracket and the text of a legend.

getSpacing() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

The spacing between the icon or bracket and the text.

getSrcAdapter() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

getSrcInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.CopyColumnDialog

getStartPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes startPanel

getStoredValue() - Method in class info.bioinfweb.treegraph.document.format.ScaleValue

Returns the stored value in millimeters or in branch length units.

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

getStringFormatterFactory() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

getStringRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel

This method initializes stringRadioButton

getStyleGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

getSubtree() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

Returns a deep copy of the subtree in the clipboard.

getSubtreeLegends() - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

Returns a deep copies of the legends attached to the ubtree in the clipboard.

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

getTable() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes table

getTable() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes table

getTableModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

getTableModel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel

This method initializes tableScrollPane

getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes tableScrollPane

getTableScrollPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes tableScrollPane

getTabRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TableSeparatorPanel

This method initializes tabRadioButton

getTabs() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ElementFormatsDialog

getTargetDataButtonGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

getTargetList() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog

This method initializes targetList

getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ColorsByNodeBranchDataDialog

getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.DistanceValuesByNodeBranchDataDialog

getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.ScaleDistanceValuesDialog

getTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog

getTargetNode() - Method in class info.bioinfweb.treegraph.document.Branch

getTargetPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog

This method initializes targetPanel

getTargetScrollPane() - Method in class info.bioinfweb.treegraph.gui.dialogs.specialformats.SpecialFormatsDialog

This method initializes targetScrollPane

getTargetTypePanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes targetTypePanel

getTerminalDataInput() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

getTerminalsPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes terminalsPanel

getText() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken

getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.BranchLengthAdapter

getText(Node) - Method in interface info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataAdapter

getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.TextElementDataAdapter

getText(Node) - Method in class info.bioinfweb.treegraph.document.nodebranchdata.UniqueNameAdapter

getText() - Method in class info.bioinfweb.treegraph.document.TextElementData

Returns the stored string value or null is no string is stored.

getText() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

getTextColor() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getTextColor(Document) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils

Returns the default text color or its inversion depending in the backgound color of the specified document.

getTextColor() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getTextColor() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getTextElement() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

getTextElements(Node) - Static method in class info.bioinfweb.treegraph.document.TreeSerializer

getTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput

getTextHeight() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getTextHeight() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getTextHeight() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getTextLabelIDs(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getTextLabelIDVector(Node) - Static method in class info.bioinfweb.treegraph.document.IDManager

getTextPos() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken

getTextPos() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

getTextStyle() - Method in class info.bioinfweb.treegraph.document.format.ConcreteTextFormats

getTextStyle() - Method in interface info.bioinfweb.treegraph.document.format.TextFormats

getTextStyle() - Method in class info.bioinfweb.treegraph.document.format.TextLabelFormats

getTitleLabel() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput

getTokens() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusCommand

getToolBarPanel() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes toolBarPanel

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

This method is overwriten to show the internal node names or label IDs as tooltip text.

getTop() - Method in class info.bioinfweb.treegraph.document.format.Margin

getTop() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

getTop() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getTop() - Method in class info.bioinfweb.treegraph.gui.dialogs.MarginInput

getTranslateInternalNodesCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

This method initializes translateInternalNodesCheckBox

getTranslateInternalsCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

This method initializes translateInternalsCheckBox

getTranslTable() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument

getTransparentCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.TransparenrtBgPrefPanel

This method initializes transparentCheckBox

getTree() - Method in class info.bioinfweb.treegraph.document.Document

getTree(int) - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument

getTree() - Method in class info.bioinfweb.treegraph.document.Legends

getTreeComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes treeComboBox

getTreeDistance() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

getTreeElement(int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getTreeScrollPane() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes scrollPane

getTreeViewInputListener() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

getTreeViewPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.TreeSelectionDialog

This method initializes treeViewPanel

getTreeViewPanel() - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeInternalFrame

This method initializes treeViewPanel

getTreeWidthRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes rightRadioButton

getType() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickToken

getType(TreePositioner) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

getType(TreePainter) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory

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

This method initializes underlineCheckBox

getUndoManager() - Method in class info.bioinfweb.treegraph.document.Document

getUndoMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes undoMenu

getUndoPresentationName() - Method in class info.bioinfweb.treegraph.document.undo.DocumentEdit

getUniqueName() - Method in class info.bioinfweb.treegraph.document.Node

The unique name is used to identify nodes in the XML-file which are associated with legends.

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

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

getUnitComboBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes unitComboBox

getUnterminatedCommentException(int) - Static method in exception info.bioinfweb.treegraph.document.io.newick.NewickException

getUnterminatedNameException(int) - Static method in exception info.bioinfweb.treegraph.document.io.newick.NewickException

getUpButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog

This method initializes upButton

getUpperBorder() - Method in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.IntervalDialog

getUpperToolBar() - Method in class info.bioinfweb.treegraph.gui.mainframe.ToolBarPanel

This method initializes fileviewWindowToolBar

getUpRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LegendPanel

This method initializes upRadioButton

getValue() - Method in class info.bioinfweb.treegraph.document.format.operate.AbstractMarginOperator

getValue(String) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction

getValue(NodeBranchDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.calculatecolumn.IDFunction

getValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput

getValue() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleValueInput

getValue(NodeBranchDataAdapter, Node) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatsTableModel

getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel

getValueAt(int, int) - Method in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel

getValues() - Method in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

getValuesPanel() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

This method initializes valuesPanel

getValueTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.editelement.AbstractTextElementDialog

This method initializes textTextField

getVector(Node, boolean, boolean, boolean, boolean) - Static method in class info.bioinfweb.treegraph.document.IDManager

Returns a vector of IDs which is sorted alphabetically.

getVersion() - Method in class info.bioinfweb.treegraph.document.Document

getVersion() - Method in class info.bioinfweb.treegraph.Main

getViewMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes viewMenu

getWarningsMessages() - Method in class info.bioinfweb.treegraph.document.undo.SaveLegendsEdit

getWhitespaceCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog

This method initializes whitespaceCheckBox

getWidth() - Method in class info.bioinfweb.treegraph.document.format.DistanceDimension

getWidth() - Method in class info.bioinfweb.treegraph.document.format.ScaleBarFormats

getWidth() - Method in class info.bioinfweb.treegraph.document.position.LegendPositionData

getWidth() - Method in class info.bioinfweb.treegraph.document.position.PositionData

getWidthTextField() - Method in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog

This method initializes widthTextField

getWikiHelp() - Method in class info.bioinfweb.treegraph.Main

getWindowListener() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

getWindowMenu() - Method in class info.bioinfweb.treegraph.gui.mainframe.MainFrame

This method initializes windowMenu

getWordsOnlyCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog

This method initializes wordsOnlyCheckBox

getWordsOnlyCheckBox() - Method in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

This method initializes wordsOnlyCheckBox

getWriter() - Method in class info.bioinfweb.treegraph.document.io.newick.NewickFactory

getWriter() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusFactory

getWriter() - Method in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLFactory

getWriter(ReadWriteFormat) - Method in class info.bioinfweb.treegraph.document.io.ReadWriteFactory

getWriter() - Method in interface info.bioinfweb.treegraph.document.io.SingleReadWriteFactory

getWriter() - Method in class info.bioinfweb.treegraph.document.io.tgf.TGFFactory

getWriter() - Method in class info.bioinfweb.treegraph.document.io.xtg.XTGFactory

getWriter() - Method in interface info.bioinfweb.treegraph.graphics.export.GraphicsFactory

getWriter(GraphicFormat) - Method in class info.bioinfweb.treegraph.graphics.export.GraphicWriterFactory

getWriter() - Method in class info.bioinfweb.treegraph.graphics.export.SingletonGraphicsFactory

getZeroLeftRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes zeroLeftRadioButton

getZeroPosGroup() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

getZeroRightRadioButton() - Method in class info.bioinfweb.treegraph.gui.dialogs.elementformats.ScaleBarPanel

This method initializes ueroRightRadioButton

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToHeightAction

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthAction

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.FitZoomToWidthHeightAction

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetUserZoomAction

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomAction

getZoom(ActionEvent, TreeInternalFrame) - Method in class info.bioinfweb.treegraph.gui.actions.view.SetZoomToOriginalAction

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

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

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

GlobalFormatsDialog - Class in info.bioinfweb.treegraph.gui.dialogs

GlobalFormatsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

GlobalFormatsEdit - Class in info.bioinfweb.treegraph.document.undo.format

GlobalFormatsEdit(Document, GlobalFormats) - Constructor for class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit

gplEditorPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

gplPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

gplScrollPane - Variable in class info.bioinfweb.treegraph.gui.dialogs.AboutDialog

GraphicFilter - Class in info.bioinfweb.treegraph.graphics.export

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

GraphicFormat - Enum in info.bioinfweb.treegraph.graphics.export

GraphicFormat() - Constructor for enum info.bioinfweb.treegraph.graphics.export.GraphicFormat

GraphicsFactory - Interface in info.bioinfweb.treegraph.graphics.export

GraphicWriter - Interface in info.bioinfweb.treegraph.graphics.export

GraphicWriterFactory - Class in info.bioinfweb.treegraph.graphics.export

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

GraphicWriterHints - Class in info.bioinfweb.treegraph.graphics.export

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

greenFactor - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit