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

C

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.AddCalculator

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.ExpCalculator

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.LogCalculator

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.MultiplyCalculator

calculate(double) - Method in interface info.bioinfweb.treegraph.gui.dialogs.datatable.math.NodeDataCalculator

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.PowerCalculator

calculate(double) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.RescaleCalculator

calculateEdgeRadiusShift(Node, float) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramPositioner

This method is overwritten to ensure that no edge radius in painted.

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

Returns the space between the right of the node and the real position of the node line dependant of the y position.

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

calculateLabelBlockDimensions(Labels, boolean) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

calculateMaxNodeData(NodeDataAdapter, Node) - Static method in class info.bioinfweb.treegraph.document.undo.format.NodeBranchDataFormatEdit

Searches for the maximal node data specified by adapter in the subtree under root.

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

calculateScale(Tree, float) - Static method in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit

Returns the branch length scale necessary for the specified tree so that the longest path to a leaf of this tree has the specified length.

calculateTaxonDimension(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

calculateTextDimension(TextElement) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

Calculates the Dimensions of this text element.

calculateWidthsHeights(Node) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

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

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

canUndo() - Method in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit

CAPACITY - Static variable in class info.bioinfweb.treegraph.document.Legends

CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.LabelLine

CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.Labels

CAPACITY_INCREMENT - Static variable in class info.bioinfweb.treegraph.document.Legends

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

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

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

caseSensitive - Variable in class info.bioinfweb.treegraph.document.undo.edit.ApplyNameTableEdit

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

caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.ApplyNameTableDialog

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

caseSensitiveCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.SearchTextDialog

changedFormats - Variable in class info.bioinfweb.treegraph.document.undo.format.OperatorsEdit

Used to store the previous format objects before they are edited to restore them in OperatorsEdit.undo().

changeHappened(ChangeEvent) - Method in interface info.bioinfweb.treegraph.document.DocumentView

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

ChangeIDDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement

ChangeIDDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.ChangeIDDialog

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

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

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

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

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

ChangePainterIDAction - Class in info.bioinfweb.treegraph.gui.actions.view

Allows the user to change the view mode.

ChangePainterIDAction(MainFrame, PositionPaintType) - Constructor for class info.bioinfweb.treegraph.gui.actions.view.ChangePainterIDAction

changeUndefined - Variable in class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit

changeUndefined - Variable in class info.bioinfweb.treegraph.document.undo.format.DistanceValuesByNodeBranchDataEdit

changeUndefinedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

changeUndefinedCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog

checkColor(Color, Color) - Method in class info.bioinfweb.treegraph.document.ContrastManager

Checks if two colors have an unsifficient contast.

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

checkPopup(MouseEvent, ConcretePaintableElement) - Method in class info.bioinfweb.treegraph.gui.treeframe.TreeEditlInputListener

CHILD_COUNT_KEY - Static variable in class info.bioinfweb.treegraph.document.NodeLadderizeComparable

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

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

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

Clears all stored data (labelList, label, subtree).

clear() - Method in class info.bioinfweb.treegraph.document.format.operate.OperatorMap

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

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

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

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

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

Clears this object.

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

Removes all tree elements including all legends from this object.

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

clear() - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataTableModel

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

clearButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.ExportNodeDataDialog

clipboard - Variable in class info.bioinfweb.treegraph.Main

ClipboardContentType - Enum in info.bioinfweb.treegraph.document.clipboard

ClipboardContentType() - Constructor for enum info.bioinfweb.treegraph.document.clipboard.ClipboardContentType

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

Clones this Branch including its Labels-object with the included Labels.

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

Implementing classes should not copy the EnumMap positions because the copy of this element will be located at another position.

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

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

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

clone() - Method in interface info.bioinfweb.treegraph.document.format.ElementFormats

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

clone() - Method in class info.bioinfweb.treegraph.document.format.LabelPositionFormats

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

Returns a deep copy of this class.

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

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

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

clone() - Method in class info.bioinfweb.treegraph.document.format.TextFormats

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

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

Returns a deep copy of this map and its contents.

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

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

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

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

Returns a deep copy of this Labels-object (including copys of all LabelLine-objects and their Labels.

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

Returns a deep copy of this legend.

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

Returns a deep copy of this node not including the subtrees.

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

Returns a deep copy of this node not including the subtrees.

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

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

clone() - Method in class info.bioinfweb.treegraph.document.TextElement

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

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

Returns a deep copy of this text label.

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

Clones this object and all objects in this subtree and its afferent branch.

CloseAction - Class in info.bioinfweb.treegraph.gui.actions.file

CloseAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.CloseAction

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

CmdProcessor - Class in info.bioinfweb.treegraph.cmd

CmdProcessor() - Constructor for class info.bioinfweb.treegraph.cmd.CmdProcessor

cmdProcessor - Variable in class info.bioinfweb.treegraph.Main

COL_BRANCH_LENGTH_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

COL_UNIQUE_NAME_DATA_TYPE - Static variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

collapseDone - Variable in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit

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

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

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

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

collapseNodeEdit - Variable in class info.bioinfweb.treegraph.document.undo.edit.RemoveSubtreeEdit

color - Variable in class info.bioinfweb.treegraph.document.format.operate.LineColorOperator

color - Variable in class info.bioinfweb.treegraph.document.format.operate.TextColorOperator

ColorAdapter - Interface in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters

ColorAdapterListModel - Class in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata

ColorAdapterListModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorAdapterListModel

colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

colorChooser - Variable in class info.bioinfweb.treegraph.gui.dialogs.GlobalFormatsDialog

colorMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.FontColorPanel

colorMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

colorPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

ColorPreviewPanel - Class in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata

ColorPreviewPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorPreviewPanel

colorPreviewPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

ColorsByNodeBranchDataAction - Class in info.bioinfweb.treegraph.gui.actions.format

ColorsByNodeBranchDataAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction

ColorsByNodeBranchDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata

ColorsByNodeBranchDataDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

ColorsByNodeBranchDataEdit - Class in info.bioinfweb.treegraph.document.undo.format

ColorsByNodeBranchDataEdit(Document, NodeDataAdapter, Color, Color, boolean, boolean, ColorAdapter[]) - Constructor for class info.bioinfweb.treegraph.document.undo.format.ColorsByNodeBranchDataEdit

comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.DecimalUnitInput

comboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput

COMMAND_PATTERN - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

COMMAND_SEPARATOR - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

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

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

COMMENT_END - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars

COMMENT_END - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

COMMENT_START - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars

COMMENT_START - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser

compareLists(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

Checks if the elements in the given lists have the same names as the elements of this list.

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

Calculates which of the two target nodes is further upwards in the tree.

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

Compares which node has more (or less) nodes in its subtree.

ComplexDocumentEdit - Class in info.bioinfweb.treegraph.document.undo

This class is the ancestor to all edits that are too complex to have an own undo() method.

ComplexDocumentEdit(Document) - Constructor for class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

compressionMethodComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.TIFFPrefPanel

compressionMethodLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.TIFFPrefPanel

ConcretePaintableElement - Class in info.bioinfweb.treegraph.document

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

confirmChange() - Method in class info.bioinfweb.treegraph.document.ContrastManager

Asks the user whether to change any colors if this was not already done.

CONFLICT_DECIMAL_FORMAT - Static variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

CONFLICT_NAME - Static variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

conflictAdapter - Variable in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

constantWidth - Variable in class info.bioinfweb.treegraph.document.format.BranchFormats

constantWidth - Variable in class info.bioinfweb.treegraph.document.format.operate.ConstantWidthOperator

constantWidthCheckBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel

constantWidthMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.BranchPanel

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

ConstantWidthOperator(boolean) - Constructor for class info.bioinfweb.treegraph.document.format.operate.ConstantWidthOperator

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

Tests whether an element is contained in the subtree of this node including all of its Nodes, Branches and Labels.

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

Returns a list of the ids of the labels that are currently selected.

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

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

Tests if the specified label is contained in the specified block (above or below the branch).

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

Tests if the specified label is contained in this object.

contains(float, float, float) - Method in class info.bioinfweb.treegraph.document.LegendPositionData

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

contains(DistanceValue, DistanceValue, float) - Method in class info.bioinfweb.treegraph.document.PositionData

contains(float, float, float) - Method in class info.bioinfweb.treegraph.document.PositionData

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

Tests if the given element is present in the tree.

contains(Node) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

contains(double, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

contains(String, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

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

containsAllNames(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

Tests if the given list contains elements with the same text values as this list.

containsAnyNameAndOther(NodeDataAdapter, AddSupportValuesEdit.LeafList, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit.LeafList

Tests if the given list contains at least one element that has the same text value as one element in this list and additionally contains at least one element with a text value that is not contained in this list.

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

containsDecimal(NodeDataAdapter, Node) - Static method in class info.bioinfweb.treegraph.document.Tree

Tests if the subtree unter root contains a node which would be able to return a decimal value to the given adapter.

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

Tests if the tree contains a node which would be able to return a decimal value to the given adapter.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Tests if the specified map contains one or more IDs that are also contained in this map.

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

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

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

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

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

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

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

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

ContrastManager - Class in info.bioinfweb.treegraph.document

Ensures that document elements (that are e.g. pasted from the clipboard) have a sufficient contrast to the document background.

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

contrastManager - Variable in class info.bioinfweb.treegraph.gui.actions.edit.PasteAction

ContrastManager.State - Enum in info.bioinfweb.treegraph.document

ContrastManager.State() - Constructor for enum info.bioinfweb.treegraph.document.ContrastManager.State

CONVERT_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor

convertToPixels(String) - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog

convertValue(JTextField, ItemEvent) - Method in class info.bioinfweb.treegraph.gui.dialogs.exporttographic.ExportToGraphicDialog

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

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

copyBranchData(Branch, Branch) - Method in class info.bioinfweb.treegraph.document.undo.edit.RerootEdit

copyButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog

copyColumn(boolean, NodeDataAdapter, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

copyDialog - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.DataTableDialog

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

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

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

copyLabelBlock(Labels, boolean) - Method in class info.bioinfweb.treegraph.document.clipboard.TreeClipboard

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

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

CopyNodeDataDialog - Class in info.bioinfweb.treegraph.gui.dialogs.datatable

CopyNodeDataDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog

copyPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.CopyNodeDataDialog

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

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

copySubtree(Node, boolean, NodeDataAdapter, NodeDataAdapter) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel

cornerRadiusInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.LinePanel

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

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

Sets all the childCount values of the contained Node-objects.

createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.HiddenDataAdapter

createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.LabelAdapter

createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter

createData(Node) - Method in class info.bioinfweb.treegraph.document.nodedata.TextElementDataAdapter

This method should create the data object if does not already exist.

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ApplyNameTableAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ChangeLabelIDAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchLengthAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditBranchNodeDataAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.EditTextElementAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.edit.ReplaceInNodeDataAction

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

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.AddSupportValuesAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToGraphicAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.ExportToNewickNexusAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.file.OpenAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.ColorsByNodeBranchDataAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.DistanceValuesByNodeBranchDataAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.EditElementFormatsAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.EditGlobalFormatsAction

createDialog() - Method in class info.bioinfweb.treegraph.gui.actions.format.ScaleBranchLengthsAction

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFactory

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFactory

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFactory

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFactory

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

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFactory

createFilter() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFactory

createGraphics(OutputStream, Dimension) - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFWriter

createGraphics(OutputStream, Dimension) - Method in class info.bioinfweb.treegraph.graphics.export.FreeHEPWriter

createInputs(int, Tree) - Method in class info.bioinfweb.treegraph.gui.dialogs.datatable.AssignImportColumnsDialog

createInstance(Document, Document, NodeDataAdapter, AddSupportValuesEdit.TargetType, String, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

Returns a new instance of AddSupportValuesEdit or null if the given source document contains internal node names that are not decimal.

createInstance(Document, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.format.ShowHideScaleBarEdit

createInstance(Document, boolean) - Static method in class info.bioinfweb.treegraph.document.undo.format.ShowRootedEdit

createLegend(Node, Legends) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils

Creates a legend to be inserted in the specified document.

createNode(Node) - Static method in class info.bioinfweb.treegraph.document.format.FormatUtils

Creates a node with an afferent branch to be inserted in the specified document.

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

Creates a node with an afferent branch to be inserted in the specified document.

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

createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog

createTargetListModel() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.FormatsByNodeBranchDataDialog

Implementing classes can specify their target list model here.

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.emf.EMFFactory

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.jpeg.JPEGFactory

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.pdf.PDFFactory

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.png.PNGFactory

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

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.svg.SVGFactory

createWriter() - Method in class info.bioinfweb.treegraph.graphics.export.tiff.TIFFFactory

CURRENT_DIR_PREF_KEY - Static variable in class info.bioinfweb.treegraph.gui.CurrentDirectoryModel

CurrentDirectoryModel - Class in info.bioinfweb.treegraph.gui

CurrentDirectoryModel() - Constructor for class info.bioinfweb.treegraph.gui.CurrentDirectoryModel

currentIDs - Variable in class info.bioinfweb.treegraph.document.undo.edit.AssignLabelIDsEdit

currentMin - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.math.RescaleCalculator

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

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

customizeComboBox(JComboBox) - Method in class info.bioinfweb.treegraph.gui.dialogs.DistanceValueInput

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

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

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

customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.ColorsByNodeBranchDataDialog

customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.DistanceValuesByNodeBranchDataDialog

customizeTarget() - Method in class info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.FormatsByNodeBranchDataDialog

This method is called from FormatsByNodeBranchDataDialog.onExecute().

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

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

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

The impelemention of this edit is the same as it is at DeleteEdit.

CutEdit(Document, ConcretePaintableElement[]) - Constructor for class info.bioinfweb.treegraph.document.undo.edit.CutEdit