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TreeGraph 2
 

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N

name - Variable in class info.bioinfweb.treegraph.document.io.nexus.NexusCommand
 
name() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
 
name() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
 
name() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
Returns the name of this view mode.
NAME_BLOCK_BEGIN - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_BLOCK_END - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_DELIMITER - Static variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
 
NAME_DELIMITER - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_NEXUS - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_SEPARATOR_PATTERN - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_TRANSL_TABLE - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NAME_TREES - Static variable in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
nameList - Variable in class info.bioinfweb.treegraph.document.io.nexus.TranslTable
 
nameManager - Variable in class info.bioinfweb.treegraph.Main
 
names - Variable in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
 
names - Variable in class info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
 
names() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
 
NAMESPACE_URI - Static variable in interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants
 
NAMESPACE_URI - Static variable in interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
 
namesToArray() - Method in class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
 
needsBrancheLengths(PositionPaintType) - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PositionPaintFactory
 
needsBranchLengths() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.PhylogramFactory
 
needsBranchLengths() - Method in class info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramFactory
 
needsBranchLengths() - Method in interface info.bioinfweb.treegraph.graphics.positionpaint.SinglePositionPaintFactory
 
negativeExampleLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.DecimalFormatPanel
 
newAnchors - Variable in class info.bioinfweb.treegraph.document.undo.format.ReanchorLegendEdit
 
newData - Variable in class info.bioinfweb.treegraph.document.undo.edit.TextElementEdit
 
NewDocumentAction - Class in info.bioinfweb.treegraph.gui.actions.file
 
NewDocumentAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.file.NewDocumentAction
 
newFormats - Variable in class info.bioinfweb.treegraph.document.undo.format.GlobalFormatsEdit
 
NewGraphicalLabelsDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
Implements basic functionalities for dialogs used to created graphical labels.
NewGraphicalLabelsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.NewGraphicalLabelsDialog
 
NewHiddenBranchDataAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
Creates a new hidden branch data column.
NewHiddenBranchDataAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenBranchDataAdapter
 
NewHiddenNodeDataAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
Creates a new hidden node data column.
NewHiddenNodeDataAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.NewHiddenNodeDataAdapter
 
NEWICK_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
 
newickDescription - Variable in class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
NewickException - Exception in info.bioinfweb.treegraph.document.io.newick
An instance of this exception is thrown if an input newick string contains a syntactical error and cannot be read.
NewickException(int, String, String) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException
 
NewickException(int, String, TokenType, TokenType) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException
 
NewickException(NewickToken, String) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException
 
NewickExceptionDialog - Class in info.bioinfweb.treegraph.gui.dialogs.io
This dialog is used to display an NewickException.
NewickExceptionDialog(Dialog) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.io.NewickExceptionDialog
 
newickExceptionDialog - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
 
NewickFactory - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickFactory() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickFactory
 
NewickFilter - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickFilter() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickFilter
 
newickFilter - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
 
NewickReader - Class in info.bioinfweb.treegraph.document.io.newick
Reads text files consisting only of Newick strings.
NewickReader() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickReader
Contructs an instance of NewickReader.
NewickReader.Status - Enum in info.bioinfweb.treegraph.document.io.newick
 
NewickReader.Status() - Constructor for enum info.bioinfweb.treegraph.document.io.newick.NewickReader.Status
 
NewickScanner - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickScanner() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickScanner
 
NewickStringChars - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickStringChars() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickStringChars
 
NewickStringReader - Class in info.bioinfweb.treegraph.document.io.newick
This class converts a tree in the Newick format to a Document.
NewickStringReader() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickStringReader
 
NewickStringWriter - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickStringWriter() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickStringWriter
 
NewickToken - Class in info.bioinfweb.treegraph.document.io.newick
 
NewickToken(TokenType, int) - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickToken
 
NewickToken(int, String, boolean) - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickToken
 
NewickToken(int, double) - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickToken
 
NewickWriter - Class in info.bioinfweb.treegraph.document.io.newick
This class writes a Document in a nexus file (contains only the newick string).
NewickWriter() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickWriter
 
NewIconLabelsAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
NewIconLabelsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.NewIconLabelsAction
 
NewIconLabelsDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
Dialog used to add a new icon label to a document.
NewIconLabelsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.NewIconLabelsDialog
 
newID(Vector<String>) - Static method in class info.bioinfweb.treegraph.document.IDManager
 
newID - Variable in class info.bioinfweb.treegraph.document.undo.edit.ChangeLabelIDEdit
 
newIDs - Variable in class info.bioinfweb.treegraph.document.undo.edit.PieChartLabelIDsEdit
 
newIDs - Variable in class info.bioinfweb.treegraph.document.undo.edit.RenameDataIDEdit
 
newIDSelected(boolean) - Method in interface info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataInputListener
This Method is called if the user selects "label with new ID" or "branch data with new ID" from the combo box of NewNodeDataInput.
NewLegendAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
NewLegendAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.NewLegendAction
 
newLength - Variable in class info.bioinfweb.treegraph.document.undo.edit.BranchLengthEdit
 
newMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
 
newNames - Variable in class info.bioinfweb.treegraph.document.undo.file.ApplyNameTableEdit
 
newNameTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.nodebranchdata.RenameIDDialog
 
NewNodeAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
NewNodeAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.NewNodeAction
 
NewNodeBranchDataInput - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
 
NewNodeBranchDataInput(JPanel, int, int, boolean) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NewNodeBranchDataInput
 
NewNodeDataAdapter - Interface in info.bioinfweb.treegraph.document.nodebranchdata
This interface should be implemented by all node data adapters that create a new node data column (e.g. a new group of labels).
newParent - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit
 
NewPieChartLabelsAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
NewPieChartLabelsAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.NewPieChartLabelsAction
 
NewPieChartLabelsDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
Dialog used to create new pie chart labels.
NewPieChartLabelsDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.NewPieChartLabelsDialog
 
newRoot - Variable in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit
 
newRoot - Variable in class info.bioinfweb.treegraph.document.undo.edit.EditNodeBranchDataEdit
 
newScale - Variable in class info.bioinfweb.treegraph.document.undo.format.ScaleBranchLengthsEdit
 
newSibling - Variable in class info.bioinfweb.treegraph.document.undo.edit.PasteSiblingEdit
 
newText - Variable in class info.bioinfweb.treegraph.document.undo.edit.ReplaceInNodeDataEdit
 
NewTextLabelAction - Class in info.bioinfweb.treegraph.gui.actions.edit
 
NewTextLabelAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.edit.NewTextLabelAction
 
NewTextLabelAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
Creates a new group of labels.
NewTextLabelAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.NewTextLabelAdapter
 
NewTextLabelDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelement
Dialog used to add a new text label to a document.
NewTextLabelDialog(Frame) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.editelement.NewTextLabelDialog
 
newUniqueName() - Method in class info.bioinfweb.treegraph.document.Tree
Generates a random unique name for a node which is currently not present in this tree.
newUniqueName() - Method in class info.bioinfweb.treegraph.document.undo.edit.LegendPaster
Returns a new unique name with is neither present in the associated document nor the unique name map.
NextDocumentAction - Class in info.bioinfweb.treegraph.gui.actions.window
 
NextDocumentAction(MainFrame) - Constructor for class info.bioinfweb.treegraph.gui.actions.window.NextDocumentAction
 
nextPosOutsideComment(String, int, char) - Static method in class info.bioinfweb.treegraph.document.io.nexus.NexusParser
Returns the index of the next occurence of character after start which is not located inside a comment.
NEXUS_OPTION - Static variable in class info.bioinfweb.treegraph.cmd.CmdProcessor
 
NexusCommand - Class in info.bioinfweb.treegraph.document.io.nexus
 
NexusCommand(String) - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusCommand
 
NexusCommand(String, String) - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusCommand
 
NexusDocument - Class in info.bioinfweb.treegraph.document.io.nexus
 
NexusDocument() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusDocument
 
NexusError - Enum in info.bioinfweb.treegraph.document.io.nexus
 
NexusError() - Constructor for enum info.bioinfweb.treegraph.document.io.nexus.NexusError
 
NexusException - Exception in info.bioinfweb.treegraph.document.io.nexus
 
NexusException(NexusError) - Constructor for exception info.bioinfweb.treegraph.document.io.nexus.NexusException
 
NexusFactory - Class in info.bioinfweb.treegraph.document.io.nexus
 
NexusFactory() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusFactory
 
NexusFilter - Class in info.bioinfweb.treegraph.document.io.nexus
Filter for Nexus files.
NexusFilter() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusFilter
 
nexusFilter - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
nexusFilter - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
 
nexusFilter - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
 
NexusParser - Class in info.bioinfweb.treegraph.document.io.nexus
 
NexusParser() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusParser
 
NexusReader - Class in info.bioinfweb.treegraph.document.io.nexus
This class reads a tree loads a tree out of a Nexus file.
NexusReader() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusReader
Constructs an instance of NexusReader.
NexusWriter - Class in info.bioinfweb.treegraph.document.io.nexus
 
NexusWriter() - Constructor for class info.bioinfweb.treegraph.document.io.nexus.NexusWriter
 
Node - Class in info.bioinfweb.treegraph.document
This class represents a node of a tree in the TreeGraph data structure.
Node() - Constructor for class info.bioinfweb.treegraph.document.Node
 
node - Variable in class info.bioinfweb.treegraph.document.NodeLadderizeComparable
 
node - Variable in class info.bioinfweb.treegraph.document.undo.edit.CollapseNodeEdit
 
node - Variable in class info.bioinfweb.treegraph.document.undo.edit.SeparateBranchEdit
 
node - Variable in class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
 
NODE_NAMES_VAR - Static variable in class info.bioinfweb.treegraph.document.undo.edit.CalculateColumnEdit
 
NodeBranchDataActionNotSupportedException - Exception in info.bioinfweb.treegraph.document.nodebranchdata
This exception is thrown by node data adapters if an unsupported operation is perfomed (e.g.
NodeBranchDataActionNotSupportedException() - Constructor for exception info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataActionNotSupportedException
 
NodeBranchDataActionNotSupportedException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataActionNotSupportedException
 
NodeBranchDataActionNotSupportedException(String) - Constructor for exception info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataActionNotSupportedException
 
NodeBranchDataActionNotSupportedException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.nodebranchdata.NodeBranchDataActionNotSupportedException
 
NodeBranchDataAdapter - Interface in info.bioinfweb.treegraph.document.nodebranchdata
 
NodeBranchDataBackup - Class in info.bioinfweb.treegraph.document.undo
Used to backup a node/branch data column beforen an edit operation.
NodeBranchDataBackup(NodeBranchDataAdapter, Node) - Constructor for class info.bioinfweb.treegraph.document.undo.NodeBranchDataBackup
 
NodeBranchDataEdit - Class in info.bioinfweb.treegraph.document.undo
Can be used as a superclass for edits which change a node/branch data column.
NodeBranchDataEdit(Document, NodeBranchDataAdapter) - Constructor for class info.bioinfweb.treegraph.document.undo.NodeBranchDataEdit
 
NodeBranchDataFormatEdit - Class in info.bioinfweb.treegraph.document.undo.format
 
NodeBranchDataFormatEdit(Document) - Constructor for class info.bioinfweb.treegraph.document.undo.format.NodeBranchDataFormatEdit
 
NodeBranchDataInput - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
 
NodeBranchDataInput(JPanel, int, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeBranchDataInput
 
nodeBranchDataMenu - Variable in class info.bioinfweb.treegraph.gui.mainframe.MainFrame
 
nodeDataButtonsPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
NodeDataComboBoxModel - Class in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
 
NodeDataComboBoxModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput.NodeDataComboBoxModel
 
nodeDataInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
NodeDataInputListener - Interface in info.bioinfweb.treegraph.gui.dialogs.nodebranchdatainput
 
nodeDataLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
 
nodeDataLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.ReplaceInNodeDataDialog
 
nodeDataPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ApplyNameTableDialog
 
nodeDataPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
nodeDataPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog
 
nodeDataRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
NodeFormats - Class in info.bioinfweb.treegraph.document.format
 
NodeFormats() - Constructor for class info.bioinfweb.treegraph.document.format.NodeFormats
 
NodeInfo - Class in info.bioinfweb.treegraph.document.undo.file.addsupportvalues
 
NodeInfo(Node, int, boolean) - Constructor for class info.bioinfweb.treegraph.document.undo.file.addsupportvalues.NodeInfo
 
NodeLadderizeComparable - Class in info.bioinfweb.treegraph.document
This class is a wrapper class for Node-objects that allowws them to be compared by their number of terminal subnodes.
NodeLadderizeComparable(Node, boolean) - Constructor for class info.bioinfweb.treegraph.document.NodeLadderizeComparable
 
NodeLineColorAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.color
 
NodeLineColorAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.color.NodeLineColorAdapter
 
NodeLineWidthAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
 
NodeLineWidthAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.NodeLineWidthAdapter
 
NodeMarginPanel - Class in info.bioinfweb.treegraph.gui.dialogs.elementformats
Panel of the ElementFormatsDialog used to edit the margin around a terminal node.
NodeMarginPanel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.elementformats.NodeMarginPanel
This is the default constructor
NodeNameAdapter - Class in info.bioinfweb.treegraph.document.nodebranchdata
 
NodeNameAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.NodeNameAdapter
 
nodeNamesDataInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog
 
nodeNamesRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog
 
NodePositionData - Class in info.bioinfweb.treegraph.document.position
 
NodePositionData() - Constructor for class info.bioinfweb.treegraph.document.position.NodePositionData
 
nodes - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportNodeDataTableModel
 
nodes - Variable in class info.bioinfweb.treegraph.gui.treeframe.DocumentTableModel
 
nodesGroup - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
NodesPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportTableDialog
 
NodeTextColorAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.color
 
NodeTextColorAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.color.NodeTextColorAdapter
 
NodeTextHeightAdapter - Class in info.bioinfweb.treegraph.document.format.adapters.distance
 
NodeTextHeightAdapter() - Constructor for class info.bioinfweb.treegraph.document.format.adapters.distance.NodeTextHeightAdapter
 
NoLinkedNodeException - Exception in info.bioinfweb.treegraph.document
Thrown when a method of a tree element is invoked which need to access the linked node, but the element does not have a linked node.
NoLinkedNodeException() - Constructor for exception info.bioinfweb.treegraph.document.NoLinkedNodeException
 
NoLinkedNodeException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.NoLinkedNodeException
 
NoLinkedNodeException(String) - Constructor for exception info.bioinfweb.treegraph.document.NoLinkedNodeException
 
NoLinkedNodeException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.NoLinkedNodeException
 
noneRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.exporttographic.ExportToGraphicDialog
 
nullLinesMonitor - Variable in class info.bioinfweb.treegraph.gui.dialogs.elementformats.IconPieChartLabelPanel
 
NullPieChartLinesOperator - Class in info.bioinfweb.treegraph.document.format.operate
 
NullPieChartLinesOperator(boolean) - Constructor for class info.bioinfweb.treegraph.document.format.operate.NullPieChartLinesOperator
 

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