Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

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

## 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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

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