Home / Development / Documentation / 2.0.44 / N-Index

Download

System requirements

How to install

License

Help

Alphabetical index

Tutorials

Categories

Random page

Development

Subversion repository

Recent changes

Source download

Documentation

Latest Javadoc

XTG format

Libraries and tools

Publications

Version 1

Subversion repository

About

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