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

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

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

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

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

NewHiddenBranchDataAdapter - Class in info.bioinfweb.treegraph.document.nodedata

NewHiddenBranchDataAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodedata.NewHiddenBranchDataAdapter

NewHiddenNodeDataAdapter - Class in info.bioinfweb.treegraph.document.nodedata

NewHiddenNodeDataAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodedata.NewHiddenNodeDataAdapter

NewickException - Exception in info.bioinfweb.treegraph.document.io.newick

NewickException(int) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException

NewickException(int, String) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException

NewickException(int, TokenType, TokenType) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException

NewickException(NewickToken) - Constructor for exception info.bioinfweb.treegraph.document.io.newick.NewickException

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

NewickReader - Class in info.bioinfweb.treegraph.document.io.newick

NewickReader() - Constructor for class info.bioinfweb.treegraph.document.io.newick.NewickReader

Contructs an instance of NewickReader with a info.bioinfweb.treegraph.document.io.newick.DefaultNewickSelector.

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

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.AssignLabelIDsEdit

newIDSelected(boolean) - Method in interface info.bioinfweb.treegraph.gui.dialogs.nodedatainput.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.

NewLabelAdapter - Class in info.bioinfweb.treegraph.document.nodedata

NewLabelAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodedata.NewLabelAdapter

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

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

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

newNameTextField - Variable in class info.bioinfweb.treegraph.gui.dialogs.RenameIDDialog

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

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

NewNodeDataAdapter - Interface in info.bioinfweb.treegraph.document.nodedata

NewNodeDataInput - Class in info.bioinfweb.treegraph.gui.dialogs.nodedatainput

NewNodeDataInput(JPanel, int, int, boolean) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NewNodeDataInput

newParent - Variable in class info.bioinfweb.treegraph.document.undo.edit.InsertSiblingEdit

newRoot - Variable in class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

newRoot - Variable in class info.bioinfweb.treegraph.document.undo.edit.EditNodeBranchDataEdit

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

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

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.

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

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

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

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

Contructs an instance of NexusReader with a info.bioinfweb.treegraph.document.io.nexus.DefaultNexusSelector.

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

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

NodeDataActionNotSupportedException - Exception in info.bioinfweb.treegraph.document.nodedata

NodeDataActionNotSupportedException() - Constructor for exception info.bioinfweb.treegraph.document.nodedata.NodeDataActionNotSupportedException

NodeDataActionNotSupportedException(String, Throwable) - Constructor for exception info.bioinfweb.treegraph.document.nodedata.NodeDataActionNotSupportedException

NodeDataActionNotSupportedException(String) - Constructor for exception info.bioinfweb.treegraph.document.nodedata.NodeDataActionNotSupportedException

NodeDataActionNotSupportedException(Throwable) - Constructor for exception info.bioinfweb.treegraph.document.nodedata.NodeDataActionNotSupportedException

NodeDataAdapter - Interface in info.bioinfweb.treegraph.document.nodedata

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

NodeDataCalculator - Interface in info.bioinfweb.treegraph.gui.dialogs.datatable.math

This interface should be implemented by all classes that are able to rescale or recalculate decimal node data in any way.

nodeDataComboBox - Variable in class info.bioinfweb.treegraph.gui.dialogs.BranchWidthFromNodeDataDialog

NodeDataComboBoxModel - Class in info.bioinfweb.treegraph.gui.dialogs.nodedatainput

NodeDataComboBoxModel() - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataComboBoxModel

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

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

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

nodeDataInput - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.OpenDialog

NodeDataInput - Class in info.bioinfweb.treegraph.gui.dialogs.nodedatainput

NodeDataInput(JPanel, int, int) - Constructor for class info.bioinfweb.treegraph.gui.dialogs.nodedatainput.NodeDataInput

NodeDataInputListener - Interface in info.bioinfweb.treegraph.gui.dialogs.nodedatainput

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

nodeDataLabel - Variable in class info.bioinfweb.treegraph.gui.dialogs.BranchWidthFromNodeDataDialog

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

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

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

nodeDataPanel - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.ExportToNewickStringDialog

nodeDataRadioButton - Variable in class info.bioinfweb.treegraph.gui.dialogs.io.AddSupportValuesDialog

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

This table model allows to display all branch and node data in a table.

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

NodeFormats - Class in info.bioinfweb.treegraph.document.format

NodeFormats() - Constructor for class info.bioinfweb.treegraph.document.format.NodeFormats

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

nodeMargin - Variable in class info.bioinfweb.treegraph.document.format.GlobalFormats

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

NodeNameAdapter - Class in info.bioinfweb.treegraph.document.nodedata

NodeNameAdapter() - Constructor for class info.bioinfweb.treegraph.document.nodedata.NodeNameAdapter

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

NodePositionData - Class in info.bioinfweb.treegraph.document

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

nodePresent - Variable in class info.bioinfweb.treegraph.gui.treeframe.TreeSelection

nodes - Variable in class info.bioinfweb.treegraph.gui.dialogs.datatable.NodeDataTableModel