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.newickThis 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.editelementDialog 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.nodebranchdataThis 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.editelementDialog 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.nodebranchdataCreates a new group of labels.NewTextLabelAdapter() -
Constructor for class info.bioinfweb.treegraph.document.nodebranchdata.NewTextLabelAdapter
NewTextLabelDialog - Class in info.bioinfweb.treegraph.gui.dialogs.editelementDialog 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.nexusFilter 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.nexusThis 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.documentThis 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.nodebranchdataThis 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.undoUsed 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.undoCan 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.documentThis 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.elementformatsPanel 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.documentThrown 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
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