Uses of Interface
info.bioinfweb.treegraph.document.nodedata.NodeDataAdapter

Packages that use NodeDataAdapter

info.bioinfweb.treegraph.document	Contains the classes that represent the data structure of TreeGraph 2 (document elements and formats) as well as all edit operations in the undo-package to manipulate the data structure and classes to read and write a document from and to different formats (io- subpackage).
info.bioinfweb.treegraph.document.io	Contains classes necessary to read and write the data structure of a TreeGraph 2 document from and to different formats.
info.bioinfweb.treegraph.document.io.newick
info.bioinfweb.treegraph.document.io.nexus
info.bioinfweb.treegraph.document.io.tgf
info.bioinfweb.treegraph.document.io.xtg
info.bioinfweb.treegraph.document.nodedata
info.bioinfweb.treegraph.document.undo.edit
info.bioinfweb.treegraph.document.undo.format
info.bioinfweb.treegraph.gui.dialogs.datatable
info.bioinfweb.treegraph.gui.dialogs.nodedatainput

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document

Methods in info.bioinfweb.treegraph.document with parameters of type NodeDataAdapter

boolean	Tree.containsDecimal(NodeDataAdapter adapter) Tests if the tree contains a node which would be able to return a decimal value to the given adapter.
static boolean	Tree.containsDecimal(NodeDataAdapter adapter, Node root) Tests if the subtree unter root contains a node which would be able to return a decimal value to the given adapter.

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.io

Methods in info.bioinfweb.treegraph.document.io with parameters of type NodeDataAdapter

Document	DocumentReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
Document	AbstractDocumentReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
Document	DocumentReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	AbstractDocumentReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes) If you want to implement file specific functionalities you should override this method.
Document	DocumentReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
Document	AbstractDocumentReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
Document	DocumentReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
void	DocumentWriter.write(Document document, File file, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)
void	AbstractDocumentWriter.write(Document document, File file, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)
void	DocumentWriter.write(Document document, OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.io.newick

Methods in info.bioinfweb.treegraph.document.io.newick with parameters of type NodeDataAdapter

private static String	NewickStringWriter.formatName(Node node, NodeDataAdapter adapter)
Document	NewickReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals)
Document	NewickReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals)
static Tree	NewickStringReader.read(String newick, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
static Tree	NewickStringReader.read(String newick, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
private static Node	NewickStringReader.readBranch(Vector<NewickToken> tokens, int start, int end, Node root, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static void	NewickStringReader.readBranchList(Vector<NewickToken> tokens, int start, int end, Node root, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static Node	NewickStringReader.readInternal(Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static void	NewickStringReader.readName(Vector<NewickToken> tokens, int previousEnd, int end, Node root, NodeDataAdapter internalAdapter, TranslTable translTable)
private static Node	NewickStringReader.readSubtree(Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static Tree	NewickStringReader.readTree(Vector<NewickToken> tokens, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
void	NewickWriter.write(Document document, OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)
static String	NewickStringWriter.write(Tree tree, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)
private static String	NewickStringWriter.writeSubtree(Node root, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.io.nexus

Methods in info.bioinfweb.treegraph.document.io.nexus with parameters of type NodeDataAdapter

Document	NexusReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	NexusReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes)
void	NexusWriter.write(Document document, OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.io.tgf

Methods in info.bioinfweb.treegraph.document.io.tgf with parameters of type NodeDataAdapter

Document

TGFReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.io.xtg

Methods in info.bioinfweb.treegraph.document.io.xtg with parameters of type NodeDataAdapter

Document	XTGReader.read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
Document	XTGReader.read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
void	XTGWriter.write(Document document, OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter) A call of this method is identical with calling XTGWriter.write(info.bioinfweb.treegraph.document.Document, java.io.OutputStream) becuase the tgx format supports writing any number of labels by default and there is no need to replace internal node names by label values.

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.nodedata

Classes in info.bioinfweb.treegraph.document.nodedata that implement NodeDataAdapter

class	AbstractIDElementAdapter Node data adapters that need to store an ID can be inherited from this abstract class.
class	BranchLengthAdapter
class	HiddenBranchDataAdapter
class	HiddenDataAdapter
class	HiddenNodeDataAdapter
class	LabelAdapter
class	NewHiddenBranchDataAdapter Creates a new hidden branch data column.
class	NewHiddenNodeDataAdapter Creates a new hidden node data column.
class	NewLabelAdapter Creates a new group of labels.
class	NodeNameAdapter
class	TextElementDataAdapter This abstract class implements basic funktionalities for adapters that deal with data stored in a TextElementData-object.
class	UniqueNameAdapter

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.undo.edit

Fields in info.bioinfweb.treegraph.document.undo.edit declared as NodeDataAdapter

private NodeDataAdapter	RescaleNodeDataEdit.adapter
private NodeDataAdapter	ReplaceInNodeDataEdit.adapter
private NodeDataAdapter	ApplyNameTableEdit.adapter
private NodeDataAdapter	AddSupportValuesEdit.conflictAdapter
private NodeDataAdapter	AddSupportValuesEdit.sourceAdapter
private NodeDataAdapter	AddSupportValuesEdit.supportAdapter
private NodeDataAdapter	AddSupportValuesEdit.terminalsAdapter

Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type NodeDataAdapter

String	AddSupportValuesEdit.LeafList.compareLists(NodeDataAdapter listAdapter, AddSupportValuesEdit.LeafList other, NodeDataAdapter otherAdapter) Checks if the elements in the given lists have the same names as the elements of this list.
boolean	AddSupportValuesEdit.LeafList.contains(double value, NodeDataAdapter adapter)
boolean	AddSupportValuesEdit.LeafList.contains(String value, NodeDataAdapter adapter)
boolean	AddSupportValuesEdit.LeafList.containsAllNames(NodeDataAdapter listAdapter, AddSupportValuesEdit.LeafList other, NodeDataAdapter otherAdapter) Tests if the given list contains elements with the same text values as this list.
boolean	AddSupportValuesEdit.LeafList.containsAnyNameAndOther(NodeDataAdapter listAdapter, AddSupportValuesEdit.LeafList other, NodeDataAdapter otherAdapter) Tests if the given list contains at least one element that has the same text value as one element in this list and additionally contains at least one element with a text value that is not contained in this list.
static AddSupportValuesEdit	AddSupportValuesEdit.createInstance(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, boolean importNodeNames) Returns a new instance of AddSupportValuesEdit or null if the given source document contains internal node names that are not decimal.
Node	AddSupportValuesEdit.LeafList.get(double value, NodeDataAdapter adapter)
Node	AddSupportValuesEdit.LeafList.get(String value, NodeDataAdapter adapter)
private static boolean	AddSupportValuesEdit.internalsAreDecimal(Node root, NodeDataAdapter adapter) Tests if all internal nodes in the subtree under root contain decimal values.

Constructors in info.bioinfweb.treegraph.document.undo.edit with parameters of type NodeDataAdapter

AddSupportValuesEdit(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, NodeDataAdapter sourceAdapter)

ApplyNameTableEdit(Document document, NodeDataAdapter adapter, List<String> oldNames, List<String> newNames, boolean ignoreWhitespaces, boolean caseSensitive, boolean parseNumericValues)

ReplaceInNodeDataEdit(Document document, NodeDataAdapter adapter, ReplaceInNodeDataEdit.InsertPosition position, String oldText, String newText, boolean caseSensitive, boolean wordsOnly)

RescaleNodeDataEdit(Document document, NodeDataAdapter adapter, double factor, double addend)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.document.undo.format

Fields in info.bioinfweb.treegraph.document.undo.format declared as NodeDataAdapter

private NodeDataAdapter	DistanceValuesByNodeBranchDataEdit.sourceAdapter
private NodeDataAdapter	ColorsByNodeBranchDataEdit.sourceAdapter

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type NodeDataAdapter

static double

NodeBranchDataFormatEdit.calculateMaxNodeData(NodeDataAdapter adapter, Node root) Searches for the maximal node data specified by adapter in the subtree under root.

Constructors in info.bioinfweb.treegraph.document.undo.format with parameters of type NodeDataAdapter

ColorsByNodeBranchDataEdit(Document document, NodeDataAdapter sourceAdapter, Color min, Color max, boolean changeUndefined, boolean inheritToTerminals, ColorAdapter[] targetAdapters)

DistanceValuesByNodeBranchDataEdit(Document document, NodeDataAdapter sourceAdapter, float min, float max, boolean changeUndefined, boolean inheritToTerminals, DistanceAdapter[] targetAdapters)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.gui.dialogs.datatable

Fields in info.bioinfweb.treegraph.gui.dialogs.datatable with type parameters of type NodeDataAdapter

private Vector<NodeDataAdapter>	NodeDataTableModel.adapters
private Vector<NodeDataAdapter>	ExportNodeDataTableModel.adapters

Methods in info.bioinfweb.treegraph.gui.dialogs.datatable that return NodeDataAdapter

NodeDataAdapter[]	AssignImportColumnsDialog.execute(int count, Tree tree)
NodeDataAdapter	ExportNodeDataTableModel.get(int index)
NodeDataAdapter	NodeDataTableModel.getAdapter(int col)
NodeDataAdapter	CopyNodeDataDialog.getDestAdapter()
NodeDataAdapter	CopyNodeDataDialog.getSrcAdapter()
NodeDataAdapter	ExportNodeDataTableModel.remove(int index)
NodeDataAdapter	ExportNodeDataTableModel.set(int index, NodeDataAdapter adapter)

Methods in info.bioinfweb.treegraph.gui.dialogs.datatable with parameters of type NodeDataAdapter

boolean	ExportNodeDataTableModel.add(NodeDataAdapter adapter)
void	NodeDataTableModel.copyColumn(boolean includeLeafs, NodeDataAdapter src, NodeDataAdapter dest)
private void	NodeDataTableModel.copySubtree(Node root, boolean includeLeafs, NodeDataAdapter src, NodeDataAdapter dest)
private void	NodeDataTableModel.deleteOutsideIntervalSubtree(Node root, NodeDataAdapter adapter, double upperBorder, double lowerBorder)
private void	NodeDataTableModel.deleteSubtree(Node root, NodeDataAdapter adapter)
boolean	NodeDataTableModel.importData(NodeDataAdapter[] adapters, String[][] data)
private void	NodeDataTableModel.rescaleSubtree(Node root, NodeDataAdapter adapter, NodeDataCalculator calculator)
NodeDataAdapter	ExportNodeDataTableModel.set(int index, NodeDataAdapter adapter)

Uses of NodeDataAdapter in info.bioinfweb.treegraph.gui.dialogs.nodedatainput

Fields in info.bioinfweb.treegraph.gui.dialogs.nodedatainput declared as NodeDataAdapter

private NodeDataAdapter

NodeDataComboBoxModel.selected

Fields in info.bioinfweb.treegraph.gui.dialogs.nodedatainput with type parameters of type NodeDataAdapter

private Vector<NodeDataAdapter>

NodeDataComboBoxModel.adapters

Methods in info.bioinfweb.treegraph.gui.dialogs.nodedatainput that return NodeDataAdapter

NodeDataAdapter	NodeDataComboBoxModel.getElementAt(int pos)
NodeDataAdapter	NodeDataComboBoxModel.getSelectedItem()
NodeDataAdapter	NodeDataInput.selectedAdapter() Returns the currently selected adapter.
NodeDataAdapter	NewNodeDataInput.selectedAdapter()

Method parameters in info.bioinfweb.treegraph.gui.dialogs.nodedatainput with type arguments of type NodeDataAdapter

boolean	NodeDataInput.setSelectedAdapter(Class<? extends NodeDataAdapter> adapterClass) Selects the adapter which is an instance (not instance of a subclass) of the given class.
boolean	NodeDataComboBoxModel.setSelectedAdapter(Class<? extends NodeDataAdapter> adapterClass) Selects the adapter which is an instance (not instance of a subclass) of the given class.