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

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

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

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(java.io.InputStream stream, NodeDataAdapter internalAdapter, 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(java.io.File file, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternalNodes)`
`Document` | `XTGReader.read(java.io.InputStream stream, NodeDataAdapter internalAdapter, TreeSelector selector, boolean translateInternalNodes)`
`void` | `XTGWriter.write(Document document, java.io.OutputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter)` 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 static NodeDataAdapter` | `AddSupportValuesEdit.SOURCE_ADAPTER`
`private NodeDataAdapter` | `AddSupportValuesEdit.supportAdapter`
`private NodeDataAdapter` | `AddSupportValuesEdit.terminalsAdapter`

Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type NodeDataAdapter
`java.lang.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(java.lang.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, java.lang.String idPrefix)` 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(java.lang.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, java.lang.String idPrefix)`
`ApplyNameTableEdit(Document document, NodeDataAdapter adapter, java.util.List<java.lang.String> oldNames, java.util.List<java.lang.String> newNames, boolean ignoreWhitespaces, boolean caseSensitive, boolean parseNumericValues)`
`ReplaceInNodeDataEdit(Document document, NodeDataAdapter adapter, ReplaceInNodeDataEdit.InsertPosition position, java.lang.String oldText, java.lang.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` | `ColorsFromNodeDataEdit.adapter`
`private NodeDataAdapter` | `BranchWidthsFromNodeDataEdit.adapter`

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type NodeDataAdapter
`static double` | `NodeDataFormatEdit.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
`BranchWidthsFromNodeDataEdit(Document document, NodeDataAdapter adapter, double min, double max, boolean changeUndefined)`
`ColorsFromNodeDataEdit(Document document, NodeDataAdapter adapter, java.awt.Color min, java.awt.Color max, boolean changeUndefined)`

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 java.util.Vector<NodeDataAdapter>` | `NodeDataTableModel.adapters`
`private java.util.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.deleteSubtree(Node root, NodeDataAdapter adapter)`
`boolean` | `NodeDataTableModel.importData(NodeDataAdapter[] adapters, java.lang.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 java.util.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(java.lang.Class<? extends NodeDataAdapter> adapterClass)` Selects the adapter which is an instance (not instance of a subclass) of the given class.
`boolean` | `NodeDataComboBoxModel.setSelectedAdapter(java.lang.Class<? extends NodeDataAdapter> adapterClass)` Selects the adapter which is an instance (not instance of a subclass) of the given class.

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