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## Uses of Class
info.bioinfweb.treegraph.document.Node

Packages that use Node
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.clipboard | Classes in this package implement the clipboard of TreeGraph 2 used to copy document elements (subtrees, labels, legends, ...) between and inside tree documents.
info.bioinfweb.treegraph.document.format | Contains classes that store format information of the different document elements.
info.bioinfweb.treegraph.document.format.adapters.color |
info.bioinfweb.treegraph.document.format.adapters.distance |
info.bioinfweb.treegraph.document.io.newick | Contains classes implementing the import from and export to the Newick format.
info.bioinfweb.treegraph.document.io.phyloxml | Contains classes implementing the import from the phyloXML format.
info.bioinfweb.treegraph.document.io.xtg | Contains classes implementing reading and writing of TreeGraph 2 documents.
info.bioinfweb.treegraph.document.nodebranchdata | Contains classes that implement the access to different data fields of the document elements over the common interface `NodeBranchDataAdapter`.
info.bioinfweb.treegraph.document.undo | Contains all document edits to manipulate the TreeGraph 2 data structure.
info.bioinfweb.treegraph.document.undo.edit |
info.bioinfweb.treegraph.document.undo.file |
info.bioinfweb.treegraph.document.undo.file.addsupportvalues |
info.bioinfweb.treegraph.document.undo.format |
info.bioinfweb.treegraph.graphics.positionpaint | The classes in this package implement the output of an TreeGraph 2 document with `Graphics2D`.
info.bioinfweb.treegraph.gui.actions.edit |
info.bioinfweb.treegraph.gui.dialogs.io |
info.bioinfweb.treegraph.gui.dialogs.specialformats |
info.bioinfweb.treegraph.gui.treeframe | Contains all classes that make up a document window.

Uses of Node in info.bioinfweb.treegraph.document

Fields in info.bioinfweb.treegraph.document declared as Node
`private Node` | `NodeLadderizeComparable.node`
`private Node` | `Tree.paintStart`
`private Node` | `Node.parent`
`private Node` | `Branch.targetNode`

Fields in info.bioinfweb.treegraph.document with type parameters of type Node
`private ArrayList<Node>` | `Node.children`

Methods in info.bioinfweb.treegraph.document that return Node
`Node` | `Node.clone()` Returns a deep copy of this node not including the subtrees.
`Node` | `Node.clone(boolean keepUniqheNames)` Returns a deep copy of this node not including the subtrees.
`Node` | `Node.cloneWithSubtree(boolean keepUniqueNames)` Clones this object and all objects in this subtree and its afferent branch.
`Node` | `TreePath.findNode(Node root)` Finds the node specidied by the stored path relative to the given root node.
`Node` | `Node.getHighestChild()` Returns the upper most subnode of this node (e.g. needed for legend positioning).
`static Node` | `Node.getInstanceWithBranch()`
`static Node[]` | `TreeSerializer.getLeafNodes(Node root)`
`static Node[]` | `TreeSerializer.getLeafNodesBetween(Node upperLeaf, Node lowerLeaf)`
`Node` | `TreeElement.getLinkedNode()`
`Node` | `Node.getLinkedNode()`
`Node` | `Label.getLinkedNode()`
`Node` | `Branch.getLinkedNode()`
`static Node` | `Tree.getLinkedNode(PaintableElement element)` Returns the linked node to the given element.
`Node` | `Node.getLowestChild()` Returns the lowest subnode of this node (e.g. needed for legend positioning).
`Node` | `Node.getNext()`
`Node` | `Node.getNextLeaf()`
`Node` | `NodeLadderizeComparable.getNode()`
`static Node` | `Tree.getNodeByUniqueName(Node root, String uniqueName)` Searches for a node with the given unique name in the subtree under root.
`Node` | `Tree.getNodeByUniqueName(String uniqueName)` Searches for a node with the given unique name in this tree.
`static Node[]` | `TreeSerializer.getNodes(Node root)`
`Node` | `Tree.getPaintStart()`
`Node` | `Node.getParent()`
`Node` | `Node.getPrevious()`
`Node` | `Node.getPreviousLeaf()`
`Node` | `Branch.getTargetNode()`
`static Node` | `Tree.mostRecentCommonAncestor(Node n1, Node n2)`

Methods in info.bioinfweb.treegraph.document that return types with arguments of type Node
`List<Node>` | `Node.getChildren()`

Methods in info.bioinfweb.treegraph.document with parameters of type Node
`private static void` | `TreeSerializer.addLabelsWithID(Vector<Label> list, Node root, String id)`
`private static void` | `TreeSerializer.addLeafNodesBetween(Vector<Node> list, Node root, int level, TreePath upperPath, TreePath lowerPath)`
`private static void` | `TreeSerializer.addSubtree(Vector<PaintableElement> list, Node root, boolean leafsOnly, boolean node, boolean branch, boolean label)`
`static void` | `NodeLadderizeComparable.addToNode(NodeLadderizeComparable[] elements, Node root)` This method is used to reinsert sorted elements in the a subtree.
`private void` | `Tree.assignUniqueNamesToSubtree(Node root)` Assigns unique names to all nodes in the subtree under root currently without one.
`static boolean` | `Tree.containsDecimal(NodeBranchDataAdapter adapter, Node root)` Tests if the subtree under `root` contains a node which would be able to return a decimal value to the given adapter.
`static boolean` | `IDManager.containsIDElements(Node root)` Test whether the subtree under `root` contains at least one ID element (label or hidden data)
`static int` | `NodeLadderizeComparable.countNodes(Node root)` Sets all the `childCount` values of the contained `Node`-objects.
`static NodeLadderizeComparable[]` | `NodeLadderizeComparable.encloseSubnodes(Node root, boolean ladderizeDown)` Encloses all direct subelements of `root` with a `NodeLadderizeComparable`- object and adds this objects to an array that is returned.
`boolean` | `ContrastManager.ensureContrast(Document document, Node root, Legend[] legends)` Checks the colors of all elements in the subtree under `root` (including `root` and its afferent branch) regarding to their contrast to the background color of the document.
`private boolean` | `ContrastManager.ensureSubtreeContrast(Document document, Node root)` Rekursive method which contains the actual implementation.
`Node` | `TreePath.findNode(Node root)` Finds the node specidied by the stored path relative to the given root node.
`static Branch[]` | `TreeSerializer.getBranches(Node root)`
`static
`<T> T[]`
` | `TreeSerializer.getElements(Node root, T[] array, boolean leafsOnly, boolean node, boolean branch, boolean label)`
`static
`<T> T[]`
` | `TreeSerializer.getElementsOfType(Node root, PaintableElement typeElement, T[] array, boolean leafsOnly)`
`static IconLabel` | `IDManager.getFirstIconLabel(Node root, String id)`
`static Label` | `IDManager.getFirstLabel(Node root, String id)`
`static TextLabel` | `IDManager.getFirstTextLabel(Node root, String id)`
`static String[]` | `IDManager.getHiddenBranchDataIDs(Node root)` Searches for all the IDs of hidden data that is assigned to a branch present in the subtree under root.
`static Vector<String>` | `IDManager.getHiddenBranchDataIDVector(Node root)`
`static String[]` | `IDManager.getHiddenNodeDataIDs(Node root)` Searches for all the IDs of hidden data that is assigned to a node present in the subtree under root.
`static Vector<String>` | `IDManager.getHiddenNodeDataIDVector(Node root)`
`static Vector<String>` | `IDManager.getIconLabelIDVector(Node root)`
`static String[]` | `IDManager.getIDs(Node root)` Searches for all IDs (hidden data and label IDs) present in the subtree under root.
`static Vector<String>` | `IDManager.getIDVector(Node root)` Searches for all IDs present in the subtree under root.
`static String[]` | `IDManager.getLabelIDs(Node root)` Searches for all label IDs present in the subtree under root.
`static Vector<String>` | `IDManager.getLabelIDVector(Node root)`
`static Label[]` | `TreeSerializer.getLabels(Node root)` Returns all labels in the subtree under root.
`static Label[]` | `TreeSerializer.getLabelsWithID(Node root, String id)`
`static Node[]` | `TreeSerializer.getLeafNodes(Node root)`
`static Node[]` | `TreeSerializer.getLeafNodesBetween(Node upperLeaf, Node lowerLeaf)`
`static Legend[]` | `TreeSerializer.getLegendsInSubtree(Tree tree, Node root)` Returns an array of all legends which are completely anchored inside the subtree under `root`.
`static LineElement[]` | `TreeSerializer.getLineElements(Node root)`
`static Node` | `Tree.getNodeByUniqueName(Node root, String uniqueName)` Searches for a node with the given unique name in the subtree under root.
`static Node[]` | `TreeSerializer.getNodes(Node root)`
`static ConcretePaintableElement[]` | `TreeSerializer.getPaintableElements(Node root)`
`static TextElement[]` | `TreeSerializer.getTextElements(Node root)`
`static String[]` | `IDManager.getTextLabelIDs(Node root)`
`static Vector<String>` | `IDManager.getTextLabelIDVector(Node root)`
`private static Vector<String>` | `IDManager.getVector(Node root, boolean includeTextLabels, boolean includeIconLabels, boolean includeNodeHiddenData, boolean includeBranchHiddenData)` Returns a vector of IDs which is sorted alphabetically.
`static boolean` | `Tree.hasAllBranchLengths(Node root, boolean needsRootLength)` Tests is there are any branches without a defined length in the subtree under `root`.
`static boolean` | `IDManager.idExists(Node root, String id)`
`boolean` | `Node.isChildOf(Node ancestor)` Tests if the specified node is an ancestor of this node.
`static double` | `Tree.longestPath(Node root, boolean includeRootBranch)` Returns the longest path to a terminal in the subtree of `root`.
`static Node` | `Tree.mostRecentCommonAncestor(Node n1, Node n2)`
`static void` | `IDManager.renameID(String oldName, String newName, Node root)` Changes all accurences of the given ID in the subtree under root.
`private static void` | `IDManager.searchIDsInSubtree(Node root, Vector<String> list, boolean includeTextLabels, boolean includeIconLabels, boolean includeNodeHiddenData, boolean includeBranchHiddenData)`
`private void` | `Node.searchLeafNames(Node root, Vector<String> names)`
`void` | `Tree.setPaintStart(Node paintStart)`
`void` | `Node.setParent(Node node)`
`private void` | `TreePath.setPath(Node end, Node ancestor)`
`void` | `Branch.setTargetNode(Node targetNode)`

Method parameters in info.bioinfweb.treegraph.document with type arguments of type Node
`private static void` | `TreeSerializer.addLeafNodesBetween(Vector<Node> list, Node root, int level, TreePath upperPath, TreePath lowerPath)`

Constructors in info.bioinfweb.treegraph.document with parameters of type Node
`Branch(Node target)`
`NodeLadderizeComparable(Node node, boolean ladderizeDown)`
`TreePath(Node leaf)` Creates a path from the specified leaf to the root of the tree.
`TreePath(Node leaf, Node ancestor)` Creates a path from the specified leaf to the specified ancestor (not including the ancestor itself).

Uses of Node in info.bioinfweb.treegraph.document.clipboard

Fields in info.bioinfweb.treegraph.document.clipboard declared as Node
`private Node` | `TreeClipboard.subtreeRoot`

Methods in info.bioinfweb.treegraph.document.clipboard that return Node
`Node` | `TreeClipboard.getSubtree()` Returns a deep copy of the subtree in the clipboard.

Methods in info.bioinfweb.treegraph.document.clipboard with parameters of type Node
`void` | `TreeClipboard.copySubtree(Tree tree, Node root)`

Uses of Node in info.bioinfweb.treegraph.document.format

Methods in info.bioinfweb.treegraph.document.format that return Node
`static Node` | `FormatUtils.createNode(Document document)` Creates a node with an afferent branch to be inserted in the specified document.
`static Node` | `FormatUtils.createNode(Node parent)` Creates a node with an afferent branch to be inserted in the specified document.
`Node` | `LegendFormats.getAnchor(int no)`

Methods in info.bioinfweb.treegraph.document.format with parameters of type Node
`static Legend` | `FormatUtils.createLegend(Node anchor, Legends legends)` Creates a legend to be inserted in the specified document.
`static Node` | `FormatUtils.createNode(Node parent)` Creates a node with an afferent branch to be inserted in the specified document.
`void` | `LegendFormats.setAnchor(int no, Node node)`

Uses of Node in info.bioinfweb.treegraph.document.format.adapters.color

Methods in info.bioinfweb.treegraph.document.format.adapters.color with parameters of type Node
`Color` | `NodeTextColorAdapter.getColor(Node node)`
`Color` | `NodeLineColorAdapter.getColor(Node node)`
`Color` | `LabelTextColorAdapter.getColor(Node node)`
`Color` | `LabelLineColorAdapter.getColor(Node node)`
`Color` | `ColorAdapter.getColor(Node node)`
`Color` | `BranchLineColorAdapter.getColor(Node node)`
`void` | `NodeTextColorAdapter.setColor(Color color, Node node)`
`void` | `NodeLineColorAdapter.setColor(Color color, Node node)`
`void` | `LabelTextColorAdapter.setColor(Color color, Node node)`
`void` | `LabelLineColorAdapter.setColor(Color color, Node node)`
`void` | `ColorAdapter.setColor(Color color, Node node)`
`void` | `BranchLineColorAdapter.setColor(Color color, Node node)`

Uses of Node in info.bioinfweb.treegraph.document.format.adapters.distance

Methods in info.bioinfweb.treegraph.document.format.adapters.distance with parameters of type Node
`float` | `NodeTextHeightAdapter.getDistance(Node node)`
`float` | `NodeLineWidthAdapter.getDistance(Node node)`
`float` | `DistanceAdapter.getDistance(Node node)` Returns the distance value in millimeters
`float` | `BranchSpaceAboveAdapter.getDistance(Node node)`
`float` | `BranchMinLengthAdapter.getDistance(Node node)`
`float` | `BranchLineWidthAdapter.getDistance(Node node)`
`float` | `AbstractLegendAdapter.getDistance(Node node)` This method always returns `Float.NaN`.
`float` | `AbstractLabelDistanceAdapter.getDistance(Node node)` Returns the distance value of the label with the specified ID in millimeters.
`float` | `AbstractDistanceValueAdapter.getDistance(Node node)`
`protected DistanceValue` | `LeafMarginTopAdapter.getDistanceValue(Node node)`
`protected DistanceValue` | `LeafMarginRightAdapter.getDistanceValue(Node node)`
`protected DistanceValue` | `LeafMarginLeftAdapter.getDistanceValue(Node node)`
`protected DistanceValue` | `LeafMarginBottomAdapter.getDistanceValue(Node node)`
`protected DistanceValue` | `CornerRadiusAdapter.getDistanceValue(Node node)`
`protected DistanceValue` | `BranchSpaceBelowAdapter.getDistanceValue(Node node)`
`protected abstract DistanceValue` | `AbstractDistanceValueAdapter.getDistanceValue(Node node)`
`void` | `NodeTextHeightAdapter.setDistance(float distance, Node node)`
`void` | `NodeLineWidthAdapter.setDistance(float distance, Node node)`
`void` | `DistanceAdapter.setDistance(float distance, Node node)`
`void` | `BranchSpaceAboveAdapter.setDistance(float distance, Node node)`
`void` | `BranchMinLengthAdapter.setDistance(float distance, Node node)`
`void` | `BranchLineWidthAdapter.setDistance(float distance, Node node)`
`void` | `AbstractLegendAdapter.setDistance(float distance, Node node)` This method does nothing.
`void` | `AbstractLabelDistanceAdapter.setDistance(float distance, Node node)`
`void` | `AbstractDistanceValueAdapter.setDistance(float distance, Node node)`

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

Methods in info.bioinfweb.treegraph.document.io.newick that return Node
`private Node` | `NewickStringReader.readBranch(int start, int end, Node root)`
`private Node` | `NewickStringReader.readInternal(int start, int end)`
`private Node` | `NewickStringReader.readLeaf(int start, int end)`
`private Node` | `NewickStringReader.readSubtree(int start, int end)`

Methods in info.bioinfweb.treegraph.document.io.newick with parameters of type Node
`private void` | `BranchLengthsScaler.calculateAverage(Node root)`
`private static String` | `NewickStringWriter.formatName(Node node, NodeBranchDataAdapter adapter)`
`void` | `CommentDataReader.read(String comment, Node node)`
`private Node` | `NewickStringReader.readBranch(int start, int end, Node root)`
`private void` | `NewickStringReader.readBranchList(int start, int end, Node root)`
`private void` | `NewickStringReader.readName(int previousEnd, int end, Node root, NodeBranchDataAdapter adapter, TranslTable translTable)`
`private static String` | `NewickStringWriter.writeSubtree(Node root, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter leafAdapter, NodeBranchDataAdapter branchLengthAdapter)`

Uses of Node in info.bioinfweb.treegraph.document.io.phyloxml

Methods in info.bioinfweb.treegraph.document.io.phyloxml that return Node
`private Node` | `PhyloXMLReader.readSubtree(StartElement rootElement, Node parent)`

Methods in info.bioinfweb.treegraph.document.io.phyloxml with parameters of type Node
`private void` | `PhyloXMLReader.readDate(Node node)`
`private void` | `PhyloXMLReader.readDistribution(Node node)`
`private void` | `PhyloXMLReader.readSequence(StartElement rootElement, Node node)`
`private Node` | `PhyloXMLReader.readSubtree(StartElement rootElement, Node parent)`
`private void` | `PhyloXMLReader.readTaxonomy(Node node)`

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

Methods in info.bioinfweb.treegraph.document.io.xtg that return Node
`private Node` | `XTGReader.readSubtree(StartElement rootElement)`

Methods in info.bioinfweb.treegraph.document.io.xtg with parameters of type Node
`private void` | `XTGWriter.writeSubtree(Node root)`

Uses of Node in info.bioinfweb.treegraph.document.nodebranchdata

Methods in info.bioinfweb.treegraph.document.nodebranchdata that return Node
`Node` | `UniqueNameAdapter.getDataElement(Node node)`
`Node` | `NodeNameAdapter.getDataElement(Node node)`
`Node` | `HiddenNodeDataAdapter.getDataElement(Node node)`

Methods in info.bioinfweb.treegraph.document.nodebranchdata with parameters of type Node
`boolean` | `TextLabelAdapter.assignData(Node node, TextElementData data)`
`abstract boolean` | `TextElementDataAdapter.assignData(Node node, TextElementData data)`
`boolean` | `NodeNameAdapter.assignData(Node node, TextElementData data)`
`boolean` | `HiddenDataAdapter.assignData(Node node, TextElementData data)`
`protected void` | `TextLabelAdapter.createData(Node node)`
`protected abstract void` | `TextElementDataAdapter.createData(Node node)` This method should create the data object if does not already exist.
`protected void` | `NodeNameAdapter.createData(Node node)`
`protected void` | `HiddenDataAdapter.createData(Node node)`
`void` | `UniqueNameAdapter.delete(Node node)`
`void` | `TextLabelAdapter.delete(Node node)`
`void` | `TextElementDataAdapter.delete(Node node)`
`void` | `NodeBranchDataAdapter.delete(Node node)`
`void` | `HiddenDataAdapter.delete(Node node)`
`void` | `BranchLengthAdapter.delete(Node node)`
`TextElementData` | `TextLabelAdapter.getData(Node node)`
`abstract TextElementData` | `TextElementDataAdapter.getData(Node node)`
`TextElementData` | `NodeNameAdapter.getData(Node node)`
`TextElementData` | `HiddenDataAdapter.getData(Node node)`
`Node` | `UniqueNameAdapter.getDataElement(Node node)`
`TextLabel` | `TextLabelAdapter.getDataElement(Node node)`
`Node` | `NodeNameAdapter.getDataElement(Node node)`
`ConcretePaintableElement` | `NodeBranchDataAdapter.getDataElement(Node node)` This method should return the tree element which contains the data which is edited with the implementation of the respective adapter.
`Node` | `HiddenNodeDataAdapter.getDataElement(Node node)`
`Branch` | `HiddenBranchDataAdapter.getDataElement(Node node)`
`Branch` | `BranchLengthAdapter.getDataElement(Node node)`
`protected HiddenDataMap` | `HiddenNodeDataAdapter.getDataMap(Node node)`
`protected abstract HiddenDataMap` | `HiddenDataAdapter.getDataMap(Node node)`
`protected HiddenDataMap` | `HiddenBranchDataAdapter.getDataMap(Node node)`
`double` | `UniqueNameAdapter.getDecimal(Node node)`
`double` | `TextElementDataAdapter.getDecimal(Node node)`
`double` | `NodeBranchDataAdapter.getDecimal(Node node)`
`double` | `BranchLengthAdapter.getDecimal(Node node)`
`DecimalFormat` | `TextLabelAdapter.getDecimalFormat(Node node)`
`abstract DecimalFormat` | `TextElementDataAdapter.getDecimalFormat(Node node)`
`DecimalFormat` | `NodeNameAdapter.getDecimalFormat(Node node)`
`DecimalFormat` | `HiddenDataAdapter.getDecimalFormat(Node node)`
`String` | `UniqueNameAdapter.getText(Node node)`
`String` | `TextElementDataAdapter.getText(Node node)`
`String` | `NodeBranchDataAdapter.getText(Node node)`
`String` | `BranchLengthAdapter.getText(Node node)`
`boolean` | `UniqueNameAdapter.isDecimal(Node node)`
`boolean` | `TextElementDataAdapter.isDecimal(Node node)`
`boolean` | `NodeBranchDataAdapter.isDecimal(Node node)`
`boolean` | `BranchLengthAdapter.isDecimal(Node node)`
`boolean` | `UniqueNameAdapter.isEmpty(Node node)`
`boolean` | `TextElementDataAdapter.isEmpty(Node node)`
`boolean` | `NodeBranchDataAdapter.isEmpty(Node node)`
`boolean` | `BranchLengthAdapter.isEmpty(Node node)`
`boolean` | `UniqueNameAdapter.isString(Node node)`
`boolean` | `TextElementDataAdapter.isString(Node node)`
`boolean` | `NodeBranchDataAdapter.isString(Node node)`
`boolean` | `BranchLengthAdapter.isString(Node node)`
`void` | `UniqueNameAdapter.setDecimal(Node node, double value)`
`void` | `TextElementDataAdapter.setDecimal(Node node, double value)`
`void` | `NodeBranchDataAdapter.setDecimal(Node node, double value)`
`void` | `BranchLengthAdapter.setDecimal(Node node, double value)`
`void` | `BranchLengthAdapter.setDecimal(Node node, double value, int decimalPlaceCount)`
`void` | `UniqueNameAdapter.setText(Node node, String value)`
`void` | `TextElementDataAdapter.setText(Node node, String value)`
`void` | `NodeBranchDataAdapter.setText(Node node, String value)`
`void` | `BranchLengthAdapter.setText(Node node, String value)`
`void` | `TextElementDataAdapter.setType(Node node, boolean decimal)`

Uses of Node in info.bioinfweb.treegraph.document.undo

Fields in info.bioinfweb.treegraph.document.undo declared as Node
`private Node` | `ComplexDocumentEdit.newRoot`
`private Node` | `ComplexDocumentEdit.oldRoot`

Methods in info.bioinfweb.treegraph.document.undo that return Node
`protected Node` | `ComplexDocumentEdit.findEquivilant(Node old)` Returns the node in the new tree (copy of the old) with the equivilant position to `old`.

Methods in info.bioinfweb.treegraph.document.undo with parameters of type Node
`private void` | `NodeBranchDataBackup.backupSubtree(Node root)`
`protected void` | `SaveLegendsEdit.editSubtreeLegends(Node root)` This method can be used to adopt the legends of a document prior to deleting a subtree.
`protected Node` | `ComplexDocumentEdit.findEquivilant(Node old)` Returns the node in the new tree (copy of the old) with the equivilant position to `old`.
`void` | `NodeBranchDataBackup.restore(Node root)` Restores the previous values of the specified column if it previously exsited.
`private int` | `NodeBranchDataBackup.restoreSubtree(Node root, int index)`

Constructors in info.bioinfweb.treegraph.document.undo with parameters of type Node
`NodeBranchDataBackup(NodeBranchDataAdapter adapter, Node root)`

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

Fields in info.bioinfweb.treegraph.document.undo.edit declared as Node
`private Node[]` | `InsertRemoveLegendEdit.anchor`
`private Node` | `InsertSiblingEdit.firstSibling`
`private Node` | `InsertSiblingEdit.newParent`
`private Node` | `EditNodeBranchDataEdit.newRoot`
`private Node` | `PasteSiblingEdit.newSibling`
`private Node` | `SeparateBranchEdit.node`
`private Node` | `CollapseNodeEdit.node`
`private Node` | `EditNodeBranchDataEdit.oldRoot`
`private Node` | `PasteSubtreeEdit.parent`
`protected Node` | `InsertRemoveSubtreeEdit.parent`
`private Node` | `CalculateColumnEdit.position`
`private Node` | `PasteSubtreeEdit.root`
`protected Node` | `MoveSubtreeEdit.root`
`private Node` | `LadderizeEdit.root`
`protected Node` | `InsertRemoveSubtreeEdit.root`
`private Node` | `DeleteSubelementsEdit.root`
`private Node[]` | `DeleteSubelementsEdit.subnodes`

Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type Node
`private void` | `CalculateColumnEdit.calculateSubtree(Node root)`
`void` | `LegendPaster.changeUniqueNames(Node root)` Changes the unique names of the subtree under `root` and the anchor names of the legends.
`private void` | `LegendPaster.changeUniqueNamesSubtree(Node root)`
`private boolean` | `DeleteEdit.containsParent(Node node)`
`private void` | `CopyColumnEdit.copySubtree(Node root)`
`private void` | `DeleteOutsideIntervalEdit.deleteOutsideIntervalSubtree(Node root)`
`static void` | `DeleteColumnEdit.deleteSubtree(Node root, NodeBranchDataAdapter adapter)`
`private void` | `LadderizeEdit.ladderize(Node root, boolean down)`
`private void` | `ReplaceInNodeDataEdit.replace(Node root)`
`void` | `RescaleNodeDataEdit.rescale(Node root)`
`protected void` | `SetColumnTypeEdit.setDataTypeInSubtree(Node root, TextElementDataAdapter adapter, boolean decimal)`

Constructors in info.bioinfweb.treegraph.document.undo.edit with parameters of type Node
`CollapseNodeEdit(Document document, Node node, boolean showWarnings)`
`DeleteSubelementsEdit(Document document, Node root, boolean showWarnings)`
`EditNodeBranchDataEdit(Document document, Node newRoot)`
`InsertLegendEdit(Document document, Legend legend, Node anchor0, Node anchor1)`
`InsertRemoveLegendEdit(Document document, Legend legend, Node anchor0, Node anchor1)`
`InsertRemoveSubtreeEdit(Document document, Node parent, Node root, int index)`
`InsertSiblingEdit(Document document, Node firstSibling, Node newSibling)`
`InsertSubtreeEdit(Document document, Node parent, Node root, int index)`
`LadderizeEdit(Document document, Node root, boolean down)`
`MoveSubtreeEdit(Document document, Node root, boolean down)`
`PasteLegendEdit(Document document, Node anchor1, Node anchor2, Legend legend)`
`PasteRootEdit(Document document, Node root, Legend[] legends)`
`PasteSiblingEdit(Document document, Node firstSibling, Node newSibling, Legend[] legends)`
`PasteSubtreeEdit(Document document, Node parent, Node root, Legend[] legends)`
`RemoveSubtreeEdit(Document document, Node parent, Node root, int index, boolean showWarnings)`

Uses of Node in info.bioinfweb.treegraph.document.undo.file

Methods in info.bioinfweb.treegraph.document.undo.file with parameters of type Node
`private void` | `AddSupportValuesEdit.addLeafFields(Node root, TextElementDataAdapter adapter)` Adds a boolean field which indicates the leafs located under `root` to the attribute map of `root`.
`private void` | `AddSupportValuesEdit.addLeafList(List<TextElementData> list, Node root, TextElementDataAdapter adapter)` Fills the specified list with the values of all leafs under `root`.
`private double` | `AddSupportValuesEdit.findHighestConflict(Node root, double highest, Node targetNode, NodeInfo info)` This method is the recursive part called by `findHighestConflict`.
`private NodeInfo` | `AddSupportValuesEdit.findSourceNodeWithAllLeafs(Node sourceRoot, LeafField targetLeafs)`
`private LeafField` | `AddSupportValuesEdit.getLeafField(Node node)`
`private double` | `AddSupportValuesEdit.getSupportValue(Node node)`
`private static boolean` | `AddSupportValuesEdit.internalsAreDecimal(Node root, NodeBranchDataAdapter adapter)` Tests if all internal nodes in the subtree under `root` contain decimal values.
`private void` | `AddSupportValuesEdit.processSubtree(Node targetRoot)` Finds the support or conflict values in the source document.
`private void` | `ApplyNameTableEdit.rename(Node root, List<String> oldNames, List<String> newNames)`
`private int` | `ApplyNameTableEdit.restoreNames(Node root, int pos)`

Uses of Node in info.bioinfweb.treegraph.document.undo.file.addsupportvalues

Fields in info.bioinfweb.treegraph.document.undo.file.addsupportvalues declared as Node
`private Node` | `NodeInfo.node`

Methods in info.bioinfweb.treegraph.document.undo.file.addsupportvalues that return Node
`Node` | `NodeInfo.getNode()`

Methods in info.bioinfweb.treegraph.document.undo.file.addsupportvalues with parameters of type Node
`void` | `NodeInfo.setNode(Node node)`

Constructors in info.bioinfweb.treegraph.document.undo.file.addsupportvalues with parameters of type Node
`NodeInfo(Node node, int additionalCount, boolean downwards)`

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

Fields in info.bioinfweb.treegraph.document.undo.format declared as Node
`private Node` | `ScaleDistanceValuesEdit.root`
`private Node` | `DistanceValuesBackup.root`

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type Node
`static double` | `NodeBranchDataFormatEdit.calculateMaxNodeData(NodeBranchDataAdapter adapter, Node root)` Searches for the maximal node data specified by `adapter` in the subtree under root.
`static void` | `AutoPositionLabelsEdit.position(Node root)`
`private int` | `DistanceValuesBackup.restoreSubtreeValues(Node root, int index)` Assigns the previously saved line widths to the branches in the subtree under root.
`private void` | `ColorsByNodeBranchDataEdit.saveOldSubtreeColors(Node root)` Saves the old colors.
`private void` | `DistanceValuesBackup.saveOldSubtreeValues(Node root)` Saves the old widths in a linear list (ordering is root, child 0..n)
`private void` | `ColorsByNodeBranchDataEdit.setNewColors(Node root)` Sets the line colors according to the specified border colors and node data.
`private void` | `ScaleDistanceValuesEdit.setNewSubtreeValues(Node root)` Sets the branch widths according to the specified rescaling factor.
`private void` | `DistanceValuesByNodeBranchDataEdit.setNewValues(Node root)` Sets the branch widths according to the specified range and node data.
`private int` | `ColorsByNodeBranchDataEdit.setOldColors(Node root, int index)` Assigns the previously saved colors in the subtree under `root`.

Constructors in info.bioinfweb.treegraph.document.undo.format with parameters of type Node
`DistanceValuesBackup(Tree tree, Node root, DistanceAdapter[] targetAdapters)`
`ScaleDistanceValuesEdit(Document document, Node root, float factor, DistanceAdapter[] targetAdapters)`

Uses of Node in info.bioinfweb.treegraph.graphics.positionpaint

Methods in info.bioinfweb.treegraph.graphics.positionpaint with parameters of type Node
`protected float` | `RectangularCladogramPositioner.calculateCornerRadiusShift(Node node, float y)` Returns the space between the right of the node and the real position of the node line dependant of the y position.
`protected float` | `PhylogramPositioner.calculateCornerRadiusShift(Node node, float y)` This method is overwritten to ensure that no corner radius in painted.
`private DistanceDimension` | `RectangularCladogramPositioner.calculateTaxonDimension(Node taxon)`
`private float` | `RectangularCladogramPositioner.calculateWidthsHeights(Node root)`
`private void` | `RectangularCladogramPositioner.moveSubtree(Node root, float dX, float dY)`
`private void` | `RectangularCladogramPainter.paintInternalNode(Node n)` Paints the given node.
`private void` | `RectangularCladogramPainter.paintLeaf(Node leaf)`
`private void` | `RectangularCladogramPainter.paintPointNode(Node n)`
`private void` | `RectangularCladogramPainter.paintSubtree(Node root)`
`private float` | `RectangularCladogramPositioner.positionElements(Node root, float overallWidth, float y0)` Positions the subtree under root.
`protected float` | `RectangularCladogramPositioner.rescaleNodeWidth(Node node, float width)` This methode can be overwritten by extending classes to define a different rescaling process.
`protected float` | `PhylogramPositioner.rescaleNodeWidth(Node node, float width)` This method is overwritten to ensure that no corner radius in painted.
`private float` | `RectangularCladogramPositioner.rescaleSubtree(Node root, float shift)` Rescales the subtree under root.
`private ConcretePaintableElement` | `RectangularCladogramPositioner.searchElementToPosition(Node root, float x, float y, float margin)`

Uses of Node in info.bioinfweb.treegraph.gui.actions.edit

Methods in info.bioinfweb.treegraph.gui.actions.edit that return Node
`protected Node` | `MoveSubtreeAction.getSelectedNode(TreeSelection selection)` Returns the node that should be moved if the selection contains this node or its afferent branch as the first element.

Methods in info.bioinfweb.treegraph.gui.actions.edit with parameters of type Node
`static boolean` | `NewNodeAction.insertSubtree(Document document, Node parent, Node root)` Inserts a new subelement as the last subelement of the given parent.
`static boolean` | `NewNodeAction.insertSubtree(Document document, Node parent, Node root, int index)` Inserts a new subelement at the given position.
`private void` | `SearchTextAction.searchSubtree(Node root)`

Uses of Node in info.bioinfweb.treegraph.gui.dialogs.io

Methods in info.bioinfweb.treegraph.gui.dialogs.io with parameters of type Node
`private String` | `ExportNodeDataTableModel.getValue(NodeBranchDataAdapter adapter, Node node)`
`void` | `ExportNodeDataTableModel.writeData(File file, Node root, ExportNodeDataTableModel.Nodes nodes)`
`void` | `ExportNodeDataTableModel.writeData(OutputStream stream, Node root, ExportNodeDataTableModel.Nodes nodes)`
`private void` | `ExportNodeDataTableModel.writeSubtree(Node root)` Writes the node data of the subtree under root as a text.

Uses of Node in info.bioinfweb.treegraph.gui.dialogs.specialformats

Methods in info.bioinfweb.treegraph.gui.dialogs.specialformats with parameters of type Node
`void` | `ColorAdapterListModel.setAdapters(Node root)` Creates all color adapters valid for the subtree under `root`.
`void` | `DistanceAdapterListModel.setAdapters(Tree tree, Node root, boolean includeLegendFormats)` Creates all distance adapters valid for the subtree under `root`.

Uses of Node in info.bioinfweb.treegraph.gui.treeframe

Fields in info.bioinfweb.treegraph.gui.treeframe with type parameters of type Node
`private Vector<Node>` | `DocumentTableModel.nodes`

Methods in info.bioinfweb.treegraph.gui.treeframe that return Node
`Node` | `TreeSelection.getFirstLeaf()`
`Node` | `TreeSelection.getFirstNode()`

Methods in info.bioinfweb.treegraph.gui.treeframe with parameters of type Node
`private void` | `DocumentTableModel.fillAdapterList(Node root)`
`private void` | `DocumentTableModel.fillNodeList(Node root)`
`int` | `DocumentTableModel.getRow(Node node)`

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