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

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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`
`private TreeMap<String,Node>`	`Tree.uniqueNameMap`

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.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()`
`Node`	`Tree.getNodeByUniqueName(String uniqueName)` Searches for a node with the given unique name in this tree.
`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



<T extends PaintableElement> 


void

TreeSerializer.addElementsOnNode(List<PaintableElement> list,
                  Node node,
                  Class<T> c)

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, Class<? extends PaintableElement> elementClass)

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 TextElementData IDManager.getDataByID(Node node, String id)
Returns the text element data specified by the given ID which is linked to this node (either from a text label, hidden node data or hidden branch data).

static



<T extends PaintableElement> 


T[]

TreeSerializer.getElementsInSubtree(Node root,
                     boolean leafsOnly,
                     Class<? extends PaintableElement> elementClass,
                     T[] array)

Returns an array of tree elements in the subtree under root

static



<T extends PaintableElement> 


T[]

TreeSerializer.getElementsInSubtree(Node root,
                     boolean leafsOnly,
                     Class<T> elementClass)

Returns an array of tree elements in the subtree under root Calling this method is equivalent to getElementsInSubtree(root, leafsOnly, elementClass, (T[])Array.newInstance(elementClass, 0)).

static



<T extends PaintableElement> 


T[]

TreeSerializer.getElementsOnNode(Node node,
                  Class<? extends PaintableElement> c,
                  T[] array)

Returns an array of tree elements linked to the specified node.

static



<T extends PaintableElement> 


T[]

TreeSerializer.getElementsOnNode(Node node,
                  Class<T> c)

Returns an array of tree elements linked to the specified node.

static IconLabel IDManager.getFirstIconLabel(Node root, String id)
Returns the first icon label with the specified ID to be found in the subtree under root.

static Label IDManager.getFirstLabel(Node root, String id)
Returns the first label with the specified ID to be found in the subtree under root.

static TextLabel IDManager.getFirstTextLabel(Node root, String id)
Returns the first text label with the specified ID to be found in the subtree under root.

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.getLabelsWithID(Node root, String id)

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 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)

private static void IDManager.renameIDSubtree(String oldName, String newName, Node root)
Changes all occurrences 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)

private static void IDManager.updatePieChartLabels(String oldName, String newName, Node root)
Updates the renamed ID if it is referenced by pie chart label in the subtree under root.

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)`
`ConcretePaintableElement`	`AbstractIDElementAdapter.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)`
`private boolean`	`RectangularCladogramPainter.subtreeVisible(Node root)`

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()`

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)`