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
info.bioinfweb.treegraph.document.format	Contains classes that store format information of the different document elements.
info.bioinfweb.treegraph.document.io.newick
info.bioinfweb.treegraph.document.io.xtg
info.bioinfweb.treegraph.document.nodedata
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.format
info.bioinfweb.treegraph.graphics.positionpaint
info.bioinfweb.treegraph.gui.actions.edit
info.bioinfweb.treegraph.gui.dialogs.datatable
info.bioinfweb.treegraph.gui.dialogs.formatbynodedata
info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters
info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters
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`	`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`	`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`	`Branch.getTargetNode()`

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.addSubtree(Vector<PaintableElement> list, Node root, boolean leafsOnly, boolean node, boolean branch, boolean textLabel, boolean iconLabel)

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(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.

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)
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)

int Node.getChildIndex(Node child)

static



<T> T[]

TreeSerializer.getElements(Node root,
            T[] array,
            boolean leafsOnly,
            boolean node,
            boolean branch,
            boolean textLabel,
            boolean iconLabel)

static



<T> T[]

TreeSerializer.getElementsOfType(Node root,
                  PaintableElement typeElement,
                  T[] array,
                  boolean leafsOnly)

static Label IDManager.getFirstLabel(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 IconLabel[] TreeSerializer.getIconLabels(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)

static Label[] TreeSerializer.getLabelsWithID(Node root, String id)

static Node[] TreeSerializer.getLeafNodes(Node 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 TextLabel[] TreeSerializer.getTextLabels(Node root)

private static Vector<String> IDManager.getVector(Node root, boolean includeLabels, boolean includeNodeHiddenData, boolean includeBranchHiddenData)

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)

static double Tree.longestPath(Node root, boolean includeRootBranch)
Returns the longest path to a terminal in the subtree of root.

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 includeLabels, 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)

void Branch.setTargetNode(Node targetNode)

Constructors in info.bioinfweb.treegraph.document with parameters of type Node
`Branch(Node target)`
`NodeLadderizeComparable(Node node, boolean ladderizeDown)`
`TreePath(Node end)`

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(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.io.newick

Methods in info.bioinfweb.treegraph.document.io.newick that return Node
`private static Node`	`NewickStringReader.readBranch(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 Node`	`NewickStringReader.readLeaf(Vector<NewickToken> tokens, int start, int end, TranslTable translTable)`
`private static Node`	`NewickStringReader.readSubtree(Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)`

Methods in info.bioinfweb.treegraph.document.io.newick with parameters of type Node
`private static String`	`NewickStringWriter.formatName(Node node, NodeDataAdapter adapter)`
`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 void`	`NewickStringReader.readName(Vector<NewickToken> tokens, int previousEnd, int end, Node root, NodeDataAdapter internalAdapter, TranslTable translTable)`
`private static String`	`NewickStringWriter.writeSubtree(Node root, NodeDataAdapter internalAdapter, NodeDataAdapter leafAdapter, NodeDataAdapter branchLengthAdapter)`

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.nodedata

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

Methods in info.bioinfweb.treegraph.document.nodedata with parameters of type Node
`abstract boolean`	`TextElementDataAdapter.assignData(Node node, TextElementData data)`
`boolean`	`NodeNameAdapter.assignData(Node node, TextElementData data)`
`boolean`	`LabelAdapter.assignData(Node node, TextElementData data)`
`boolean`	`HiddenDataAdapter.assignData(Node node, TextElementData data)`
`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`	`LabelAdapter.createData(Node node)`
`protected void`	`HiddenDataAdapter.createData(Node node)`
`void`	`UniqueNameAdapter.delete(Node node)`
`void`	`TextElementDataAdapter.delete(Node node)`
`void`	`NodeDataAdapter.delete(Node node)`
`void`	`LabelAdapter.delete(Node node)`
`void`	`HiddenDataAdapter.delete(Node node)`
`void`	`BranchLengthAdapter.delete(Node node)`
`abstract TextElementData`	`TextElementDataAdapter.getData(Node node)`
`TextElementData`	`NodeNameAdapter.getData(Node node)`
`TextElementData`	`LabelAdapter.getData(Node node)`
`TextElementData`	`HiddenDataAdapter.getData(Node node)`
`Node`	`UniqueNameAdapter.getDataElement(Node node)`
`Node`	`NodeNameAdapter.getDataElement(Node node)`
`ConcretePaintableElement`	`NodeDataAdapter.getDataElement(Node node)` This method should return the tree element which contains the data which is edited with the implementation of the respective adapter.
`Label`	`LabelAdapter.getDataElement(Node node)`
`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`	`NodeDataAdapter.getDecimal(Node node)`
`double`	`BranchLengthAdapter.getDecimal(Node node)`
`abstract DecimalFormat`	`TextElementDataAdapter.getDecimalFormat(Node node)`
`DecimalFormat`	`NodeNameAdapter.getDecimalFormat(Node node)`
`DecimalFormat`	`LabelAdapter.getDecimalFormat(Node node)`
`DecimalFormat`	`HiddenDataAdapter.getDecimalFormat(Node node)`
`String`	`UniqueNameAdapter.getText(Node node)`
`String`	`TextElementDataAdapter.getText(Node node)`
`String`	`NodeDataAdapter.getText(Node node)`
`String`	`BranchLengthAdapter.getText(Node node)`
`boolean`	`UniqueNameAdapter.isDecimal(Node node)`
`boolean`	`TextElementDataAdapter.isDecimal(Node node)`
`boolean`	`NodeDataAdapter.isDecimal(Node node)`
`boolean`	`BranchLengthAdapter.isDecimal(Node node)`
`boolean`	`UniqueNameAdapter.isEmpty(Node node)`
`boolean`	`TextElementDataAdapter.isEmpty(Node node)`
`boolean`	`NodeDataAdapter.isEmpty(Node node)`
`boolean`	`BranchLengthAdapter.isEmpty(Node node)`
`boolean`	`UniqueNameAdapter.isString(Node node)`
`boolean`	`TextElementDataAdapter.isString(Node node)`
`boolean`	`NodeDataAdapter.isString(Node node)`
`boolean`	`BranchLengthAdapter.isString(Node node)`
`void`	`UniqueNameAdapter.setDecimal(Node node, double value)`
`void`	`TextElementDataAdapter.setDecimal(Node node, double value)`
`void`	`NodeDataAdapter.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`	`NodeDataAdapter.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
`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`.

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`	`SeparateBranchEdit.node`
`private Node`	`CollapseNodeEdit.node`
`private Node`	`EditNodeBranchDataEdit.oldRoot`
`private Node`	`PasteSubtreeEdit.parent`
`protected Node`	`InsertRemoveSubtreeEdit.parent`
`private Node`	`PasteSubtreeEdit.root`
`protected Node`	`MoveSubtreeEdit.root`
`private Node`	`LadderizeEdit.root`
`protected Node`	`InsertRemoveSubtreeEdit.root`
`private Node`	`DeleteSubelementsEdit.root`
`private Node[]`	`DeleteSubelementsEdit.subnodes`

Fields in info.bioinfweb.treegraph.document.undo.edit with type parameters of type Node
`private Vector<Node>`	`AddSupportValuesEdit.LeafList.list`

Methods in info.bioinfweb.treegraph.document.undo.edit that return Node
`private Node`	`AddSupportValuesEdit.findDeepestNodeWithLeafs(AddSupportValuesEdit.LeafList leafs)` Finds the deepest node in the source document which has a subtree that contains all the specified leafs.
`private Node`	`AddSupportValuesEdit.findSubnodeWithLeafs(AddSupportValuesEdit.LeafList leafs, Node parent)` Finds the direct subnode under `root` that contains all the specified leafs.
`Node`	`AddSupportValuesEdit.LeafList.get(double value, NodeDataAdapter adapter)`
`Node`	`AddSupportValuesEdit.LeafList.get(int pos)`
`Node`	`AddSupportValuesEdit.LeafList.get(String value, NodeDataAdapter adapter)`

Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type Node
`boolean`	`AddSupportValuesEdit.LeafList.add(Node n)`
`private void`	`AddSupportValuesEdit.addLeafReferences(Node root)` Adds direkt references to all leaves of the subtree under `root` to the attribute map of `root`.
`private void`	`AssignLabelIDsEdit.assignIDsToSubtree(Node root)`
`boolean`	`AddSupportValuesEdit.LeafList.contains(Node n)`
`private boolean`	`DeleteEdit.containsParent(Node node)`
`private double`	`AddSupportValuesEdit.findHighestConflict(Node root, AddSupportValuesEdit.LeafList leafs)` Finds the highest conflicting support value in the subtree under `root`.
`private double`	`AddSupportValuesEdit.findHighestConflictRek(Node root, double highest, AddSupportValuesEdit.LeafList leafs)` This method is the recursive part called by `findHighestConflict`.
`private Node`	`AddSupportValuesEdit.findSubnodeWithLeafs(AddSupportValuesEdit.LeafList leafs, Node parent)` Finds the direct subnode under `root` that contains all the specified leafs.
`private AddSupportValuesEdit.LeafList`	`AddSupportValuesEdit.getLeafList(Node node)` Returns the leaf list of `node` that is stored in its attribute map.
`private double`	`AddSupportValuesEdit.getSupportValue(Node node)`
`private static boolean`	`AddSupportValuesEdit.internalsAreDecimal(Node root, NodeDataAdapter adapter)` Tests if all internal nodes in the subtree under `root` contain decimal values.
`private void`	`LadderizeEdit.ladderize(Node root, boolean down)`
`private void`	`AddSupportValuesEdit.processSubtree(Node root)` Finds the support or conflict values in the source document.
`private void`	`ApplyNameTableEdit.rename(Node root, List<String> oldNames, List<String> newNames)`
`private void`	`ReplaceInNodeDataEdit.replace(Node root)`
`void`	`RescaleNodeDataEdit.rescale(Node root)`
`private int`	`ApplyNameTableEdit.restoreNames(Node root, int pos)`

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 anchor, Legend legend)`
`PasteRootEdit(Document document, Node root)`
`PasteSiblingEdit(Document document, Node firstSibling, Node newSibling)`
`PasteSubtreeEdit(Document document, Node parent, Node root)`
`RemoveSubtreeEdit(Document document, Node parent, Node root, int index, boolean showWarnings)`

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

Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type Node
`static double`	`NodeBranchDataFormatEdit.calculateMaxNodeData(NodeDataAdapter adapter, Node root)` Searches for the maximal node data specified by `adapter` in the subtree under root.
`private void`	`ColorsByNodeBranchDataEdit.saveOldSubtreeColors(Node root)` Saves the old colors.
`private void`	`DistanceValuesByNodeBranchDataEdit.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`	`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`.
`private int`	`DistanceValuesByNodeBranchDataEdit.setOldWidths(Node root, int index)` Assigns the previously saved line widths to the branches in the subtree under root.

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

Methods in info.bioinfweb.treegraph.graphics.positionpaint with parameters of type Node
`protected float`	`RectangularCladogramPositioner.calculateEdgeRadiusShift(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.calculateEdgeRadiusShift(Node node, float y)` This method is overwritten to ensure that no edge 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 edge 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.datatable

Fields in info.bioinfweb.treegraph.gui.dialogs.datatable with type parameters of type Node
`private Vector<Node>`	`NodeDataTableModel.nodes`

Methods in info.bioinfweb.treegraph.gui.dialogs.datatable with parameters of type Node
`void`	`NodeDataTableModel.assignTree(Node root)` Assigns the node data in the subtree under root to this model.
`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)`
`private void`	`NodeDataTableModel.fillAdapterList(Node root)`
`private void`	`NodeDataTableModel.fillNodeList(Node root)`
`private void`	`NodeDataTableModel.rescaleSubtree(Node root, NodeDataAdapter adapter, NodeDataCalculator calculator)`
`private void`	`NodeDataTableModel.setDataTypeInSubtree(Node root, TextElementDataAdapter adapter, boolean decimal)`
`void`	`ExportNodeDataTableModel.writeData(File file, Node root)`
`void`	`ExportNodeDataTableModel.writeData(OutputStream stream, Node root)`
`private void`	`ExportNodeDataTableModel.writeSubtree(OutputStreamWriter writer, Node root)` Writes the node data of the subtree under root as a text.

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

Methods in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata with parameters of type Node
`void`	`DistanceAdapterListModel.setAdapters(Node root)` Creates all distance adapters valid for the subtree under `root`.
`void`	`ColorAdapterListModel.setAdapters(Node root)` Creates all color adapters valid for the subtree under `root`.

Uses of Node in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters

Methods in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.coloradapters with parameters of type Node
`Color`	`NodeTextColorAdapter.getColor(Node node)`
`Color`	`NodeLineColorAdapter.getColor(Node node)`
`Color`	`LabelTextColorAdapter.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`	`ColorAdapter.setColor(Color color, Node node)`
`void`	`BranchLineColorAdapter.setColor(Color color, Node node)`

Uses of Node in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters

Methods in info.bioinfweb.treegraph.gui.dialogs.formatbynodedata.distanceadapters with parameters of type Node
`float`	`NodeTextHeightAdapter.getDistance(Node node)`
`float`	`NodeLineWidthAdapter.getDistance(Node node)`
`float`	`LabelTextHeightAdapter.getDistance(Node node)` Returns the text height of the label with the specified ID in millimeters.
`float`	`DistanceAdapter.getDistance(Node node)` Returns the distance value in millimeters
`float`	`BranchSpaceBelowAdapter.getDistance(Node node)`
`float`	`BranchSpaceAboveAdapter.getDistance(Node node)`
`float`	`BranchMinLengthAdapter.getDistance(Node node)`
`float`	`BranchLineWidthAdapter.getDistance(Node node)`
`void`	`NodeTextHeightAdapter.setDistance(float distance, Node node)`
`void`	`NodeLineWidthAdapter.setDistance(float distance, Node node)`
`void`	`LabelTextHeightAdapter.setDistance(float distance, Node node)`
`void`	`DistanceAdapter.setDistance(float distance, Node node)`
`void`	`BranchSpaceBelowAdapter.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)`

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

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