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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.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 java.util.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, java.lang.String uniqueName)` Searches for a node with the given unique name in the subtree under root.
`Node` | `Tree.getNodeByUniqueName(java.lang.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
`java.util.List<Node>` | `Node.getChildren()`

Methods in info.bioinfweb.treegraph.document with parameters of type Node
`private static void` | `TreeSerializer.addLabelsWithID(java.util.Vector<Label> list, Node root, java.lang.String id)`
`private static void` | `TreeSerializer.addSubtree(java.util.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, java.lang.String id)`
`static java.lang.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 java.util.Vector<java.lang.String>` | `IDManager.getHiddenBranchDataIDVector(Node root)`
`static java.lang.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 java.util.Vector<java.lang.String>` | `IDManager.getHiddenNodeDataIDVector(Node root)`
`static IconLabel[]` | `TreeSerializer.getIconLabels(Node root)`
`static java.lang.String[]` | `IDManager.getIDs(Node root)` Searches for all IDs (hidden data and label IDs) present in the subtree under root.
`static java.util.Vector<java.lang.String>` | `IDManager.getIDVector(Node root)` Searches for all IDs present in the subtree under root.
`static java.lang.String[]` | `IDManager.getLabelIDs(Node root)` Searches for all label IDs present in the subtree under root.
`static java.util.Vector<java.lang.String>` | `IDManager.getLabelIDVector(Node root)`
`static Label[]` | `TreeSerializer.getLabels(Node root)`
`static Label[]` | `TreeSerializer.getLabelsWithID(Node root, java.lang.String id)`
`static Node[]` | `TreeSerializer.getLeafNodes(Node root)`
`static LineElement[]` | `TreeSerializer.getLineElements(Node root)`
`static Node` | `Tree.getNodeByUniqueName(Node root, java.lang.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 java.util.Vector<java.lang.String>` | `IDManager.getVector(Node root, boolean includeLabels, boolean includeNodeHiddenData, boolean includeBranchHiddenData)`
`static boolean` | `Tree.hasAllBranchLengths(Node root)` Tests is there are any branches without a defined length in the subtree under `root`.
`static boolean` | `IDManager.idExists(Node root, java.lang.String id)`
`static void` | `IDManager.renameID(java.lang.String oldName, java.lang.String newName, Node root)` Changes all accurences of the given ID in the subtree under root.
`private static void` | `IDManager.searchIDsInSubtree(Node root, java.util.Vector<java.lang.String> list, boolean includeLabels, boolean includeNodeHiddenData, boolean includeBranchHiddenData)`
`private void` | `Node.searchLeafNames(Node root, java.util.Vector<java.lang.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(java.util.Vector<NewickToken> tokens, int start, int end, Node root, NodeDataAdapter internalAdapter, TranslTable translTable, boolean translateInternals)`
`private static Node` | `NewickStringReader.readInternal(java.util.Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, TranslTable translTable, boolean translateInternals)`
`private static Node` | `NewickStringReader.readLeaf(java.util.Vector<NewickToken> tokens, int start, int end, TranslTable translTable)`
`private static Node` | `NewickStringReader.readSubtree(java.util.Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, TranslTable translTable, boolean translateInternals)`

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

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(javax.xml.stream.events.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 java.text.DecimalFormat` | `TextElementDataAdapter.getDecimalFormat(Node node)`
`java.text.DecimalFormat` | `NodeNameAdapter.getDecimalFormat(Node node)`
`java.text.DecimalFormat` | `LabelAdapter.getDecimalFormat(Node node)`
`java.text.DecimalFormat` | `HiddenDataAdapter.getDecimalFormat(Node node)`
`java.lang.String` | `UniqueNameAdapter.getText(Node node)`
`java.lang.String` | `TextElementDataAdapter.getText(Node node)`
`java.lang.String` | `NodeDataAdapter.getText(Node node)`
`java.lang.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, java.lang.String value)`
`void` | `TextElementDataAdapter.setText(Node node, java.lang.String value)`
`void` | `NodeDataAdapter.setText(Node node, java.lang.String value)`
`void` | `BranchLengthAdapter.setText(Node node, java.lang.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 java.util.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(java.lang.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, java.util.List<java.lang.String> oldNames, java.util.List<java.lang.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` | `NodeDataFormatEdit.calculateMaxNodeData(NodeDataAdapter adapter, Node root)` Searches for the maximal node data specified by `adapter` in the subtree under root.
`private void` | `ColorsFromNodeDataEdit.saveOldColors(Node root)` Saves the old branch and node line colors in two linear list (ordering is root, child 0..n)
`private void` | `BranchWidthsFromNodeDataEdit.saveOldWidths(Node root)` Saves the old widths in a linear list (ordering is root, child 0..n)
`private void` | `ColorsFromNodeDataEdit.setNewColors(Node root)` Sets the line colors according to the specified border colors and node data.
`private void` | `BranchWidthsFromNodeDataEdit.setNewWidths(Node root)` Sets the branch widths according to the specified range and node data.
`private int` | `ColorsFromNodeDataEdit.setOldColors(Node root, int index)` Assigns the previously saved line colors to the branches and nodes in the subtree under root.
`private int` | `BranchWidthsFromNodeDataEdit.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 java.util.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.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(java.io.File file, Node root)`
`void` | `ExportNodeDataTableModel.writeData(java.io.OutputStream stream, Node root)`
`private void` | `ExportNodeDataTableModel.writeSubtree(java.io.OutputStreamWriter writer, Node root)` Writes the node data of the subtree under root as a text.

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

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

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