info.bioinfweb.treegraph.document.undo.edit
Class AddSupportValuesEdit

java.lang.Object
  info.bioinfweb.treegraph.document.undo.DocumentEdit
      info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit
          info.bioinfweb.treegraph.document.undo.edit.AddSupportValuesEdit

All Implemented Interfaces:

UndoableEdit

public class AddSupportValuesEdit
extends ComplexDocumentEdit

Nested Class Summary

private class	AddSupportValuesEdit.LeafList
static class	AddSupportValuesEdit.TargetType

Field Summary

static DecimalFormat	CONFLICT_DECIMAL_FORMAT
static String	CONFLICT_NAME
private NodeDataAdapter	conflictAdapter
static String	KEY_LEAF_REFERENCE
static int	MAX_TERMINAL_ERROR_COUNT
private NodeDataAdapter	sourceAdapter
private Document	src
static DecimalFormat	SUPPORT_DECIMAL_FORMAT
static String	SUPPORT_NAME
private NodeDataAdapter	supportAdapter
private NodeDataAdapter	terminalsAdapter

Fields inherited from class info.bioinfweb.treegraph.document.undo.DocumentEdit

document

Constructor Summary

private

AddSupportValuesEdit(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, NodeDataAdapter sourceAdapter)

Method Summary

private void	addLeafReferences(Node root) Adds direkt references to all leaves of the subtree under root to the attribute map of root.
static AddSupportValuesEdit	createInstance(Document document, Document src, NodeDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, boolean importNodeNames) Returns a new instance of AddSupportValuesEdit or null if the given source document contains internal node names that are not decimal.
private Node	findDeepestNodeWithLeafs(AddSupportValuesEdit.LeafList leafs) Finds the deepest node in the source document which has a subtree that contains all the specified leafs.
private double	findHighestConflict(Node root, AddSupportValuesEdit.LeafList leafs) Finds the highest conflicting support value in the subtree under root.
private double	findHighestConflictRek(Node root, double highest, AddSupportValuesEdit.LeafList leafs) This method is the recursive part called by findHighestConflict.
private Node	findSubnodeWithLeafs(AddSupportValuesEdit.LeafList leafs, Node parent) Finds the direct subnode under root that contains all the specified leafs.
private AddSupportValuesEdit.LeafList	getLeafList(Node node) Returns the leaf list of node that is stored in its attribute map.
String	getPresentationName()
private double	getSupportValue(Node node)
private static boolean	internalsAreDecimal(Node root, NodeDataAdapter adapter) Tests if all internal nodes in the subtree under root contain decimal values.
protected void	performRedo()
private void	processSubtree(Node root) Finds the support or conflict values in the source document.

Methods inherited from class info.bioinfweb.treegraph.document.undo.ComplexDocumentEdit

findEquivilant, findEquivilant, redo, undo

Methods inherited from class info.bioinfweb.treegraph.document.undo.DocumentEdit

addEdit, canRedo, canUndo, die, getRedoPresentationName, getUndoPresentationName, isSignificant, replaceEdit

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SUPPORT_NAME

public static final String SUPPORT_NAME

See Also:

Constant Field Values

CONFLICT_NAME

public static final String CONFLICT_NAME

See Also:

Constant Field Values

SUPPORT_DECIMAL_FORMAT

public static final DecimalFormat SUPPORT_DECIMAL_FORMAT

CONFLICT_DECIMAL_FORMAT

public static final DecimalFormat CONFLICT_DECIMAL_FORMAT

KEY_LEAF_REFERENCE

public static final String KEY_LEAF_REFERENCE

MAX_TERMINAL_ERROR_COUNT

public static final int MAX_TERMINAL_ERROR_COUNT

See Also:

Constant Field Values

sourceAdapter

private NodeDataAdapter sourceAdapter

src

private Document src

terminalsAdapter

private NodeDataAdapter terminalsAdapter

supportAdapter

private NodeDataAdapter supportAdapter

conflictAdapter

private NodeDataAdapter conflictAdapter

Constructor Detail

AddSupportValuesEdit

private AddSupportValuesEdit(Document document,
                             Document src,
                             NodeDataAdapter terminalsAdapter,
                             AddSupportValuesEdit.TargetType targetType,
                             String idPrefix,
                             NodeDataAdapter sourceAdapter)

Method Detail

createInstance

public static AddSupportValuesEdit createInstance(Document document,
                                                  Document src,
                                                  NodeDataAdapter terminalsAdapter,
                                                  AddSupportValuesEdit.TargetType targetType,
                                                  String idPrefix,
                                                  boolean importNodeNames)

Returns a new instance of AddSupportValuesEdit or null if the given source document contains internal node names that are not decimal.

Parameters:

document - - the document to add the support values to

src - - the document to obtain the support values frim

terminalsAdapter - - the adapter to obtain the terminal names from the target document

targetType - - the type of node data to store the new support values

idPrefix - - the prefix of the IDs that will be given to the new support (and conflict values)

importNodeNames - - If true the internal node names are imported as support valus, otherwise the internal branch lengths are used.

Returns:

a new instance of AddSupportValuesEdit or null

internalsAreDecimal

private static boolean internalsAreDecimal(Node root,
                                           NodeDataAdapter adapter)

Tests if all internal nodes in the subtree under root contain decimal values.

Parameters:

root - - the root of the subtree to be checked

adapter - - the adapter to obtain the data from the nodes

Returns:

true if only decimal values are found

getLeafList

private AddSupportValuesEdit.LeafList getLeafList(Node node)

Returns the leaf list of node that is stored in its attribute map.

Parameters:

node - - the node of the returned leaf list

Returns:

the leaf list instance or null if the node contains no leaf list

addLeafReferences

private void addLeafReferences(Node root)

Adds direkt references to all leaves of the subtree under root to the attribute map of root.

Parameters:

root - - the root of the subtree

findSubnodeWithLeafs

private Node findSubnodeWithLeafs(AddSupportValuesEdit.LeafList leafs,
                                  Node parent)

Finds the direct subnode under root that contains all the specified leafs.

Note that this method should only be used with nodes of the source document because of the correct use of the NodeDataAdapters.

Parameters:

leafs - - the leaf list of a node from the target document

parent - - the direct parent node of the nodes to be searched (a node of the source document)

Returns:

the according subnode or null if none is found

findDeepestNodeWithLeafs

private Node findDeepestNodeWithLeafs(AddSupportValuesEdit.LeafList leafs)

Finds the deepest node in the source document which has a subtree that contains all the specified leafs.

Parameters:

leafs - - the leaf list of a node from the target document

Returns:

the deepest node in the source document

getSupportValue

private double getSupportValue(Node node)

findHighestConflict

private double findHighestConflict(Node root,
                                   AddSupportValuesEdit.LeafList leafs)

Finds the highest conflicting support value in the subtree under root. (Root itsself is not included.) Conflicting nodes have to contain at least one leaf node of the leafs the original node had and at least one leaf node the original node did not have.

Parameters:

root - - the root of the subtree to be searched (a node in the source document)

highest - - the initial support value

leafs - - the leaf list of the node of the target document

Returns:

the node with the highest support value found (in the source document)

findHighestConflictRek

private double findHighestConflictRek(Node root,
                                      double highest,
                                      AddSupportValuesEdit.LeafList leafs)

This method is the recursive part called by findHighestConflict. The only difference between the two is that this method can return the support value of root itsself as findHighestConflict does not.

Parameters:

root - - the root of the subtree to be searched (a node in the source document)

highest - - the initial support value

leafs - - the leaf list of the node of the target document

Returns:

the node with the highest support value found (in the source document)

processSubtree

private void processSubtree(Node root)

Finds the support or conflict values in the source document.

Parameters:

root - - the root of the subtree to add support values to (a node of the target document)

performRedo

protected void performRedo()

Specified by:

performRedo in class ComplexDocumentEdit

getPresentationName

public String getPresentationName()