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

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

All Implemented Interfaces:

UndoableEdit

public class AddSupportValuesEdit
extends ComplexDocumentEdit

Nested Class Summary

static class

AddSupportValuesEdit.TargetType

Field Summary

static DecimalFormat	CONFLICT_DECIMAL_FORMAT
static String	CONFLICT_NAME
private TextElementDataAdapter	conflictAdapter The node/branch data column to write imported conflict values to
static String	KEY_LEAF_REFERENCE
private Vector<TextElementData>	leafValues
static int	MAX_TERMINAL_ERROR_COUNT
private boolean	processRooted
static NodeNameAdapter	SOURCE_LEAFS_ADAPTER
private NodeBranchDataAdapter	sourceAdapter The node/branch data to be imported (node names or branch lengths)
private Document	src
static DecimalFormat	SUPPORT_DECIMAL_FORMAT
static String	SUPPORT_NAME
private TextElementDataAdapter	supportAdapter The node/branch data column to write imported support values to
private TextElementDataAdapter	targetLeafsAdapter The column that contains the terminal identifiers in the target document (usually nodes names)

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

document

Constructor Summary

AddSupportValuesEdit(Document document, Document src, TextElementDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, NodeBranchDataAdapter sourceAdapter, boolean processRooted)

Method Summary

private void	addLeafFields(Node root, TextElementDataAdapter adapter) Adds a boolean field which indicates the leafs located under root to the attribute map of root.
private void	addLeafList(List<TextElementData> list, Node root, TextElementDataAdapter adapter) Fills the specified list with the values of all leafs under root.
private String	compareLeafs()
static AddSupportValuesEdit	createInstance(Document document, Document src, TextElementDataAdapter terminalsAdapter, AddSupportValuesEdit.TargetType targetType, String idPrefix, boolean importNodeNames, boolean processRooted) Returns a new instance of AddSupportValuesEdit or null if the given source document contains internal node names that are not decimal.
private double	findHighestConflict(Node root, double highest, Node targetNode, NodeInfo info) This method is the recursive part called by findHighestConflict.
private NodeInfo	findSourceNodeWithAllLeafs(Node sourceRoot, LeafField targetLeafs)
private LeafField	getLeafField(Node node)
private int	getLeafIndex(TextElementData value)
String	getPresentationName()
private double	getSupportValue(Node node)
private static boolean	internalsAreDecimal(Node root, NodeBranchDataAdapter adapter) Tests if all internal nodes in the subtree under root contain decimal values.
protected void	performRedo()
private void	processSubtree(Node targetRoot) 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, getIsSubedit, getRedoPresentationName, getUndoPresentationName, isSignificant, replaceEdit, setIsSubedit

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

SOURCE_LEAFS_ADAPTER

public static final NodeNameAdapter SOURCE_LEAFS_ADAPTER

src

private Document src

targetLeafsAdapter

private TextElementDataAdapter targetLeafsAdapter

The column that contains the terminal identifiers in the target document (usually nodes names)

sourceAdapter

private NodeBranchDataAdapter sourceAdapter

The node/branch data to be imported (node names or branch lengths)

supportAdapter

private TextElementDataAdapter supportAdapter

The node/branch data column to write imported support values to

conflictAdapter

private TextElementDataAdapter conflictAdapter

The node/branch data column to write imported conflict values to

leafValues

private Vector<TextElementData> leafValues

processRooted

private boolean processRooted

Constructor Detail

AddSupportValuesEdit

public AddSupportValuesEdit(Document document,
                            Document src,
                            TextElementDataAdapter terminalsAdapter,
                            AddSupportValuesEdit.TargetType targetType,
                            String idPrefix,
                            NodeBranchDataAdapter sourceAdapter,
                            boolean processRooted)

Method Detail

internalsAreDecimal

private static boolean internalsAreDecimal(Node root,
                                           NodeBranchDataAdapter 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

createInstance

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

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.

processRooted - defines whether the two specified trees shall be merged rooted or not (no matter if the specified documents are rooted or not)

Returns:

a new instance of AddSupportValuesEdit or null

performRedo

protected void performRedo()

Specified by:

performRedo in class ComplexDocumentEdit

addLeafList

private void addLeafList(List<TextElementData> list,
                         Node root,
                         TextElementDataAdapter adapter)

Fills the specified list with the values of all leafs under root.

Parameters:

list -

root -

adapter -

compareLeafs

private String compareLeafs()

getLeafField

private LeafField getLeafField(Node node)

getLeafIndex

private int getLeafIndex(TextElementData value)

addLeafFields

private void addLeafFields(Node root,
                           TextElementDataAdapter adapter)

Adds a boolean field which indicates the leafs located under root to the attribute map of root.

Parameters:

root - the root of the subtree

findSourceNodeWithAllLeafs

private NodeInfo findSourceNodeWithAllLeafs(Node sourceRoot,
                                            LeafField targetLeafs)

getSupportValue

private double getSupportValue(Node node)

findHighestConflict

private double findHighestConflict(Node root,
                                   double highest,
                                   Node targetNode,
                                   NodeInfo info)

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

targetNode - the node in the target document to attach a support value to

info - information about the node in the source document which contains all terminals of targetNode in its subtree

Returns:

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

processSubtree

private void processSubtree(Node targetRoot)

Finds the support or conflict values in the source document.

Parameters:

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

getPresentationName

public String getPresentationName()