fr.orsay.lri.varna.models.treealign
Class TreeAlign<ValueType1,ValueType2>

java.lang.Object
  fr.orsay.lri.varna.models.treealign.TreeAlign<ValueType1,ValueType2>

Type Parameters:

ValueType1 - The type of values on nodes in the first tree.

ValueType2 - The type of values on nodes in the second tree.

public class TreeAlign<ValueType1,ValueType2>
extends Object

Tree alignment algorithm. This class implements the tree alignment algorithm for ordered trees explained in article: T. Jiang, L. Wang, K. Zhang, Alignment of trees - an alternative to tree edit, Theoret. Comput. Sci. 143 (1995). Other references: - Claire Herrbach, Alain Denise and Serge Dulucq. Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. Theoretical Computer Science 411 (2010) 2423-2432. Our implementation supposes that the trees will never have more than 32000 nodes and that the total distance will never require more significant digits that a float (single precision) has.

Author:

Raphael Champeimont

Nested Class Summary

private class	TreeAlign.Aligner For arrays that take at least O(|T1|*|T2|) we take care not to use too big data types.
private class	TreeAlign.ConvertTreeToArray<ValueType>
private class	TreeAlign.TreeData<ValueType>

Field Summary

private TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2>

labelDist The distance function between labels.

Constructor Summary

TreeAlign(TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2> labelDist)
Create a TreeAlignSymmetric object, which can align trees.

Method Summary

TreeAlignResult<ValueType1,ValueType2>	align(Tree<ValueType1> T1, Tree<ValueType2> T2) Align T1 with T2, computing both the distance and the alignment.
float	distanceFromAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment) Takes a alignment, and compute the distance between the two original trees.

Methods inherited from class java.lang.Object

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

Field Detail

labelDist

private TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2> labelDist

The distance function between labels.

Constructor Detail

TreeAlign

public TreeAlign(TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2> labelDist)

Create a TreeAlignSymmetric object, which can align trees. The distance function will be called only once on every pair of nodes. The result is then kept in a matrix, so you need not manage yourself a cache of f(value1, value2). Note that it is permitted to have null values on nodes, so comparing a node with a non-null value with a node with a null value will give the same cost as to insert the first node. This can be useful if you tree has "fake" nodes.

Parameters:

labelDist - The label distance.

Method Detail

align

public TreeAlignResult<ValueType1,ValueType2> align(Tree<ValueType1> T1,
                                                    Tree<ValueType2> T2)
                                             throws TreeAlignException

Align T1 with T2, computing both the distance and the alignment. Time: O(|T1|*|T2|*(deg(T1)+deg(T2))^2) Space: O(|T1|*|T2|*(deg(T1)+deg(T2))) Average (over possible trees) time: O(|T1|*|T2|)

Parameters:

T1 - The first tree.

T2 - The second tree.

Returns:

The distance and the alignment.

Throws:

TreeAlignException

distanceFromAlignment

public float distanceFromAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment)

Takes a alignment, and compute the distance between the two original trees. If you have called align(), the result object already contains the distance D and the alignment A. If you call distanceFromAlignment on the alignment A it will compute the distance D.