org.biojava.nbio.alignment

Class GuideTree<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.alignment.GuideTree<S,C>

Type Parameters:

S - each Sequence in the tree is of type S

C - each element of a Sequence is a Compound of type C

All Implemented Interfaces:

java.lang.Iterable<GuideTreeNode<S,C>>

public class GuideTree<S extends Sequence<C>,C extends Compound>
extends java.lang.Object
implements java.lang.Iterable<GuideTreeNode<S,C>>

Implements a data structure for a guide tree used during progressive multiple sequence alignment. Leaf GuideTree.Nodes correspond to single Sequences. Internal GuideTree.Nodes correspond to multiple sequence alignments. The root GuideTree.Node corresponds to the full multiple sequence alignment.

Author:

Mark Chapman

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	GuideTree.Node Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.

Constructor Summary

Constructors

Constructor and Description
GuideTree(java.util.List<S> sequences, java.util.List<PairwiseSequenceScorer<S,C>> scorers) Creates a guide tree for use during progressive multiple sequence alignment.

Method Summary

Modifier and Type	Method and Description
double[]	getAllPairsScores() Returns a sequence pair score for all Sequence pairs in the given List.
double[][]	getDistanceMatrix() Returns the distance matrix used to construct this guide tree.
GuideTree.Node	getRoot() Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.
double[][]	getScoreMatrix() Returns the similarity matrix used to construct this guide tree.
java.util.List<S>	getSequences() Returns the Sequences which make up the leaves of this tree.
java.util.Iterator<GuideTreeNode<S,C>>	iterator() Returns a post-order Iterator that traverses the tree from leaves to root.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

GuideTree

public GuideTree(java.util.List<S> sequences,
                 java.util.List<PairwiseSequenceScorer<S,C>> scorers)

Creates a guide tree for use during progressive multiple sequence alignment.

Parameters:

sequences - the List of Sequences to align

scorers - list of sequence pair scorers, one for each pair of sequences given

Method Detail

getAllPairsScores

public double[] getAllPairsScores()

Returns a sequence pair score for all Sequence pairs in the given List.

Returns:

list of sequence pair scores

getDistanceMatrix

public double[][] getDistanceMatrix()

Returns the distance matrix used to construct this guide tree. The scores have been normalized.

Returns:

the distance matrix used to construct this guide tree

getRoot

public GuideTree.Node getRoot()

Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.

Returns:

the root node

getScoreMatrix

public double[][] getScoreMatrix()

Returns the similarity matrix used to construct this guide tree. The scores have not been normalized.

Returns:

the similarity matrix used to construct this guide tree

getSequences

public java.util.List<S> getSequences()

Returns the Sequences which make up the leaves of this tree.

Returns:

the sequences which make up the leaves of this tree

iterator

public java.util.Iterator<GuideTreeNode<S,C>> iterator()

Returns a post-order Iterator that traverses the tree from leaves to root.

Specified by:

iterator in interface java.lang.Iterable<GuideTreeNode<S extends Sequence<C>,C extends Compound>>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object