S
- each Sequence
in the tree is of type SC
- each element of a Sequence
is a Compound
of type Cpublic class GuideTree<S extends Sequence<C>,C extends Compound> extends java.lang.Object implements java.lang.Iterable<GuideTreeNode<S,C>>
GuideTree.Node
s correspond to single Sequence
s. Internal GuideTree.Node
s correspond to multiple sequence
alignments. The root GuideTree.Node
corresponds to the full multiple sequence alignment.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 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.
|
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
Sequence s 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() |
public GuideTree(java.util.List<S> sequences, java.util.List<PairwiseSequenceScorer<S,C>> scorers)
sequences
- the List
of Sequence
s to alignscorers
- list of sequence pair scorers, one for each pair of sequences givenpublic double[] getAllPairsScores()
Sequence
pairs in the given List
.public double[][] getDistanceMatrix()
public GuideTree.Node getRoot()
GuideTree.Node
which corresponds to the full multiple sequence alignment.public double[][] getScoreMatrix()
public java.util.List<S> getSequences()
Sequence
s which make up the leaves of this tree.public java.util.Iterator<GuideTreeNode<S,C>> iterator()
Iterator
that traverses the tree from leaves to root.public java.lang.String toString()
toString
in class java.lang.Object