|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava3.alignment.GuideTree<S,C>
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>
Implements a data structure for a guide tree used during progressive multiple sequence alignment. Leaf
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.
Nested Class Summary | |
---|---|
class |
GuideTree.Node
Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment. |
Constructor Summary | |
---|---|
GuideTree(List<S> sequences,
List<PairwiseSequenceScorer<S,C>> scorers)
Creates a guide tree for use during progressive multiple sequence alignment. |
Method Summary | |
---|---|
int[] |
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. |
int[][] |
getScoreMatrix()
Returns the similarity matrix used to construct this guide tree. |
List<S> |
getSequences()
Returns the Sequence s which make up the leaves of this tree. |
Iterator<GuideTreeNode<S,C>> |
iterator()
Returns a post-order Iterator that traverses the tree from leaves to root. |
String |
toString()
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public GuideTree(List<S> sequences, List<PairwiseSequenceScorer<S,C>> scorers)
sequences
- the List
of Sequence
s to alignscorers
- list of sequence pair scorers, one for each pair of sequences givenMethod Detail |
---|
public int[] 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 int[][] getScoreMatrix()
public List<S> getSequences()
Sequence
s which make up the leaves of this tree.
public Iterator<GuideTreeNode<S,C>> iterator()
Iterator
that traverses the tree from leaves to root.
iterator
in interface Iterable<GuideTreeNode<S extends Sequence<C>,C extends Compound>>
public String toString()
toString
in class Object
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |