GuideTree

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 Description

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

Nested Classes
Modifier and Type	Class	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	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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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()`

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- 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<S extends Sequence<C>>
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

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

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Constructor Detail

GuideTree

Method Detail

getAllPairsScores

getDistanceMatrix

getRoot

getScoreMatrix

getSequences

iterator

toString