jebl.evolution.align

Class BartonSternberg

java.lang.Object

jebl.evolution.align.BartonSternberg

All Implemented Interfaces:

MultipleAligner

public class BartonSternberg
extends java.lang.Object
implements MultipleAligner

Version:

$Id: BartonSternberg.java 1025 2009-10-23 01:29:48Z matt_kearse $ Implements the BartonSternberg multiple sequence alignment algorithm. Note: this is not yet complete, it does not create an initial ordering in which to add sequences to the profile. Also, after creating the profile, it just removes and adds each sequence back into the profile a fixed number of times(currently two).

Author:

Matt Kearse

Constructor Summary

Constructors

Constructor and Description
BartonSternberg(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String[]	align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
Alignment	doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment	doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment	doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Scores	getEstimatedScores()
double	getScore()
static void	main(java.lang.String[] arguments)

Methods inherited from class java.lang.Object

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

Constructor Detail

BartonSternberg

public BartonSternberg(Scores scores,
               float gapOpen,
               float gapExtend,
               int refinementIterations,
               boolean freeGapsAtEnds,
               boolean fastGuide)

Method Detail

getEstimatedScores

public Scores getEstimatedScores()

align

public final java.lang.String[] align(java.util.List<Sequence> sourceSequences,
                       ProgressListener progress,
                       boolean refineOnly,
                       boolean estimateMatchMismatchCosts)
                               throws CannotBuildDistanceMatrixException

Parameters:

sourceSequences -

progress -

refineOnly - if specified, then the input sequences are assumed to be aligned already, and this function will only refine the alignment.

Throws:

CannotBuildDistanceMatrixException

main

public static void main(java.lang.String[] arguments)
                 throws java.io.IOException,
                        ImportException

Throws:

java.io.IOException

ImportException

doAlign

public Alignment doAlign(java.util.List<Sequence> seqs,
                RootedTree guideTree,
                ProgressListener progress)

Specified by:

doAlign in interface MultipleAligner

doAlign

public Alignment doAlign(Alignment a1,
                Alignment a2,
                ProgressListener progress)

Specified by:

doAlign in interface MultipleAligner

doAlign

public Alignment doAlign(Alignment alignment,
                Sequence sequence,
                ProgressListener progress)

Specified by:

doAlign in interface MultipleAligner

getScore

public double getScore()