jebl.evolution.align
Class BartonSternberg

java.lang.Object
  jebl.evolution.align.BartonSternberg

All Implemented Interfaces:

MultipleAligner

public class BartonSternberg
extends Object
implements MultipleAligner

Author:

Matt Kearse

Constructor Summary

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

Method Summary

String[]	align(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(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Scores	getEstimatedScores()
static void	main(String[] arguments)

Methods inherited from class java.lang.Object

clone, equals, finalize, 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 String[] align(List<Sequence> sourceSequences,
                      ProgressListener progress,
                      boolean refineOnly,
                      boolean estimateMatchMIsmatchCosts)

Parameters:

sourceSequences -

progress -

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

main

public static void main(String[] arguments)
                 throws IOException,
                        ImportException

Throws:

IOException

ImportException

doAlign

public Alignment doAlign(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