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 |
BartonSternberg(Scores scores,
float gapOpen,
float gapExtend,
int refinementIterations,
boolean freeGapsAtEnds,
boolean fastGuide)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BartonSternberg
public BartonSternberg(Scores scores,
float gapOpen,
float gapExtend,
int refinementIterations,
boolean freeGapsAtEnds,
boolean fastGuide)
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()
http://code.google.com/p/jebl2/