Package 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 Description BartonSternberg(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide)
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String[]
align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
Alignment
doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Scores
getEstimatedScores()
double
getScore()
static void
main(java.lang.String[] arguments)
-
-
-
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 interfaceMultipleAligner
-
doAlign
public Alignment doAlign(Alignment a1, Alignment a2, ProgressListener progress)
- Specified by:
doAlign
in interfaceMultipleAligner
-
doAlign
public Alignment doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
- Specified by:
doAlign
in interfaceMultipleAligner
-
getScore
public double getScore()
-
-