jebl.evolution.align
public class BartonSternberg extends java.lang.Object implements MultipleAligner
Constructor and Description |
---|
BartonSternberg(Scores scores,
float gapOpen,
float gapExtend,
int refinementIterations,
boolean freeGapsAtEnds,
boolean fastGuide) |
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) |
public BartonSternberg(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide)
public Scores getEstimatedScores()
public final java.lang.String[] align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts) throws CannotBuildDistanceMatrixException
sourceSequences
- progress
- refineOnly
- if specified, then the input sequences are assumed to be aligned already,
and this function will only refine the alignment.CannotBuildDistanceMatrixException
public static void main(java.lang.String[] arguments) throws java.io.IOException, ImportException
java.io.IOException
ImportException
public Alignment doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
doAlign
in interface MultipleAligner
public Alignment doAlign(Alignment a1, Alignment a2, ProgressListener progress)
doAlign
in interface MultipleAligner
public Alignment doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
doAlign
in interface MultipleAligner
public double getScore()
http://code.google.com/p/jebl2/