public class SoftAlignmentScoreAlgorithm extends AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
Modifier and Type | Class and Description |
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static class |
SoftAlignmentScoreAlgorithm.ScoreEntry |
Modifier and Type | Field and Description |
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static double |
DEFAULTBETA |
Constructor and Description |
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SoftAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
Modifier and Type | Method and Description |
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SoftAlignmentScoreAlgorithm.ScoreEntry |
createDelInitial(SoftAlignmentScoreAlgorithm.ScoreEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
SoftAlignmentScoreAlgorithm.ScoreEntry |
createInitial()
This method should not be called from outside!
|
SoftAlignmentScoreAlgorithm.ScoreEntry |
createInsInitial(SoftAlignmentScoreAlgorithm.ScoreEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
SoftAlignmentScoreAlgorithm.ScoreEntry |
createNewEntry(SoftAlignmentScoreAlgorithm.ScoreEntry delOld,
SoftAlignmentScoreAlgorithm.ScoreEntry insOld,
SoftAlignmentScoreAlgorithm.ScoreEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
double |
getApproxThreshold()
For more information on the ApproxThreshold have a look at the
Softmin class.
|
double |
getBeta() |
void |
setApproxThreshold(double approxThreshold)
For more information on the ApproxThreshold have a look at the
Softmin class.
|
void |
setBeta(double beta) |
Double |
transformToResult(SoftAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
calculateAlignment, calculateDeletionCosts, calculateInsertionCosts, calculateReplacementCosts, createGenericArray, createGenericMatrix, getEntryClass, getLastAlignmentMatrix, getResultClass, getSpecification, getWeightThreshold, setWeightThreshold
public static final double DEFAULTBETA
public SoftAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification)
alignmentSpecification
- an AlignmentSpecification.public void setBeta(double beta)
beta
- The parameter defining the "softness" of the alignment. For
beta towards infinity this alignment becomes closer to the strict
alignment. For beta = 0 all possible alignments are equally considered
and softmin returns the average. Please note that a low beta value might
lead to a very rough approximation and that for higher sequence lengths
beta has to be higher, too.public double getBeta()
public double getApproxThreshold()
public void setApproxThreshold(double approxThreshold)
approxThreshold
- public SoftAlignmentScoreAlgorithm.ScoreEntry createInitial()
createInitial
in class AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
public SoftAlignmentScoreAlgorithm.ScoreEntry createDelInitial(SoftAlignmentScoreAlgorithm.ScoreEntry delOld, int i, double delLocal)
createDelInitial
in class AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
delOld
- the matrix entry (i,0)i
- i+1delLocal
- the local deletion cost, defined as the weighted sum over
all comparator deletion costs.public SoftAlignmentScoreAlgorithm.ScoreEntry createInsInitial(SoftAlignmentScoreAlgorithm.ScoreEntry insOld, int j, double insLocal)
createInsInitial
in class AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
insOld
- the matrix entry (0,j+1)j
- j+1insLocal
- the local insertion cost, defined as the weighted sum
over all comparator insertion costs.public SoftAlignmentScoreAlgorithm.ScoreEntry createNewEntry(SoftAlignmentScoreAlgorithm.ScoreEntry delOld, SoftAlignmentScoreAlgorithm.ScoreEntry insOld, SoftAlignmentScoreAlgorithm.ScoreEntry repOld, int i, int j, double delLocal, double insLocal, double repLocal)
createNewEntry
in class AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
delOld
- the matrix entry (i,j+1)insOld
- the matrix entry (i+1,j)repOld
- the matrix entry (i,j)i
- i+1j
- j+1delLocal
- the local deletion cost, defined as the weighted sum over
all comparator deletion costs.insLocal
- the local insertion cost, defined as the weighted sum
over all comparator insertion costs.repLocal
- the local replacement cost, defined as the weighted sum
over all comparator replacement costs.public Double transformToResult(SoftAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix, Sequence a, Sequence b)
transformToResult
in class AbstractGapAlignmentAlgorithm<SoftAlignmentScoreAlgorithm.ScoreEntry,Double>
alignmentMatrix
- the alignment matrix.a
- the first sequence.b
- th second sequence.Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, Georg Zentgraf, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs