public class SoftLocalAlignmentScoreAlgorithm extends AbstractLocalAlignmentAlgorithm<Double>
AbstractLocalAlignmentAlgorithm.Recurrence
Modifier and Type | Field and Description |
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static double |
DEFAULTBETA |
Constructor and Description |
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SoftLocalAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification) |
Modifier and Type | Method and Description |
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double |
choice(double... choices)
This implements the strict maximum of the given input doubles.
|
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.
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void |
setBeta(double beta) |
Double |
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
calculateAlignment, calculateSkipDeletionCosts, calculateSkipInsertionCosts, getMinMiddleSkips, getResultClass, getSpecification, getWeightThreshold, setMinMiddleSkips, setWeightThreshold
public static final double DEFAULTBETA
public SoftLocalAlignmentScoreAlgorithm(AlignmentSpecification 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 double choice(double... choices)
choice
in class AbstractLocalAlignmentAlgorithm<Double>
choices
- the costs of all choices.public Double transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables, double[][] compareMatrix, double[] deletionMatrix, double[] insertionMatrix, double[] skipDeletionMatrix, double[] skipInsertionMatrix, Sequence a, Sequence b)
transformToResult
in class AbstractLocalAlignmentAlgorithm<Double>
dp_tables
- the dynamic programming matrices used during
calculation.compareMatrix
- the local cost for replacing node i from the first
sequence with node j from the second sequence.deletionMatrix
- the local cost for deleting node i from the first
sequence.insertionMatrix
- the local cost for inserting node j from the
second sequence into the first sequence.skipDeletionMatrix
- the local cost for skipping node i in the
first sequence.skipInsertionMatrix
- the local cost for skipping node j in the
second sequence.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