public class SoftLocalPathModel extends Object implements AlignmentDerivativeAlgorithm
Constructor and Description |
---|
SoftLocalPathModel(double beta,
AlignmentSpecification specification,
int minMiddleSkips,
double score,
EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
Modifier and Type | Method and Description |
---|---|
<X extends Value,Y> |
calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
double[] |
calculateWeightDerivative()
Calculates the derivative for each keyword weight.
|
double |
getBeta() |
double[][] |
getCompareMatrix() |
double[] |
getDeletionMatrix() |
EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> |
getDp_tables() |
double[] |
getInsertionMatrix() |
Sequence |
getLeftSequence() |
int |
getMinMiddleSkips() |
Sequence |
getRightSequence() |
double |
getScore() |
double[] |
getSkipDeletionMatrix() |
double[] |
getSkipInsertionMatrix() |
AlignmentSpecification |
getSpecification() |
public SoftLocalPathModel(double beta, AlignmentSpecification specification, int minMiddleSkips, double score, EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables, double[][] compareMatrix, double[] deletionMatrix, double[] insertionMatrix, double[] skipDeletionMatrix, double[] skipInsertionMatrix, Sequence leftSequence, Sequence rightSequence)
public double getBeta()
public AlignmentSpecification getSpecification()
public int getMinMiddleSkips()
public double getScore()
public EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> getDp_tables()
public double[][] getCompareMatrix()
public double[] getDeletionMatrix()
public double[] getInsertionMatrix()
public double[] getSkipDeletionMatrix()
public double[] getSkipInsertionMatrix()
public Sequence getLeftSequence()
public Sequence getRightSequence()
public <X extends Value,Y> double[] calculateRawParameterDerivative(DerivableComparator<X,Y> comp, String keyword)
calculateRawParameterDerivative
in interface AlignmentDerivativeAlgorithm
X
- the values the given comparator can compare.comp
- the DerivableComparator that provides functionality to
calculate local derivatives.keyword
- the keyword for which the given comparator was used in
the Alignment.public <X extends Value,Y> Y calculateParameterDerivative(DerivableComparator<X,Y> comp, String keyword)
calculateParameterDerivative
in interface AlignmentDerivativeAlgorithm
X
- the values the given comparator can compare.Y
- the result format for derivatives of the given comparator.comp
- the DerivableComparator that provides functionality to
calculate local derivatives.keyword
- the keyword for which the given comparator was used in
the Alignment.public double[] calculateWeightDerivative()
calculateWeightDerivative
in interface AlignmentDerivativeAlgorithm
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