public class SoftPathModel extends Object implements AlignmentDerivativeAlgorithm
Modifier and Type | Class and Description |
---|---|
static class |
SoftPathModel.SoftMatrixEntry |
Constructor and Description |
---|
SoftPathModel(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double score,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
Modifier and Type | Method and Description |
---|---|
<X extends Value,Y> |
calculateParameterDerivative(DerivableComparator<X,Y> comp)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
calculateRawParameterDerivative(DerivableComparator<X,Y> comp)
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()
The parameter defining the "softness" of the alignment.
|
Sequence |
getLeft()
Returns the left input sequence.
|
SoftPathModel.SoftMatrixEntry[][] |
getPathMatrix()
This is the dynamic programming matrix calculated by a
SoftAlignmentAlgorithm.
|
Sequence |
getRight()
Returns the right input sequence.
|
double |
getScore()
Returns the soft alignment score between the two input sequences,
normalized between 0 and 1, where 0 means a perfect similarity and 1 a
absolute dissimilarity.
|
AlignmentSpecification |
getSpecificaton()
Returns the AlignmentSpecification that was basis for this Alignment.
|
public SoftPathModel(AlignmentSpecification specificaton, Sequence left, Sequence right, double score, double beta, SoftPathModel.SoftMatrixEntry[][] pathMatrix)
public Sequence getLeft()
public Sequence getRight()
public AlignmentSpecification getSpecificaton()
public double getScore()
public double getBeta()
public SoftPathModel.SoftMatrixEntry[][] getPathMatrix()
public <X extends Value,Y> Y calculateParameterDerivative(DerivableComparator<X,Y> comp)
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.public <X extends Value,Y> double[] calculateRawParameterDerivative(DerivableComparator<X,Y> comp)
calculateRawParameterDerivative
in interface AlignmentDerivativeAlgorithm
X
- the values the given comparator can compare.comp
- the DerivableComparator that provides functionality to
calculate local derivatives.public double[] calculateWeightDerivative()
calculateWeightDerivative
in interface AlignmentDerivativeAlgorithm
Copyright © 2014. All rights reserved.