Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
de.unibi.citec.tcs.alignment.wrappers |
Modifier and Type | Method and Description |
---|---|
AlignmentSpecification |
DynamicTimeWarpingAlgorithm.getSpecification() |
AlignmentSpecification |
AlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
AbstractGapAlignmentAlgorithm.getSpecification() |
AlignmentSpecification |
SoftDTWModel.getSpecificaton()
Returns the AlignmentSpecification that was basis for this Alignment.
|
AlignmentSpecification |
SoftPathModel.getSpecificaton()
Returns the AlignmentSpecification that was basis for this Alignment.
|
AlignmentSpecification |
AlignmentPath.getSpecificaton() |
Modifier and Type | Method and Description |
---|---|
static double[] |
AbstractGapAlignmentAlgorithm.calculateDeletionCosts(Node a,
AlignmentSpecification specification)
This calculates the non-weighted costs for deleting the single values in
node a.
|
static double[] |
AbstractGapAlignmentAlgorithm.calculateInsertionCosts(Node b,
AlignmentSpecification specification)
This calculates the non-weighted costs for inserting the single values of
node b.
|
static double[] |
AbstractGapAlignmentAlgorithm.calculateReplacementCosts(Node a,
Node b,
AlignmentSpecification specification)
This calculates the non-weighted costs for replacing the single values in
node a by the values in node b.
|
Constructor and Description |
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AbstractGapAlignmentAlgorithm(AlignmentSpecification alignmentSpecification,
Class<X> entryClass,
Class<R> resultClass) |
AlignmentPath(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double score) |
DynamicTimeWarpingAlgorithm(AlignmentSpecification alignmentSpecification) |
SoftAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
SoftAlignmentSamplingAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
SoftAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
SoftDTWModel(AlignmentSpecification specificaton,
Sequence x,
Sequence y,
double[][] similarityMatrix) |
SoftPathModel(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double score,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
StrictAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
StrictAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
StrictAllOptimalAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
StrictKPathAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
Modifier and Type | Method and Description |
---|---|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace)
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace,
double[][] scoringScheme)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace,
double matchCost,
double mismatchCost,
double gapCost)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
|
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