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 |
AbstractGapAlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
DynamicTimeWarpingAlgorithm.getSpecification() |
AlignmentSpecification |
AlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
AbstractStrictDTWAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
SoftLocalPathModel.getSpecification() |
AlignmentSpecification |
SoftPathModel.getSpecification()
Returns the AlignmentSpecification that was basis for this Alignment.
|
AlignmentSpecification |
AbstractLocalAlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
AlignmentPath.getSpecificaton() |
AlignmentSpecification |
SoftDTWModel.getSpecificaton()
Returns the AlignmentSpecification that was basis for this Alignment.
|
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.
|
static double[] |
AbstractLocalAlignmentAlgorithm.calculateSkipDeletionCosts(Node a,
AlignmentSpecification specification)
This calculates the non-weighted costs for skip-deleting the single
values in node a.
|
static double[] |
AbstractLocalAlignmentAlgorithm.calculateSkipInsertionCosts(Node b,
AlignmentSpecification specification)
This calculates the non-weighted costs for skip-inserting the single
values of node b.
|
Constructor and Description |
---|
AbstractGapAlignmentAlgorithm(AlignmentSpecification alignmentSpecification,
Class<X> entryClass,
Class<R> resultClass) |
AbstractLocalAlignmentAlgorithm(Class<R> resultClass,
AlignmentSpecification alignmentSpecification) |
AbstractStrictDTWAlgorithm(Class<R> resultClass,
AlignmentSpecification specification) |
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) |
SoftLocalAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification) |
SoftLocalAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification) |
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) |
SoftPathModel(AlignmentSpecification specification,
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.
|
StrictDTWFullAlgorithm(AlignmentSpecification spec) |
StrictDTWScoreAlgorithm(AlignmentSpecification spec) |
StrictKPathAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
StrictLocalAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification) |
StrictLocalAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification) |
Modifier and Type | Method and Description |
---|---|
static AlignmentSpecification |
RandomSequenceGenerator.generateSpecification(int K)
This generates an AlignmentSpecification and implicitly a
NodeSpecification for K keywords.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace)
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
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.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
GapComparator[] comparators)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
GapComparator[] comparators,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
GapComparator<VectorialValue> comparator)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
GapComparator<VectorialValue> comparator,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
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