Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
de.citec.tcs.alignment.adp |
This package contains a more general approach to construct
AlignmentAlgorithms by relying on the theoretical concept of Algebraic
Dynamic Programming (ADP) as developed by Giegerich et al.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Method and Description |
---|---|
AlignmentSpecification |
AbstractAffineAlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
SoftPathModel.getSpecification()
Returns the AlignmentSpecification that was basis for this Alignment.
|
AlignmentSpecification |
SoftAffinePathModel.getSpecification()
Returns the AlignmentSpecification that was used to compute this
SoftAffinePathModel.
|
AlignmentSpecification |
AbstractGapAlignmentAlgorithm.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 |
KernelDTWFullAlgorithm.getSpecification() |
AlignmentSpecification |
AlignmentAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
SoftDTWModel.getSpecificaton()
Returns the AlignmentSpecification that was basis for this Alignment.
|
AlignmentSpecification |
AlignmentPath.getSpecificaton() |
Modifier and Type | Method and Description |
---|---|
static double[] |
Operation.calculateComparatorDistances(OperationType op,
Node left,
Node right,
AlignmentSpecification spec) |
Constructor and Description |
---|
AbstractAffineAlignmentAlgorithm(Class<R> resultClass,
AlignmentSpecification alignmentSpecification) |
AbstractGapAlignmentAlgorithm(AlignmentSpecification alignmentSpecification,
Class<X> entryClass,
Class<R> resultClass) |
AbstractStrictDTWAlgorithm(Class<R> resultClass,
AlignmentSpecification specification) |
AlignmentPath(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double distance) |
AlignmentSpecification(AlignmentSpecification other)
Constructs a copy of the given other AlignmentSpecification.
|
KernelDTWFullAlgorithm(AlignmentSpecification alignmentSpecification) |
SoftAffineAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification) |
SoftAffineAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification) |
SoftAffinePathModel(double beta,
AlignmentSpecification specification,
int minMiddleSkips,
double distance,
EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
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 specification,
Sequence left,
Sequence right,
double distance,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
StrictAffineAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification) |
StrictAffineAlignmentScoreAlgorithm(AlignmentSpecification alignmentSpecification) |
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.
|
Modifier and Type | Method and Description |
---|---|
AlignmentSpecification |
AbstractADPAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
SparseAbstractADPAlgorithm.getSpecification()
This should return the specification that is used for this Algorithm.
|
AlignmentSpecification |
SoftADPPathModel.getSpecification()
Returns the AlignmentSpecification that was used to compute this
SoftAffinePathModel.
|
Constructor and Description |
---|
AbstractADPAlgorithm(Grammar<N> grammar,
Class<R> resultClass,
AlignmentSpecification alignmentSpecification) |
SoftADPFullAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification)
Creates a new SoftFullAlgorithm based on the given ADP grammar
and the given AlignmentSpecification/algebra.
|
SoftADPPathModel(AlignmentSpecification specification,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
SoftADPScoreAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
SparseAbstractADPAlgorithm(SparseGrammar<N> grammar,
Class<R> resultClass,
AlignmentSpecification alignmentSpecification) |
SparseStrictADPFullAlgorithm(SparseGrammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
SparseStrictADPScoreAlgorithm(SparseGrammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
StrictADPFullAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
StrictADPScoreAlgorithm(Grammar<N> grammar,
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 |
VectorialSequences.setUpSpecification(Sequence[] dataSpace)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace)
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
|
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) 2013-2015 Benjamin Paaßen, 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 . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/