Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
de.unibi.citec.tcs.alignment.sequence |
This package contains the definition of input Sequences for
AlignmentAlgorithms.
|
de.unibi.citec.tcs.alignment.visualization | |
de.unibi.citec.tcs.alignment.wrappers |
Modifier and Type | Method and Description |
---|---|
Sequence |
SoftPathModel.getLeft()
Returns the left input sequence.
|
Sequence |
AlignmentPath.getLeft() |
Sequence |
SoftLocalPathModel.getLeftSequence() |
Sequence |
SoftPathModel.getRight()
Returns the right input sequence.
|
Sequence |
AlignmentPath.getRight() |
Sequence |
SoftLocalPathModel.getRightSequence() |
Sequence[] |
ParallelProcessingEngine.getSequences() |
Sequence |
SoftDTWModel.getX()
Returns the first input sequence.
|
Sequence |
SoftDTWModel.getY()
Returns the second input sequence.
|
Modifier and Type | Method and Description |
---|---|
R |
AbstractGapAlignmentAlgorithm.calculateAlignment(Sequence a,
Sequence b)
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
|
SoftDTWModel |
DynamicTimeWarpingAlgorithm.calculateAlignment(Sequence a,
Sequence b)
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
|
R |
AlignmentAlgorithm.calculateAlignment(Sequence a,
Sequence b)
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
|
R |
AbstractStrictDTWAlgorithm.calculateAlignment(Sequence a,
Sequence b)
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
|
R |
AbstractLocalAlignmentAlgorithm.calculateAlignment(Sequence a,
Sequence b)
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
|
abstract R |
AbstractStrictDTWAlgorithm.transformToResult(double[][] dtwMatrix,
Sequence a,
Sequence b)
This method has to be implemented by sub classes to transform
a calculated dynamic programming matrix to a valid result of
that implementation.
|
Double |
StrictDTWScoreAlgorithm.transformToResult(double[][] dtwMatrix,
Sequence a,
Sequence b)
This method has to be implemented by sub classes to transform
a calculated dynamic programming matrix to a valid result of
that implementation.
|
AlignmentPath |
StrictDTWFullAlgorithm.transformToResult(double[][] dtwMatrix,
Sequence a,
Sequence b)
This method has to be implemented by sub classes to transform
a calculated dynamic programming matrix to a valid result of
that implementation.
|
Double |
StrictLocalAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Double |
SoftLocalAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
AlignmentPath |
StrictLocalAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
SoftLocalPathModel |
SoftLocalAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
abstract R |
AbstractLocalAlignmentAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Double |
SoftAlignmentScoreAlgorithm.transformToResult(SoftAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
SoftPathModel |
SoftAlignmentFullAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
PathList |
SoftAlignmentSamplingAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
AlignmentPath |
StrictAlignmentFullAlgorithm.transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Double |
StrictAlignmentScoreAlgorithm.transformToResult(StrictAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
PathList |
StrictAllOptimalAlgorithm.transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
PathMap |
StrictKPathAlgorithm.transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
abstract R |
AbstractGapAlignmentAlgorithm.transformToResult(X[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Constructor and Description |
---|
AlignmentPath(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double score) |
AlignmentSpecification(Sequence sequence)
Initializes an alignment specification using the node specification
inside.
|
ParallelProcessingEngine(AlignmentAlgorithm<R> algorithm,
Sequence[] sequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
SoftDTWModel(AlignmentSpecification specificaton,
Sequence x,
Sequence y,
double[][] similarityMatrix) |
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) |
Modifier and Type | Method and Description |
---|---|
Sequence |
Node.getSequence()
Returns the sequence this node belongs to.
|
Constructor and Description |
---|
Node(Sequence sequence) |
Modifier and Type | Method and Description |
---|---|
void |
ExternalContent.add(SpecialHTMLTransformer hTransForm,
Sequence seq)
Adds content for the key to this ExternalContent.
|
Modifier and Type | Method and Description |
---|---|
static Sequence[] |
RandomSequenceGenerator.generateSequences(int N,
int L,
int K)
This generates N random sequences of length L each with K keywords.
|
static Sequence[] |
RandomSequenceGenerator.generateSequences(int N,
int L,
NodeSpecification nodeSpec)
This generates N random sequences of length L each according to
the given NodeSpecification.
|
static Sequence[] |
StringEditDistance.toSequences(Collection<String> strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
|
static Sequence[] |
StringEditDistance.toSequences(Collection<String> strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
|
static Sequence[] |
VectorialSequences.toSequences(double[][] arrays)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays,
String[] keywords)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays,
String[] keywords,
int[] propertyDist)
Transforms the given arrays to sequences.
|
static Sequence[] |
StringEditDistance.toSequences(String[] strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
|
static Sequence[] |
StringEditDistance.toSequences(String[] strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
StringEditDistance.calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm> algorithm,
Sequence a,
Sequence b)
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
|
static <R extends AlignmentDerivativeAlgorithm> |
StringEditDistance.calculateDerivatives(AlignmentAlgorithm<R> algorithm,
Sequence[] dataSpace,
int threadNum)
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
|
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