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.csv |
This module permits exporting and importing of Sequence objects to CSV files.
|
de.citec.tcs.alignment.learning |
This module is a custom implementation of the Large Margin
Nearest Neighbor classification scheme of Weinberger, Saul, et al.
|
de.citec.tcs.alignment.sequence |
This module contains the sequence datastructure of the
TCS Alignment Toolbox.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Method and Description |
---|---|
Sequence |
SoftPathModel.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
SoftAffinePathModel.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
SoftDTWModel.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
PathList.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
PathMap.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
AlignmentDerivativeAlgorithm.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
AlignmentPath.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
SoftPathModel.getRight()
Returns the right sequence of this derivative.
|
Sequence |
SoftAffinePathModel.getRight()
Returns the right sequence of this derivative.
|
Sequence |
SoftDTWModel.getRight()
Returns the right sequence of this derivative.
|
Sequence |
PathList.getRight()
Returns the right sequence of this derivative.
|
Sequence |
PathMap.getRight()
Returns the right sequence of this derivative.
|
Sequence |
AlignmentDerivativeAlgorithm.getRight()
Returns the right sequence of this derivative.
|
Sequence |
AlignmentPath.getRight()
Returns the right sequence of this derivative.
|
Sequence[] |
ParallelProcessingEngine.getSequences() |
Modifier and Type | Method and Description |
---|---|
R |
AbstractAffineAlignmentAlgorithm.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 |
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.
|
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.
|
SoftDTWModel |
KernelDTWFullAlgorithm.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.
|
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.
|
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.
|
abstract R |
AbstractAffineAlignmentAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
SoftAffinePathModel |
SoftAffineAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
StrictAffineAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
AlignmentPath |
StrictAffineAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
SoftAffineAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
SoftAlignmentScoreAlgorithm.transformToResult(SoftAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
SoftPathModel |
SoftAlignmentFullAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
PathList |
SoftAlignmentSamplingAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
AlignmentPath |
StrictAlignmentFullAlgorithm.transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
StrictAlignmentScoreAlgorithm.transformToResult(StrictAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
PathList |
StrictAllOptimalAlgorithm.transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
PathMap |
StrictKPathAlgorithm.transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
abstract R |
AbstractGapAlignmentAlgorithm.transformToResult(X[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Constructor and Description |
---|
AlignmentPath(AlignmentSpecification specificaton,
Sequence left,
Sequence right,
double distance) |
ParallelProcessingEngine(AlignmentAlgorithm<R> algorithm,
Sequence[] sequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
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) |
SoftDTWModel(AlignmentSpecification specificaton,
Sequence x,
Sequence y,
double[][] similarityMatrix) |
SoftPathModel(AlignmentSpecification specification,
Sequence left,
Sequence right,
double distance,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
Modifier and Type | Method and Description |
---|---|
Sequence |
SoftADPPathModel.getLeft()
Returns the left sequence of this derivative.
|
Sequence |
SoftADPPathModel.getRight()
Returns the right sequence of this derivative.
|
Modifier and Type | Method and Description |
---|---|
R |
AbstractADPAlgorithm.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 |
SparseAbstractADPAlgorithm.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.
|
static double |
AbstractADPAlgorithm.normalizeDissimilarity(double dissimilarity,
Sequence a,
Sequence b) |
abstract R |
AbstractADPAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
SoftADPPathModel<N> |
SoftADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
StrictADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
SoftADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
AlignmentPath |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Double |
SparseStrictADPScoreAlgorithm.transformToResult(EnumMap<N,HashMap<MatrixEngine.MatrixCoordinate,Double>> dpTables,
HashMap<MatrixEngine.MatrixCoordinate,Double> compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
abstract R |
SparseAbstractADPAlgorithm.transformToResult(EnumMap<N,HashMap<MatrixEngine.MatrixCoordinate,Double>> dpTables,
HashMap<MatrixEngine.MatrixCoordinate,Double> compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
AlignmentPath |
SparseStrictADPFullAlgorithm.transformToResult(EnumMap<N,HashMap<MatrixEngine.MatrixCoordinate,Double>> dpTables,
HashMap<MatrixEngine.MatrixCoordinate,Double> compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence a,
Sequence b) |
Constructor and Description |
---|
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) |
Modifier and Type | Method and Description |
---|---|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
File csvFile)
This imports a sequence from a CSV file using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
File csvFile,
String valueDelimiterString)
This imports a sequence from a CSV file using the given delimiter string.
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
Reader in)
This imports a sequence from a Reader using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
Reader in,
String valueDelimiterString)
This imports a sequence from a Reader containing CSV data using the
given delimiter string.
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
String csvFileName)
This imports a sequence from a CSV file using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
String csvFileName,
String valueDelimiterString)
This imports a sequence from a CSV file using the given delimiter string.
|
Modifier and Type | Method and Description |
---|---|
static void |
CSVExporter.exportSequence(Sequence seq,
File csvFile)
This exports a sequence to a file of comma-separated values (CSV).
|
static void |
CSVExporter.exportSequence(Sequence seq,
File csvFile,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
static void |
CSVExporter.exportSequence(Sequence seq,
String csvFileName)
This exports a sequence to a file of comma-separated values (CSV).
|
static void |
CSVExporter.exportSequence(Sequence seq,
String csvFileName,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
static void |
CSVExporter.exportSequence(Sequence seq,
Writer out)
This exports a sequence to a Writer as CSV data.
|
static void |
CSVExporter.exportSequence(Sequence seq,
Writer out,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
Modifier and Type | Method and Description |
---|---|
Sequence[] |
LMNNGradientCalculator.getData()
Returns the training data points as Sequences.
|
Constructor and Description |
---|
LMNNGradientCalculator(Sequence[] data,
int[] trainingLabels,
AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm> algo) |
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 |
---|---|
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 |
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/