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 |
SoftPathModel.getRight()
Returns the right input sequence.
|
Sequence |
AlignmentPath.getRight() |
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 |
---|---|
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 |
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.
|
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 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) |
SoftPathModel(AlignmentSpecification specificaton,
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[] |
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[] |
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 |
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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