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.comparators |
This module defines the interfaces for Comparators in the TCS Alignment Toolbox.
|
Modifier and Type | Method and Description |
---|---|
boolean |
AbstractStrictDTWAlgorithm.requires(OperationType type) |
boolean |
AbstractStrictAlignmentAlgorithm.requires(OperationType type) |
boolean |
AlignmentAlgorithm.requires(OperationType type)
This method should return true if and only if this AlignmentAlgorithm uses the given
operation.
|
Constructor and Description |
---|
Operation(X left,
Y right,
OperationType type,
double distance)
This constructs an Operation within an AlignmentPath.
|
Modifier and Type | Method and Description |
---|---|
OperationType[] |
ProductionRule.getOperations()
Returns the operations that are applied in this production rule.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SparseAbstractADPAlgorithm.requires(OperationType type) |
boolean |
Grammar.requires(OperationType type)
This method should return true if and only if this Grammar uses the given OperationType.
|
boolean |
GlobalAsymmetricGrammar.requires(OperationType type) |
boolean |
SakoeChibaDTWGrammar.requires(OperationType type) |
boolean |
FlexibleGrammar.requires(OperationType type) |
boolean |
DTWGrammar.requires(OperationType type) |
boolean |
AbstractADPAlgorithm.requires(OperationType type) |
boolean |
AffineGrammar.requires(OperationType type) |
boolean |
GlobalGrammar.requires(OperationType type) |
Modifier and Type | Method and Description |
---|---|
SoftADPPathModel |
SoftADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
SoftADPPathModel |
SoftADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
SoftADPPathModel |
SoftADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
StrictADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
StrictADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
StrictADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SoftADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SoftADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SoftADPScoreAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
CooptimalModel<X,Y> |
StrictADPCooptimalAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
CooptimalModel<X,Y> |
StrictADPCooptimalAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
CooptimalModel<X,Y> |
StrictADPCooptimalAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
abstract R |
AbstractADPAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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 |
AbstractADPAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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 |
AbstractADPAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> 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.
|
Alignment<X,Y> |
SparseStrictADPFullAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
SparseStrictADPFullAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
SparseStrictADPFullAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SparseStrictADPScoreAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SparseStrictADPScoreAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Double |
SparseStrictADPScoreAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Constructor and Description |
---|
ProductionRule(OperationType[] operations,
N nonterminal)
Creates a new production rule of the form
A → operation_1( ...
|
ProductionRule(OperationType operation,
N nonterminal)
Creates a new production rule of the form
A → operation(left, B, right)
|
Constructor and Description |
---|
SoftADPPathModel(Comparator<X,Y> comparator,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> left,
List<Y> right) |
SoftADPPathModel(Comparator<X,Y> comparator,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> left,
List<Y> right) |
SoftADPPathModel(Comparator<X,Y> comparator,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> left,
List<Y> right) |
Modifier and Type | Method and Description |
---|---|
static OperationType[] |
OperationType.getDeletions()
Returns an array containing the Deletion OperationTypes, namely DELETION and SKIPDELETION.
|
static OperationType[] |
OperationType.getGaps()
Returns an array containing the gap OperationTypes, namely DELETION and INSERTION.
|
static OperationType[] |
OperationType.getInsertions()
Returns an array containing the Insertion OperationTypes, namely INSERTION and SKIPINSERTION.
|
static OperationType[] |
OperationType.getReplacements()
Returns an array containing the Replacement OperationTypes, namely REPLACEMENT,
DELETIONREPLACEMENT and INSERTIONREPLACEMENT.
|
static OperationType[] |
OperationType.getSkips()
Returns an array containing the skip OperationTypes, namely SKIPDELETION and SKIPINSERTION.
|
static OperationType |
OperationType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static OperationType[] |
OperationType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
double[] |
AlignmentSpecification.calculateComparatorDistances(OperationType type,
Node a,
Node b)
Calculates the distances returned by every single Comparator in this AlignmentSpecification.
|
double |
AlignmentSpecification.compare(OperationType type,
Node a,
Node b) |
double |
AbstractValueComparatorWrapper.compare(OperationType type,
Node a,
Node b) |
double |
SquareReplacementMatrixComparator.compare(OperationType type,
X a,
X b) |
double |
SkipExtendedComparator.compare(OperationType type,
X a,
Y b) |
double |
ComparisonBasedSkipExtendedComparator.compare(OperationType type,
X a,
Y b) |
double |
Comparator.compare(OperationType type,
X a,
Y b)
This method returns a dissimilarity between x and y using the alignment operation op with the
following restrictions:
compare(op,x,y) ≥ 0 (non-negativity)
compare(op,x,y) ≤ 1 (normalization)
x = y ⇒ compare(op,x,y) = 0 (equality)
Further, this function guarantees consistency with respect to null inputs, that is, for any
operation op ∈ {REPLACEMENT, DELETIONREPLACEMENT, INSERTIONREPLACEMENT} it holds:
d(op, x, null) = d(DELETION, x, null)
d(op, null, y) = d(INSERTION, null, y)
and for any operation it holds:
d(op, null, null) = 0
Please note that a and b might be null if this alignment uses gaps or
skips.
|
Gradient |
AlignmentSpecification.computeGradient(OperationType type,
Node a,
Node b) |
Gradient |
AbstractDerivableValueComparatorWrapper.computeGradient(OperationType type,
Node a,
Node b) |
Gradient |
SquareReplacementMatrixComparator.computeGradient(OperationType type,
X a,
X b) |
Gradient |
SkipExtendedComparator.computeGradient(OperationType type,
X a,
Y b) |
Gradient |
DerivableComparator.computeGradient(OperationType type,
X a,
Y b)
Computes the gradient of this comparator function w.r.t.
|
Gradient |
ComparisonBasedSkipExtendedComparator.computeGradient(OperationType type,
X a,
Y b) |
boolean |
SquareReplacementMatrixComparator.supports(OperationType type) |
boolean |
SkipExtendedComparator.supports(OperationType type) |
boolean |
Comparator.supports(OperationType type)
This method should return true if and only if this Comparator supports the given alignment
operation.
|
boolean |
AlignmentSpecification.supports(OperationType type) |
boolean |
AbstractValueComparatorWrapper.supports(OperationType type) |
Copyright (C) 2016 Benjamin Paaßen, 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/