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 |
---|---|
<X extends Value,Y> |
SoftAffinePathModel.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftPathModel.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftDTWModel.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
AlignmentDerivativeAlgorithm.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
PathMap.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
PathList.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
AlignmentPath.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftAffinePathModel.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftPathModel.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftDTWModel.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
AlignmentDerivativeAlgorithm.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
PathMap.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
PathList.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
AlignmentPath.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
Constructor and Description |
---|
ParallelDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries,
DerivableComparator<?,Y> comparator,
String keyword) |
ParallelDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,Y> comparator,
String keyword) |
ParallelRawDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries,
DerivableComparator<?,?> comparator,
String keyword) |
ParallelRawDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,?> comparator,
String keyword) |
Modifier and Type | Method and Description |
---|---|
<X extends Value,Y> |
SoftADPPathModel.calculateParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
<X extends Value,Y> |
SoftADPPathModel.calculateRawParameterDerivative(DerivableComparator<X,Y> comp,
String keyword)
This returns the derivatives for all parameters of the given comparator
according to the implementation.
|
Modifier and Type | Interface and Description |
---|---|
interface |
SparseDerivableComparator<X extends Value,Y>
Some derivable comparators have the special property that in each alignment
step only a small subset of parameters is needed.
|
Modifier and Type | Class and Description |
---|---|
class |
CharStatComparator
This compares strings using statistics over the number of letters inside.
|
class |
ComparisonBasedSkipExtendedComparator<V extends Value>
This is an abstract class allowing to define a dynamic method to
extend a simple Comparator to a SkipComparator.
|
class |
DTWKernelComparator
implements halved gauss-kernel k:
k = exp(-1/2sigma^2 * |x-y|^2) /2, with |.| beeing the weighted euclidian
distance
k is positive definite
|
class |
EuclideanComparator
Compares vectors using the L2-Norm.
|
class |
L1NormComparator
Compares vectors using the L1-Norm.
|
class |
NCDComparator
This compares strings using normalized compression distance.
|
class |
ReplacementComparator
This comparator defines explicit replacement (and deletion/insertion) costs
for comparison of symbolic values.
|
class |
SkipExtendedComparator<V extends Value>
This is an abstract class to be used for Comparators that are only
to be used for comparisons per se but can be extended for use with
gaps and skips.
|
class |
TrivialEditComparator
This is a Comparator for SymbolicValues that just specifies a score for:
the deletion of a symbol (1 per default)
the insertion of a symbol (1 per default)
the skip deletion of a symbol (0.5 per default)
the skip insertion of a symbol (0.5 per default)
a match between the same symbols (0 per default)
a mismatch between different symbols (1 per default)
Please note that this is just a special case of the much more general
ReplacementComparator.
|
class |
ZeroNormComparator
This comparator works on basis of the zero norm.
|
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