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.parallel |
This module provides a very basic support for the parallel
computing of tasks (Engine class) and entries of a matrix (MatrixEngine).
|
de.citec.tcs.alignment.trees |
This package contains an implementation of the Tree Edit Distance according to Zhang & Shasha (1989).
|
Modifier and Type | Method and Description |
---|---|
Map<MatrixEngine.MatrixCoordinate,OperationType[][]> |
CooptimalModel.getCooptimals()
A Map of matrix coordinates to an array of sequences of operations that can be co-optimally
applied at the given position of the dynamic programming matrix.
|
Map<MatrixEngine.MatrixCoordinate,DerivableAlignmentDistance<X,Y>> |
ParallelGradientEngine.getDistances()
Returns the DerivableAlignmentDistance objects used for derivative calculation.
|
Modifier and Type | Method and Description |
---|---|
Callable<R> |
SquareParallelProcessingEngine.createCallable(MatrixEngine.MatrixCoordinate ident) |
Callable<R> |
ParallelProcessingEngine.createCallable(MatrixEngine.MatrixCoordinate ident) |
Callable<double[]> |
ParallelGradientEngine.createCallable(MatrixEngine.MatrixCoordinate ident) |
Constructor and Description |
---|
ParallelGradientEngine(Collection<Engine.CalculationResult<? extends MatrixEngine.MatrixCoordinate,? extends DerivableAlignmentDistance<X,Y>>> results,
int M,
int N,
DerivableComparator<X,Y> comparator)
Creates a ParallelGradientEngine that computes gradients for several
DeriableAlignmentDistance objects in parallel.
|
ParallelGradientEngine(Map<MatrixEngine.MatrixCoordinate,DerivableAlignmentDistance<X,Y>> derivableMatrixEntries,
int M,
int N,
DerivableComparator<X,Y> comparator)
Creates a ParallelGradientEngine that computes gradients for several
DeriableAlignmentDistance objects in parallel.
|
Modifier and Type | Method and Description |
---|---|
NavigableSet<MatrixEngine.MatrixCoordinate> |
SparseGrammar.entries(int M,
int N) |
NavigableSet<MatrixEngine.MatrixCoordinate> |
SakoeChibaDTWGrammar.entries(int M,
int N) |
Modifier and Type | Method and Description |
---|---|
int |
MatrixEngine.MatrixCoordinate.compareTo(MatrixEngine.MatrixCoordinate t) |
void |
MatrixEngine.setSpecificTasks(MatrixEngine.MatrixCoordinate[] coords)
Clears all current calculation tasks and instead adds a task for every
given matrix coordinate.
|
Modifier and Type | Method and Description |
---|---|
void |
MatrixEngine.setSpecificTasks(Collection<MatrixEngine.MatrixCoordinate> coords)
Clears all current calculation tasks and instead adds a task for every
given matrix coordinate.
|
Modifier and Type | Method and Description |
---|---|
Callable<R> |
TreeSquareParallelProcessingEngine.createCallable(MatrixEngine.MatrixCoordinate ident) |
Callable<R> |
TreeParallelProcessingEngine.createCallable(MatrixEngine.MatrixCoordinate ident) |
Modifier and Type | Method and Description |
---|---|
static double |
CooptimalMatrix.editDistance(Map<? extends MatrixEngine.MatrixCoordinate,Double> p_rep,
double[] p_del,
double[] p_ins,
double[][] rep,
double[] del,
double[] ins)
Returns the edit distance corresponding to the given frequency matrix P and the given costs
for replacement, deletion and insertion.
|
static double |
CooptimalMatrix.editDistance(Map<? extends MatrixEngine.MatrixCoordinate,Double> p_rep,
double[] p_del,
double[] p_ins,
Map<? extends MatrixEngine.MatrixCoordinate,Double> rep,
double[] del,
double[] ins)
Returns the edit distance corresponding to the given frequency matrix P and the given costs
for replacement, deletion and insertion.
|
static double |
CooptimalMatrix.editDistance(Map<? extends MatrixEngine.MatrixCoordinate,Double> p_rep,
double[] p_del,
double[] p_ins,
Map<? extends MatrixEngine.MatrixCoordinate,Double> rep,
double[] del,
double[] ins)
Returns the edit distance corresponding to the given frequency matrix P and the given costs
for replacement, deletion and insertion.
|
Constructor and Description |
---|
CooptimalMatrix(Map<? extends MatrixEngine.MatrixCoordinate,Double> p_rep,
double[] p_del,
double[] p_ins,
List<X> left,
List<Y> right,
double distance,
double K)
Initializes a CooptimalMatrix with the given operation frequencies.
|
SparseMatrix(Comparator<? super MatrixEngine.MatrixCoordinate> comparator) |
SparseMatrix(Map<? extends MatrixEngine.MatrixCoordinate,? extends Double> m) |
SparseMatrix(SortedMap<MatrixEngine.MatrixCoordinate,? extends Double> m) |
Copyright (C) 2016-2018 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/