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).
|
Modifier and Type | Method and Description |
---|---|
Callable<R> |
AbstractParallelDerivativeEngine.createCallable(MatrixEngine.MatrixCoordinate ident)
A method that should create a Callable (computation job) for the given
identifier object.
|
Callable<R> |
ParallelProcessingEngine.createCallable(MatrixEngine.MatrixCoordinate ident)
A method that should create a Callable (computation job) for the given
identifier object.
|
Constructor and Description |
---|
AbstractParallelDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
Class<R> resultClass) |
ParallelDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,Y> comparator,
String keyword) |
ParallelRawDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,?> comparator,
String keyword) |
ParallelWeightDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N) |
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 |
---|---|
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.
|
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.
|
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) |
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) |
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.
|
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/