Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
Modifier and Type | Method and Description |
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static AbstractAffineAlignmentAlgorithm.Recurrence |
AbstractAffineAlignmentAlgorithm.Recurrence.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static AbstractAffineAlignmentAlgorithm.Recurrence[] |
AbstractAffineAlignmentAlgorithm.Recurrence.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> |
SoftAffinePathModel.getDp_tables()
Returns the dynamic programming tables that constitute the (soft) affine
alignment of both input sequences.
|
Modifier and Type | Method and Description |
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abstract R |
AbstractAffineAlignmentAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
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.
|
SoftAffinePathModel |
SoftAffineAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
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 |
StrictAffineAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
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 |
StrictAffineAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
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 |
SoftAffineAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
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.
|
Constructor and Description |
---|
SoftAffinePathModel(double beta,
AlignmentSpecification specification,
int minMiddleSkips,
double distance,
EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
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/