Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
Modifier and Type | Method and Description |
---|---|
static AbstractLocalAlignmentAlgorithm.Recurrence |
AbstractLocalAlignmentAlgorithm.Recurrence.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static AbstractLocalAlignmentAlgorithm.Recurrence[] |
AbstractLocalAlignmentAlgorithm.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<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> |
SoftLocalPathModel.getDp_tables() |
Modifier and Type | Method and Description |
---|---|
Double |
StrictLocalAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
Double |
SoftLocalAlignmentScoreAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
AlignmentPath |
StrictLocalAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
SoftLocalPathModel |
SoftLocalAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
abstract R |
AbstractLocalAlignmentAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
Constructor and Description |
---|
SoftLocalPathModel(double beta,
AlignmentSpecification specification,
int minMiddleSkips,
double score,
EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, 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