public class StrictAffineAlignmentFullAlgorithm extends AbstractAffineAlignmentAlgorithm<AlignmentPath>
AbstractAffineAlignmentAlgorithm.Recurrence
Constructor and Description |
---|
StrictAffineAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification) |
Modifier and Type | Method and Description |
---|---|
double |
choice(double... choices)
This implements the strict maximum of the given input doubles.
|
OperationType[] |
getPreferredCooptimal()
This allows to specify an order in which operations shall be preferred if
cooptimal alignments occur.
|
void |
setPreferredCooptimal(OperationType[] preferredCooptimal)
This allows to specify an order in which operations shall be preferred if
cooptimal alignments occur.
|
AlignmentPath |
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.
|
calculateAlignment, getMinMiddleSkips, getResultClass, getSpecification, getWeightThreshold, setMinMiddleSkips, setWeightThreshold
public StrictAffineAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification)
public void setPreferredCooptimal(OperationType[] preferredCooptimal)
preferredCooptimal
- public OperationType[] getPreferredCooptimal()
public double choice(double... choices)
choice
in class AbstractAffineAlignmentAlgorithm<AlignmentPath>
choices
- the costs of all choices.public AlignmentPath transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables, double[][] compareMatrix, double[] deletionMatrix, double[] insertionMatrix, double[] skipDeletionMatrix, double[] skipInsertionMatrix, Sequence a, Sequence b)
transformToResult
in class AbstractAffineAlignmentAlgorithm<AlignmentPath>
dp_tables
- the dynamic programming matrices used during
calculation.compareMatrix
- the local cost for replacing node i from the first
sequence with node j from the second sequence.deletionMatrix
- the local cost for deleting node i from the first
sequence.insertionMatrix
- the local cost for inserting node j from the
second sequence into the first sequence.skipDeletionMatrix
- the local cost for skipping node i in the
first sequence.skipInsertionMatrix
- the local cost for skipping node j in the
second sequence.a
- the first sequence.b
- th second sequence.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