public class StrictAllOptimalAlgorithm extends AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
Modifier and Type | Class and Description |
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static class |
StrictAllOptimalAlgorithm.FullMatrixEntry |
Modifier and Type | Field and Description |
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static int |
DEFAULTPATHLIMIT |
Constructor and Description |
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StrictAllOptimalAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
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Modifier and Type | Method and Description |
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StrictAllOptimalAlgorithm.FullMatrixEntry |
createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createInitial()
This method should not be called from outside!
|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry delOld,
StrictAllOptimalAlgorithm.FullMatrixEntry insOld,
StrictAllOptimalAlgorithm.FullMatrixEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
int |
getPathLimit()
Please refer to the corresponding setter-method for more information.
|
void |
setPathLimit(int pathLimit)
The total number of co-optimal alignments can be very huge as multiple
co-optimal operations lead to a combinatorial explosion of possible
alignments.
|
PathList |
transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
calculateAlignment, calculateDeletionCosts, calculateInsertionCosts, calculateReplacementCosts, createGenericArray, createGenericMatrix, getEntryClass, getLastAlignmentMatrix, getResultClass, getSpecification, getWeightThreshold, setWeightThreshold
public static final int DEFAULTPATHLIMIT
public StrictAllOptimalAlgorithm(AlignmentSpecification alignmentSpecification)
alignmentSpecification
- an AlignmentSpecification.public int getPathLimit()
public void setPathLimit(int pathLimit)
pathLimit
- a maximum number of co-optimal paths that shall be
calculated.public StrictAllOptimalAlgorithm.FullMatrixEntry createInitial()
createInitial
in class AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
public StrictAllOptimalAlgorithm.FullMatrixEntry createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry delOld, int i, double delLocal)
createDelInitial
in class AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
delOld
- the matrix entry (i,0)i
- i+1delLocal
- the local deletion cost, defined as the weighted sum over
all comparator deletion costs.public StrictAllOptimalAlgorithm.FullMatrixEntry createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry insOld, int j, double insLocal)
createInsInitial
in class AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
insOld
- the matrix entry (0,j+1)j
- j+1insLocal
- the local insertion cost, defined as the weighted sum
over all comparator insertion costs.public StrictAllOptimalAlgorithm.FullMatrixEntry createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry delOld, StrictAllOptimalAlgorithm.FullMatrixEntry insOld, StrictAllOptimalAlgorithm.FullMatrixEntry repOld, int i, int j, double delLocal, double insLocal, double repLocal)
createNewEntry
in class AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
delOld
- the matrix entry (i,j+1)insOld
- the matrix entry (i+1,j)repOld
- the matrix entry (i,j)i
- i+1j
- j+1delLocal
- the local deletion cost, defined as the weighted sum over
all comparator deletion costs.insLocal
- the local insertion cost, defined as the weighted sum
over all comparator insertion costs.repLocal
- the local replacement cost, defined as the weighted sum
over all comparator replacement costs.public PathList transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][] alignmentMatrix, Sequence a, Sequence b)
transformToResult
in class AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
alignmentMatrix
- the alignment matrix.a
- the first sequence.b
- th second sequence.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