public class StrictAllOptimalAlgorithm extends AbstractGapAlignmentAlgorithm<StrictAllOptimalAlgorithm.FullMatrixEntry,PathList>
Modifier and Type | Class and Description |
---|---|
static class |
StrictAllOptimalAlgorithm.FullMatrixEntry |
Modifier and Type | Field and Description |
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static int |
DEFAULTPATHLIMIT |
Constructor and Description |
---|
StrictAllOptimalAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
Modifier and Type | Method and Description |
---|---|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createInitial()
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
|
StrictAllOptimalAlgorithm.FullMatrixEntry |
createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
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!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
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!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
calculateAlignment, 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) 2013-2015 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/