public class StrictAlignmentFullAlgorithm extends AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
Modifier and Type | Class and Description |
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static class |
StrictAlignmentFullAlgorithm.FullMatrixEntry |
Constructor and Description |
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StrictAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification)
This sets up an AlignmentAlgorithm instance according to the given
specification.
|
calculateAlignment, calculateDeletionCosts, calculateInsertionCosts, calculateReplacementCosts, createGenericArray, createGenericMatrix, getEntryClass, getLastAlignmentMatrix, getResultClass, getSpecification, getWeightThreshold, setWeightThreshold
public StrictAlignmentFullAlgorithm(AlignmentSpecification alignmentSpecification)
alignmentSpecification
- an AlignmentSpecification.public StrictAlignmentFullAlgorithm.FullMatrixEntry createInitial()
createInitial
in class AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
public StrictAlignmentFullAlgorithm.FullMatrixEntry createDelInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry delOld, int i, double delLocal)
createDelInitial
in class AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
delOld
- the matrix entry (i,0)i
- i+1delLocal
- the local deletion cost, defined as the weighted sum over
all comparator deletion costs.public StrictAlignmentFullAlgorithm.FullMatrixEntry createInsInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry insOld, int j, double insLocal)
createInsInitial
in class AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
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 StrictAlignmentFullAlgorithm.FullMatrixEntry createNewEntry(StrictAlignmentFullAlgorithm.FullMatrixEntry delOld, StrictAlignmentFullAlgorithm.FullMatrixEntry insOld, StrictAlignmentFullAlgorithm.FullMatrixEntry repOld, int i, int j, double delLocal, double insLocal, double repLocal)
createNewEntry
in class AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
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 AlignmentPath transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][] alignmentMatrix, Sequence a, Sequence b)
transformToResult
in class AbstractGapAlignmentAlgorithm<StrictAlignmentFullAlgorithm.FullMatrixEntry,AlignmentPath>
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