X
- the class of the elements in the left input sequence.Y
- the class of the elements in the right input sequence.public class StrictAlignmentAllOptimalAlgorithm<X,Y> extends AbstractStrictAlignmentAlgorithm<X,Y,AlignmentList>
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_ALIGNMENT_LIMIT |
Constructor and Description |
---|
StrictAlignmentAllOptimalAlgorithm(Comparator<X,Y> comparator) |
Modifier and Type | Method and Description |
---|---|
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.
|
AlignmentList<X,Y> |
transformToResult(double[][] alignMat,
double[][] repCosts,
double[] delCosts,
double[] insCosts,
List<X> a,
List<Y> b)
This method has to be implemented by sub classes to transform a calculated dynamic
programming matrix to a valid result of that implementation.
|
calculateAlignment, getComparator, getLastAlignmentMatrix, getResultClass, normalizeDissimilarity, requires, setComparator
public static final int DEFAULT_ALIGNMENT_LIMIT
public StrictAlignmentAllOptimalAlgorithm(@NonNull Comparator<X,Y> comparator)
public void setPathLimit(int pathLimit)
pathLimit
- a maximum number of co-optimal paths that shall be calculated.public AlignmentList<X,Y> transformToResult(double[][] alignMat, @NonNull double[][] repCosts, @NonNull double[] delCosts, @NonNull double[] insCosts, List<X> a, List<Y> b)
AbstractStrictAlignmentAlgorithm
transformToResult
in class AbstractStrictAlignmentAlgorithm<X,Y,AlignmentList>
alignMat
- a dynamic programming matrix calculated with respect to both input
sequences.repCosts
- the matrix of pairwise REPLACEMENT costs for each pairwise combination of
elements in the input sequences.delCosts
- the vector of DELETION costs for each element of the left input sequence.insCosts
- the vector of INSERTION costs for each element of the right input sequence.a
- the first input sequence.b
- the second input sequence.Copyright (C) 2016-2018 Benjamin Paaßen, 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/