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Fix local align score vector #1036

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Merged
josemduarte merged 3 commits into from
Sep 30, 2022
Merged

Fix local align score vector #1036

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bff5de7
Fix pointers[y] is null error
Jul 26, 2022
8a64963
Fix pointers[y] is null error
Jul 26, 2022
2781293
Test local, linear scheme alignment
Jul 26, 2022
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2 changes: 1 addition & 1 deletion 2 biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -581,7 +581,7 @@ public static Last[][] setScoreVector(int x, int xb, int yb, int ye, int gep, in
if (x == xb) {
pointers = new Last[ye + 1][1];
} else {
pointers = new Last[ye + 1][];
pointers = new Last[ye + 1][1];
pointers[0] = new Last[1];
for (int y = 1; y < scores[x].length; y++) {
pointers[y][0] = setScorePoint(x, y, gep, subs[y], scores);
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12 changes: 12 additions & 0 deletions 12 biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
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Expand Up @@ -165,4 +165,16 @@ public void testLinearAlignment() throws CompoundNotFoundException {
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);
Assert.assertEquals(String.format("GTAAAA-G----------%nG-AAAACGTTTTTTTTTT%n"), aligner.getPair().toString());;
}
/**
* @author aegugup
*/
@Test
public void testLinearAlignmentLocal() throws CompoundNotFoundException {
DNASequence query = new DNASequence("TGTTACGG", DNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("GGTTGACTA", DNACompoundSet.getDNACompoundSet());
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
SimpleGapPenalty gapP = new SimpleGapPenalty((short)0, (short)8);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);
Assert.assertEquals(String.format("GTT-AC%nGTTGAC%n"), aligner.getPair().toString());;
}
}
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