[Biojava-l] IndexOutOfBounds Exception when performing Pairwise Alignment

[Hannes Brandstätter-Müller]

Hah, I got some not-null results:


On Tue, Dec 6, 2011 at 09:20, Hannes Brandstätter-Müller
<biojava at hannes.oib.com> wrote:
>
> public void testPSA() {
>        String targetSeq =
> "CACGTTTCTTGTGGCAGCTTAAGTTTGAATGTCATTTCTTCAATGGGACGGA"
>                +
> "GCGGGTGCGGTTGCTGGAAAGATGCATCTATAACCAAGAGGAGTCCGTGCGCTTCGACAGC"
>                +
> "GACGTGGGGGAGTACCGGGCGGTGACGGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACA"
>                +
> "GCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGCGGTGGACACCTACTGCAGACACAACTA"
>                + "CGGGGTTGGTGAGAGCTTCACAGTGCAGCGGCGAG";
>        DNASequence target = new DNASequence(targetSeq,
> AmbiguityDNACompoundSet.getDNACompoundSet());
>        String querySeq =
> "ACGAGTGCGTGTTTTCCCGCCTGGTCCCCAGGCCCCCTTTCCGTCCTCAGGAA"
>                +
> "GACAGAGGAGGAGCCCCTCGGGCTGCAGGTGGTGGGCGTTGCGGCGGCGGCCGGTTAAGGT"
>                +
> "TCCCAGTGCCCGCACCCGGCCCACGGGAGCCCCGGACTGGCGGCGTCACTGTCAGTGTCTT"
>                +
> "CTCAGGAGGCCGCCTGTGTGACTGGATCGTTCGTGTCCCCACAGCACGTTTCTTGGAGTAC"
>                +
> "TCTACGTCTGAGTGTCATTTCTTCAATGGGACGGAGCGGGTGCGGTTCCTGGACAGATACT"
>                +
> "TCCATAACCAGGAGGAGAACGTGCGCTTCGACAGCGACGTGGGGGAGTTCCGGGCGGTGAC"
>                +
> "GGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGACATCCTGGAAGACGAG"
>                +
> "CGGGCCGCGGTGGACACCTACTGCAGACACAACTACGGGGTTGTGAGAGCTTCACCGTGCA"
>                + "GCGGCGAGACGCACTCGT";
>        DNASequence query = new DNASequence(querySeq);

query.setCompoundSet(AmbiguityDNACompoundSet.getDNACompoundSet()); //
inserting that helps.

>        SubstitutionMatrix<NucleotideCompound> matrix =
> SubstitutionMatrixHelper.getNuc4_4();
>        SequencePair<DNASequence, NucleotideCompound> psa =
> Alignments.getPairwiseAlignment(query, target,
> PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);
>        assertNotNull(psa);
>    }

But when I try something similar in my production code, I get an
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 again

dnaSequence.setCompoundSet(AmbiguityDNACompoundSet.getDNACompoundSet());
// If I remove this line, the exception is gone again, but I get NULL
result.
psa = Alignments.getPairwiseAlignment(dnaSequence, target,
PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);

the dnaSequence in that case is something that is passed to this
method, and is a sequence generated by a fasta reader - should have no
ambiguity in there, just plain ACGT. It has a plain DNACompoundSet
too.

Hannes