another update: that most recent exception was caused by a reference sequence consisting only of "NNNN" - looks like something that should be handled more gracefully to me :)
Hannes On Tue, Dec 6, 2011 at 09:59, Hannes Brandstätter-Müller <[email protected]> wrote: > Hah, I got some not-null results: > > > On Tue, Dec 6, 2011 at 09:20, Hannes Brandstätter-Müller > <[email protected]> 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
