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
