Yes, that fixed that exception. Now, I'm getting null return value - must be still something wrong in the parameters...
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4(); Alignments.getPairwiseAlignment(dnaSequence, target, PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix); Where should I start looking for that? Is there a simple way to align (or score, don't need the full alignment) a single DNA sequence against a List of sequences? I only found the "How to concurrently create a PSA for each pair in a sequence list in BioJava" cookbook entry, but that calculates a bunch of (for me) useless PSAs. would it be better to perform a blast search (custom "library" to search against) for that? Thanks, Hannes On Fri, Dec 2, 2011 at 23:04, Andreas Prlic <[email protected]> wrote: > Hi Hannes, > > Did you make sure to use the correct substitution matrix for the > alignment? You need substitution scores for all nucleotides in your > sequence to be present in the matrix... > > Andreas > > On Thu, Dec 1, 2011 at 4:59 AM, Hannes Brandstätter-Müller > <[email protected]> wrote: >> What am I doing wrong? I get: >> >> Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: >> 0, Size: 0 >> at java.util.ArrayList.RangeCheck(ArrayList.java:547) >> at java.util.ArrayList.get(ArrayList.java:322) >> at >> org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:362) >> at >> org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88) >> at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118) >> at >> org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86) >> at >> org.biojava3.alignment.SmithWaterman.setProfile(SmithWaterman.java:71) >> at >> org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) >> at >> org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) >> at >> org.biojava3.alignment.Alignments.getPairwiseAlignment(Alignments.java:208) >> >> when calling Alignments.getPairwiseAlignment(dnaSequence, target, >> PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix); >> >> where matrix = new SimpleSubstitutionMatrix<NucleotideCompound>();, >> sequence and target are both DNASequence >> >> Possible causes I can think of: target might contain IUB-Codes (not >> just ACGTU, but also RYKM...) >> >> Hannes >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
