[Biojava-l] IndexOutOfBounds Exception when performing Pairwise Alignment

[Andreas Prlic]

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
<biojava at hannes.oib.com> 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
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