[Biojava-l] IndexOutOfBounds Exception when performing Pairwise Alignment

[Hannes Brandstätter-Müller]

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