I believe I figured it out.
The constructor of DNASequence can take a CompoundSet and passing an
AmbiguityDNACompoundSet in there seems to work. There's not a lot of
documentation in the javadoc, but it seems to give the behaviour I want.
cheers
Wim
On 28-03-11 16:46, Wim De Smet wrote:
Hi
(sorry if you get 2 copies, I sent this to -request by mistake)
Apologies if this has come up before, a quick search didn't turn
anything up.
I'm attempting to do a pairwise alignment between two DNA sequences
using biojava 3. When I try to construct a DNASequence from a string
that contains an ambiguous base though (in this case 'y'), I get the
following stacktrace.
Exception in thread "main"
org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found
for: Cannot find compound for: y
at
org.biojava3.core.sequence.storage.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:196)
at
org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88)
at org.biojava3.core.sequence.DNASequence.<init>(DNASequence.java:64)
Should I attempt to mask them somehow? What's the best way to deal with
these?
cheers
Wim
--
Wim De Smet
http://www.straininfo.net/
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