Hi Bruce,
I've done a lot with Genbank files, and the problem isn't actually in
SimpleSequenceBuilder, that's just the symptom. The feature table renderer
builds a stranded feature by default, and that's not acceptable for
proteins. I'll look into your case, and try to get a fix into CVS later
today.
Greg
-----Original Message-----
From: Bruce Ling [mailto:[EMAIL PROTECTED]]
Sent: Sunday, July 22, 2001 11:17 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: [Biojava-l] need help for SimpleSequenceBuilder class
Hi, Thomas,
As I saw the doc says you are the author of SimpleSequenceBuilder class, I
am asking for help with the following problem?
I am in the way of using biojava GenbankFormat class, the code is as
following:
{
SequenceFormat gFormat = new GenbankFormat();
SequenceBuilderFactory sbFact =
new GenbankProcessor.Factory(SimpleSequenceBuilder.FACTORY);
//Alphabet alpha = DNATools.getDNA();
//this following line does not work for protein, need more work to figure
out the library
Alphabet alpha = ProteinTools.getAlphabet();
SymbolParser rParser = alpha.getParser("token");
seqI =
new StreamReader(gReader, gFormat, rParser, sbFact);
}
see the commented out part, if I am using a DNA genbank file as the one
sample in the demo part it works fine. But if I want to use the above code
to use PROTEIN alphabet and parse a protein record in genbank format such
as:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=NP_005154
<http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=NP_005154&form=6&db
=p&Dopt=g> &form=6&db=p&Dopt=g
it gives the exception shown at the end of the email.
I have traced down and problem is at:
SimpleSequenceBuilder class TemplateWithChildren. It seems by default it
assumes this is a DNA genbank record. that is why it is trying to create a
strand feature which protein record does not have it.
public Sequence makeSequence() {
SymbolList symbols = slBuilder.makeSymbolList();
Sequence seq = new SimpleSequence(symbols, uri, name, annotation);
try {
for (Iterator i = rootFeatures.iterator(); i.hasNext(); ) {
TemplateWithChildren twc = (TemplateWithChildren) i.next();
Feature f = seq.createFeature(twc.template);
if (twc.children != null) {
makeChildFeatures(f, twc.children);
}
}
} catch (Exception ex) {
throw new BioError(ex, "Couldn't create feature");
}
return seq;
}
==================================
java Exceptions
==================================
java.lang.reflect.InvocationTargetException:
org.biojava.bio.symbol.IllegalAlphabetException: Can not create a stranded
feature within a sequence of type PROTEIN
at
org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.
java:76)
at java.lang.reflect.Constructor.newInstance(Native Method)
at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature
Realizer.java:136)
rethrown as org.biojava.bio.BioException: Couldn't realize feature
at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature
Realizer.java:138)
at
org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealiz
er.java:92)
at
org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:1
76)
at
org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:18
2)
at
org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuil
der.java:154)
rethrown as org.biojava.bio.BioError: Couldn't create feature
at
org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuil
der.java:160)
at
org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFil
ter.java:98)
at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100)
Thanks.
Bruce Ling, Ph.D.
Director, Bioinformatics
Tularik, Inc -- http://www.tularik.com <http://www.tularik.com/>
Email: [EMAIL PROTECTED]
Phone: 650-825-7143
fax: 1-435-804-4009
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