[Biojava-l] need help for SimpleSequenceBuilder class

[Cox, Greg]

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:xling@tularik.com]
Sent: Sunday, July 22, 2001 11:17 AM
To: td2@sanger.ac.uk
Cc: biojava-l@biojava.org
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: bruce@tularik.com
Phone: 650-825-7143
fax: 1-435-804-4009