[Biojava-l] need help for SimpleSequenceBuilder class

[Bruce Ling]

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&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(SimpleFeatureRealizer.java:136)

 

rethrown as org.biojava.bio.BioException: Couldn't realize feature

 

 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138)

 

 at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:92)

 

 at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:176)

 

 at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:182)

 

 at org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuilder.java:154)

 

rethrown as org.biojava.bio.BioError: Couldn't create feature

 

 at org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuilder.java:160)

 

 at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.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
Email: [EMAIL PROTECTED]
Phone: 650-825-7143
fax: 1-435-804-4009