[Biojava-dev] RichSequence.Tools.enrich(..)generateNoSuchElementException

[Richard HOLLAND]

Done and committed to biojava-live in CVS. It compiles but I haven't had
the chance to test functionality. Volunteers please?

See:
	org.biojavax.bio.db.RichSequenceDBLite
	org.biojavax.bio.db.RichSequenceDB
	org.biojavax.bio.db.AbstractRichSequenceDB
	org.biojavax.bio.db.HashRichSequenceDB

The biojavax version of GenbankFormat has changed to use the new
interfaces and abstract classes, but its behaviour and previous
interface implementations remain the same.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at novartis.com 
> [mailto:mark.schreiber at novartis.com] 
> Sent: Monday, January 23, 2006 10:52 AM
> To: Richard HOLLAND
> Cc: biojava-dev at biojava.org; 
> biojava-dev-bounces at portal.open-bio.org; Janko Diminic
> Subject: RE: [Biojava-dev] 
> RichSequence.Tools.enrich(..)generateNoSuchElementException
> 
> 
> Good idea,
> 
> We need a RichSequenceDB and a RichSequenceDBLite to extend the 
> appropriate biojava interfaces.
> 
> - Mark
> 
> 
> 
> 
> 
> "Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 01/23/2006 10:42 AM
> 
>  
>         To:     Mark Schreiber/GP/Novartis at PH, "Janko 
> Diminic" <jdiminic at gmail.com>
>         cc:     biojava-dev at biojava.org
>         Subject:        RE: [Biojava-dev] 
> RichSequence.Tools.enrich(..) 
> generateNoSuchElementException
> 
> 
> Hello all.
> 
> There was indeed a bug (in the constructor of SimpleRichFeature) which
> is now fixed, but Mark is right about using the appropriate BioJavaX
> parser instead to do this task.
> 
> I've added a new module in biojava-live in CVS -
> org.biojavax.bio.seq.db.ncbi.GenbankSequenceDB. See the
> getRichSequence(), getRichSequenceDB() and getRichSequences() methods
> for details.
> 
> Your sample code will work with the new module after you do this:
> 
>                  1.              Import 
> org.biojavax.bio.seq.db.ncbi.GenbankSequenceDB
> instead of org.biojava.bio.seq.db.GenbankSequenceDB
>                  2.              change
>                                                  Sequence seq = 
> sequenceIterator.nextSequence();
>                                  to
>                                                  RichSequence seq =
> (RichSequence)sequenceIterator.nextSequence();
>                  3.              delete the line that calls enrich().
> 
> (Note: GenbankSequenceDB should probably be tidied up a 
> little and made
> to implement some kind of common interface, maybe RichSequenceDB?
> Comments please.)
> 
> cheers,
> Richard
> 
> Richard Holland
> Bioinformatics Specialist
> GIS extension 8199
> ---------------------------------------------
> This email is confidential and may be privileged. If you are not the
> intended recipient, please delete it and notify us immediately. Please
> do not copy or use it for any purpose, or disclose its content to any
> other person. Thank you.
> ---------------------------------------------
> 
> 
> > -----Original Message-----
> > From: mark.schreiber at novartis.com 
> > [mailto:mark.schreiber at novartis.com] 
> > Sent: Monday, January 23, 2006 10:03 AM
> > To: Janko Diminic
> > Cc: biojava-dev at biojava.org; Richard HOLLAND
> > Subject: Re: [Biojava-dev] RichSequence.Tools.enrich(..) 
> > generateNoSuchElementException
> > 
> > 
> > Hi -
> > 
> > Will have a look into this.
> > 
> > However, the enrich method is not the ideal way to do this. 
> > The method 
> > will do it's best to make a Sequence into a RichSequence but 
> > it usually 
> > cannot do a great job. Your best bet would be to use NCBI 
> > eutils to get 
> > sequences in GenBank or XML and then put them through the 
> appropriate 
> > parser to directly generate a RichSequence.
> > 
> > As a todo, we should update GenbankSequenceDB to provide 
> RichSequence 
> > instances (or deprecate it and provide an alternative).
> > 
> > - Mark
> > 
> > 
> > 
> > 
> > 
> > Janko Diminic <jdiminic at gmail.com>
> > Sent by: biojava-dev-bounces at portal.open-bio.org
> > 01/21/2006 02:52 PM
> > 
> > 
> >         To:     biojava-dev at biojava.org
> >         cc:     (bcc: Mark Schreiber/GP/Novartis)
> >         Subject:        [Biojava-dev] 
> > RichSequence.Tools.enrich(..) generate 
> > NoSuchElementException
> > 
> > 
> > Hi, RichSequence.Tools.enrich(seq) generate NoSuchElementException 
> > exception:
> > 
> > // Samples.java class
> > 
> >     Set param = new HashSet();
> >     param.add("AJ278573");   // NCBI accession
> > 
> >     GenbankSequenceDB genBank = new GenbankSequenceDB();
> >     SequenceDB sequences = genBank.getSequences(param);
> > 
> >     sequenceIterator = sequences.sequenceIterator();
> > 
> > while (sequenceIterator.hasNext()) {
> >         try {
> >               Sequence seq = sequenceIterator.nextSequence();
> >               RichSequence enrichSeq = 
> RichSequence.Tools.enrich(seq);
> >   //line:92,  here throw NoSuchElementException ???
> > 
> >               session.saveOrUpdate("Sequence", enrichSeq);
> > 
> >               } catch (NoSuchElementException e) {
> >                      e.printStackTrace();
> >               }
> >         }
> > 
> > 
> > 
> > java.util.NoSuchElementException
> >     at 
> > java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHas
> hMap.java:367)
> >     at 
> > java.util.LinkedHashMap$KeyIterator.next(LinkedHashMap.java:376)
> >     at 
> > org.biojavax.bio.seq.SimpleRichFeature.<init>(SimpleRichFeatur
> > e.java:96)
> >     at 
> > org.biojavax.bio.seq.SimpleRichSequence.createFeature(SimpleRi
> > chSequence.java:323)
> >     at 
> > 
> org.biojavax.bio.seq.RichSequence$Tools.enrich(RichSequence.java:434)
> >     at hr.Samples.main(Samples.java:92)
> > 
> > 
> > Do you know way?
> > Thanks for the help.
> > 
> > 
> > 
> > --
> > Janko Diminic
> > 
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-dev
> > 
> > 
> > 
> > 
> 
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