[Biojava-l] Parsing SwissProt flat file through BioJava

Schreiber, Mark mark.schreiber@agresearch.co.nz
Fri, 5 Jul 2002 10:48:04 +1200


Just a thought -

If you want to visualize the feature/ annotation structure of a sequence
or SequenceDB then use the FeatureTree.java from the org.biojava.bio.gui
package. This class extends JTree and provides a way of viewing features
sequence and annotations in a nested structure.

- Mark


> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com] 
> Sent: Thursday, 4 July 2002 1:46 a.m.
> To: Schreiber, Mark; Santosh Kumar
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] Parsing SwissProt flat file through BioJava
> 
> 
> To get the contents of the FT lines, use Sequence.features() 
> to get an iterator over them.  The iterator will return 
> Feature type objects.  
> 
> The SQ data can be accessed via the SymbolList interface.  To 
> get a string of the sequence data, Sequence.seqString() will do it.
> 
> Greg
> 
> > -----Original Message-----
> > From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> > Sent: Wednesday, July 03, 2002 12:54 AM
> > To: Santosh Kumar
> > Cc: biojava-l@biojava.org
> > Subject: RE: [Biojava-l] Parsing SwissProt flat file through BioJava
> > 
> > 
> > Hi -
> > 
> > Possibly this info has ended up in the Annotation object of the 
> > sequence. Does anyone else have an explanation for this?
> > 
> > - Mark
> > 
> > 
> > > -----Original Message-----
> > > From: Santosh Kumar [mailto:santosh@molecularconnections.com]
> > > Sent: Wednesday, 3 July 2002 4:31 p.m.
> > > To: Schreiber, Mark
> > > Subject: RE: [Biojava-l] Parsing SwissProt flat file 
> through BioJava
> > > 
> > > 
> > > 
> > > 
> > > Hey ,
> > > 
> > > I am able to retrieve the data from SwissProt flat files but
> > > was surprised when I didn't get the data corresponding to FT 
> > > & SQ from the same flat file.I donn't know the reason.
> > > 
> > > Plz let me know if I am missing same points.
> > > 
> > > regards
> > > 
> > > Santosh
> > > 
> > > -----Original Message-----
> > > From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> > > Sent: Wednesday, June 26, 2002 5:18 AM
> > > To: Rahul Deshpande; biojava-l@biojava.org
> > > Cc: Santosh Kumar
> > > Subject: RE: [Biojava-l] Parsing SwissProt flat file 
> through BioJava
> > > 
> > > 
> > > >From Memory I think there is a static method in the class
> > SeqIOTools
> > > that can do this for you.
> > > 
> > > - Mark
> > > 
> > > > -----Original Message-----
> > > > From: Rahul Deshpande [mailto:rahul@molecularconnections.com]
> > > > Sent: Tuesday, 25 June 2002 6:21 p.m.
> > > > To: biojava-l@biojava.org
> > > > Cc: Santosh Kumar
> > > > Subject: [Biojava-l] Parsing SwissProt flat file through BioJava
> > > >
> > > >
> > > > Hello,
> > > >
> > > > I am Rahul Deshpande. I work for a bio informatics company.
> > > Recently I
> > > > came across biojava. I have a question about biojava.
> > > >
> > > > How can we read the SwissProt flat files using biojava? The
> > > closest we
> > > > could come was org.biojava.bio.seq.io.EmblLikeFormat class
> > > which has
> > > > methods to return the two letter code and the remaining
> > data in the
> > > > line. Can we retrieve the data for each protein in the 
> SwissProt 
> > > > flat file instead of reading each line by each line? 
> Are there any 
> > > > methods like that?
> > > >
> > > > Regards,
> > > > Rahul Deshpande
> > > > Molecularconnections Pvt. Ltd.
> > > > A203, Blue Cross Chambers,
> > > > Infantry Road Cross,
> > > > Bangalore 560001
> > > > Ph: +(91)-80-5598502, 5327919
> > > >
> > > > _______________________________________________
> > > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > > http://biojava.org/mailman/listinfo/biojava-l
> > > >
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