[Biojava-l] Parsing SwissProt flat file through BioJava

[Cox, Greg]

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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