[Biojava-l] removeGap problem with SimpleGappedSequence

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Wed Feb 11 20:07:18 EST 2004

Hi -

The problem seems to be that

   DNATools.createDNASequence("ACT--GGACCTAAGG", "test");

Creates a SimpleSequence and not a gapped sequence. Then when you call 

  SimpleGappedSequence s = new SimpleGappedSequence(sequence);

You get back a view onto sequence. The view can only remove gaps that are 
introduced in that view. I guess that DNATools.createDNASequence and 
createDNA methods may need modification. There is a method in DNATools 
called createGappedDNASequence which will do what you want but it would be 
nice if the other two could call it as appropriate.

Probably need to add a createGappedDNA as well.

If no one gets to this in the next few days I'll have a hack at it.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910

"david de beule" <daviddebeule at pandora.be>
Sent by: biojava-l-bounces at portal.open-bio.org
02/12/2004 03:57 AM

        To:     <biojava-l at biojava.org>
        Subject:        [Biojava-l] removeGap problem with SimpleGappedSequence


I have got another small problem with SimpleGappedSequence.

This code:

Sequence sequence = DNATools.createDNASequence("ACT--GGACCTAAGG", "test");
SimpleGappedSequence s = new SimpleGappedSequence(sequence);

results in:

org.biojava.bio.symbol.IllegalSymbolException: Attempted to remove a gap 
a non-gap index: 4 -> []

Is this intented or a bug ?

Thanks in advance,
David De Beule

----- Original Message -----
From: "David Huen" <david.huen at ntlworld.com>
To: <biojava-l at biojava.org>
Sent: Tuesday, January 06, 2004 2:56 PM
Subject: Re: [Biojava-l] biojava doubts and problems

> On Tuesday 06 Jan 2004 11:33 am, nandakumar sridharan wrote:
> > any reference books available for the biojava docs and tutorials.
> Please look at www.biojava.org for some material.  Follow the link there
> "Biojava In Anger" for further useful cookbook style materials.
> > GCContent .java gives exception "usage: java GCContent filename.fa" 
> > to solve it
> >
> The above is not an exception but a Unix-style way of telling you that 
> command line format for invoking the code.
> In this case, it appears to be saying you need to provide it a file in
> format:-
> java GCContent <name of some file in FASTA format goes here!>
> Regards,
> David Huen
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

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