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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
02/12/2004 03:57 AM
To: <[EMAIL PROTECTED]>
cc:
Subject: [Biojava-l] removeGap problem with SimpleGappedSequence
Hi,
I have got another small problem with SimpleGappedSequence.
This code:
Sequence sequence = DNATools.createDNASequence("ACT--GGACCTAAGG", "test");
SimpleGappedSequence s = new SimpleGappedSequence(sequence);
s.removeGap(4);
results in:
org.biojava.bio.symbol.IllegalSymbolException: Attempted to remove a gap
at
a non-gap index: 4 -> []
at
org.biojava.bio.symbol.SimpleGappedSymbolList.removeGap(SimpleGappedSymbolLi
st.java:426)
Is this intented or a bug ?
Thanks in advance,
David De Beule
----- Original Message -----
From: "David Huen" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
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
to
> "Biojava In Anger" for further useful cookbook style materials.
>
> > GCContent .java gives exception "usage: java GCContent filename.fa"
how
> > to solve it
> >
> The above is not an exception but a Unix-style way of telling you that
the
> command line format for invoking the code.
>
> In this case, it appears to be saying you need to provide it a file in
FASTA
> format:-
> java GCContent <name of some file in FASTA format goes here!>
>
> Regards,
> David Huen
>
> _______________________________________________
> Biojava-l mailing list - [EMAIL PROTECTED]
> http://biojava.org/mailman/listinfo/biojava-l
>
>
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