[Biojava-l] removeGap problem with SimpleGappedSequence

[david de beule]

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" <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
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
>
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>