[Biojava-l] removeGap problem with SimpleGappedSequence

[daviddebeule at pandora.be]

Hi,

'createGappedDNASequence' would solve the problem in this example but in fact it was just an example, in the real application the sequences are not always created with DNATools and a lot of time we create a SimpleGappedSequence from a Sequence.
I was wondering if it would be possible to let SimpleGappedSequence(sequence) create a view that immediately contains the gaps available in the original sequence.  With that view it would be possible to remove the gaps in the original sequence and add/remove new gaps.

David

>----- Oorspronkelijk bericht -----
>Van
: mark.schreiber at group.novartis.com [mailto:mark.schreiber at group.novartis.com]
>Verzonden
: donderdag
, februari
 12, 2004 01:07 AM
>Aan
: 'david de beule'
>CC
: biojava-l at biojava.org
>Onderwerp
: Re: [Biojava-l] removeGap problem with SimpleGappedSequence
>
>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>
>        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" <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
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at biojava.org
>> http://biojava.org/mailman/listinfo/biojava-l
>>
>>
>
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