Sounds like a pretty sensible suggestion. Can anyone think of why this
might not be a 'good idea'?
If not, i'll add it to the list of things to fix :)
- Mark
[EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
02/12/2004 05:04 PM
To: [EMAIL PROTECTED]
cc:
Subject: Re: [Biojava-l] removeGap problem with SimpleGappedSequence
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
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
>Verzonden
: donderdag
, februari
12, 2004 01:07 AM
>Aan
: 'david de beule'
>CC
: [EMAIL PROTECTED]
>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" <[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
>>
>> _______________________________________________
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>> http://biojava.org/mailman/listinfo/biojava-l
>>
>>
>
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>
>
>
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