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 >> >> _______________________________________________ >> Biojava-l mailing list - [EMAIL PROTECTED] >> http://biojava.org/mailman/listinfo/biojava-l >> >> > >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l > > > > > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
