[Biojava-l] Editing a RichSequence

[Mark Schreiber]

I wonder if Edits on Chunked or BitPacked lists are possible (theoretically
possible).

If they are we should really allow them.

- Mark

On Fri, Feb 15, 2008 at 11:16 PM, Richard Holland <holland at ebi.ac.uk> wrote:

> I think it's because sequences are constructed internally in a
> ChunkedSymbolListFactory which compresses large sequences whereas small
> sequences are stored as normal uncompressed ones. Compressed sequences
> extend AbstractSymbolList, which is immutable (and therefore uneditable)
> whereas uncompressed ones do not, and hence are editable.
>
> You can disable the use of compressed sequences by using readGenbank()
> instead of readGenbankDNA() and passing in the DNA alphabet and the
> non-compressed sequence factory (see the static constants in
> RichSequenceBuilderFactory).
>
> If this still doesn't work, please could you post the full stacktrace so
> that we can see which class is throwing the exception and at what line
> etc.
>
> cheers,
> Richard
>
> On Fri, February 15, 2008 2:44 pm, Jolyon Holdstock wrote:
> > Hi
> >
> >
> > Hi,
> >
> > I am trying to edit a Genbank sequence.
> > The code I'm using is as follows:
> >
> > [code]
> > richSeq = RichSequence.IOTools.readGenbankDNA(new BufferedReader(new
> > FileReader(new File("U00096.gbk"))), null).nextRichSequence();
> >
> > SymbolList sl1 = DNATools.createDNA("AAAGGGTTTCCC");
> > Edit editOne = new Edit(47078, 2690, sl1);
> > richSeq.edit(editOne);
> >
> > [/code]
> >
> > When it runs it gives the following error
> >
> > ChangeVetoException: org.biojava.utils.ChangeVetoException:
> > AbstractSymbolList is immutable
> >
> >
> > I have used the code for a smaller sequence (15kb, compared with 4Mb)
> > and it works.
> >
> > Does anyone have an idea why this is not working?
> >
> > Thanks,
> >
> > Jolyon
> >
> >
> >
> >
> >
> > Jolyon Holdstock Ph.D.
> > Senior Computational Biologist,
> > Oxford Gene Technology,
> > Begbroke Science Park,
> > Sandy Lane, Yarnton
> > Oxford, OX5 1PF
> >
> > Tel: +44 (0)1865 856852
> > Fax: +44 (0)1865 842116
> >
> > Oxford Gene Technology (Operations) Ltd. Registered in England
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>
> --
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK
>
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