As far as I'm aware no there shouldn't be a problem with this solution. However have you investigated any other mechanisms for doing this kind of contig editing/assembly work? I know that people at the Sanger Centre use a program called gap4 which has powered just about every assembly they have done. It's available from:
http://www.sanger.ac.uk/Software/production/staden/ (bit of info here) http://staden.sourceforge.net/staden_home.html Have a look at it as I feel that this is exactly what you are attempting to do. Andy Ashika Umanga Umagiliya wrote: > Cheers. > > > I still haven't implemented the editor.I assume for basecall editing, I > can use 'Edit' class. > > Like: > > ABIFChromatogram a; > .. > .. > a.getBaseCalls().edit(new Edit(.......)) > > > And for Quality values, I am hoping to read and store Qualitly files > generated by 'phred'.And when user edit the basecall, I am planing to > edit stored quality values accordinly. > Finally the fasta file is generated using > ABIFChromatogram.getBaseCalls()... > and Quality file will be generated using the structure I used above. > > Any issues with this approach? > > Many thanks, > Umanga > > > Russ Kepler wrote: >> On Thursday 19 February 2009 22:48:45 Ashika Umanga Umagiliya wrote: >> >> >>> My problem is can I use the same Quality files ,with the modified >>> callbases ? >>> >> >> Edit the quality data in parallel with the chromatogram. I would >> assume that the editor is relatively sure of their edits, so I would >> give them a high confidence level when I generate the trace fasta and >> quality file. >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
