Some code examples like this would be great on the biojava.org cookbook. If people could add their GUI code that would be excellent.
- Mark On Fri, Mar 14, 2008 at 7:27 AM, Andrew Farmer <[EMAIL PROTECTED]> wrote: > Eric- > thanks very much for your insights, the phred -c trick might in fact be > exactly what I need. If not, I will check out the other code you have > sent and follow up off-list if I have further questions. > > > Andrew > > > Eric Haugen wrote: > > > > Hi Andrew, > > > > It looks like what I did three years ago was turn off the > > ChromatogramGraphic's call boxes: > > > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS, > > Boolean.FALSE ); > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE ); > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE ); > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE ); > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE ); > > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, > > Boolean.FALSE ); > > > > then set the range based on the chromat positions in the phred file: > > > > graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, > > startIndex ); > > graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex ); > > > > and finally just draw Phred's base calls myself based on the chromat > > position scale. > > > > I don't know if you'll find it useful, but I've attached > > PhdSequence.java and support code which I use as an alternative to > > PhredSequence currently in biojava, which I think ignores chromat > > positions. > > > > But the easiest solution may be to have "phred -c" convert your ABI > > chromats to SCF files containing the phred base calls. > > > > -- > > Eric Haugen > > Software Engineer > > University of Washington Genome Center > > [EMAIL PROTECTED] > > (206) 616-7582 > > > > On Thu, 13 Mar 2008, Andrew Farmer wrote: > > > >> Hi all- > >> I have been trying to use the ChromatogramGraphic class to display ABI > >> chromatogram data, whilst relating this to alignments of sequences > >> called from these trace files with phred. For example, if the user > >> clicks a putatively polymorphic base in an alignment viewer, to scroll > >> and highlight the region of the ChromatogramGraphic corresponding to > >> the ase call. However, I seem to be having some difficulty in > >> establishing correspondences between the phred base calls and the > >> information shown in the graphic. > >> > >> As far as I understand what is being displayed by ChromatogramGraphic, > >> it is drawing "callboxes" around peaks corresponding to calls that are > >> stored by Chromatogram, which in turn is storing information about the > >> base calls that was encoded in the ABI file. These tend to differ > >> substantially (e.g. in lower-quality areas) from the calls made by > >> phred- e.g. an untrimmed phred-called sequence might have 1300 bases > >> to the abi-called version's 900 bases. So, I am trying to find some > >> way to get the ChromatogramGraphic callboxes to reflect the calls made > >> by phred. > >> > >> Has anyone else encountered this type of situation before? It appears > >> that phred's phd output encodes a trace offset for each of its calls, > >> so I would guess that one could conceivably overlay the phred calls > >> into a chromatogram produced by the abi parser in order to get the > >> callboxes to reflect phred's interpretation of the trace data. > >> > >> I could be way off-base (no pun intended) in my interpretation, and > >> would appreciate any insights from the gurus out there. And if this is > >> more or less correct, and there is not yet a canned solution, any > >> advice on how to go about coding it in a way that could be contributed > >> back to the project would be great. > >> > >> Thanks in advance > >> -- > >> > >> Andrew Farmer > >> [EMAIL PROTECTED] > >> (505) 995-4464 > >> Database Administrator/Software Developer > >> National Center for Genome Resources > >> > >> --- > >> "To live in the presence of great truths and eternal laws, > >> to be led by permanent ideals- > >> that is what keeps a man patient when the world ignores him, > >> and calm and unspoiled when the world praises him." > >> -Balzac > >> --- > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l@lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > -- > > Andrew Farmer > [EMAIL PROTECTED] > (505) 995-4464 > Database Administrator/Software Developer > National Center for Genome Resources > > --- > "To live in the presence of great truths and eternal laws, > to be led by permanent ideals- > that is what keeps a man patient when the world ignores him, > and calm and unspoiled when the world praises him." > -Balzac > --- > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l