[Biojava-dev] traceviewer and phred scores

[Jun Wan]

Hi folks,
I intended to write a sequence traceviewer with phred scores displayed
underneath each base calls. The approach would be writing a new renderer
that displays phred scores, and add it, along with AbiTraceRenderer, to the
MultiLineRenderer, the problem is:
the base calls generated by phred program is slighly different from the
sequences returned by org.biojava.bio.program.abi.ABITrace.getSequence(),
including some insertions and deletions at both ends where chromatogram is
not as good, how can I align the phred scores/base-calls properly with the
chromatogram and sequences from ABITrace.getSequence()? I don't see the
alignment functions in biojava-1.3pre1, for Java 1.3.
I just started to look at this package, and it was very impressive. But
please pardon me if I missed something here.
You guys have done a great job. Thanks!


Jun Wan
Database Developer and Administrator
Phylos, Inc.
781-862-6400 x359