[Biojava-l] SCF and ABI chromatogram read error

[Heather Kent]

Hi!
im also having a problem creating a chromatogram object from abi or scf
files.  The abi files i have are sequences that have been processed for
heterozygotes so there are symbols for incompletely specified bases in the
sequence (for instance r or y).  The ABI and SCF parsers in biojava apear to
only parse the DNA atomic symbols or a gap symbol.  Right now im in the
middle of trying to override the  decodeDNAToken method in the
ABIFParser.java class.  I'll create my own finite alphabet with the other
symbols i need the parser to recognize.  Am i heading in the right direction
here or is there an easier way?? The SCF parser is set up the same way so
i'll have to override it too....

any help would be appreciated!!
thanx
heather