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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
