Hi, I was trying to create a protein sequence using ProteinTools; I've found a couple of oddities:
1. There's a method called createDNASequence(..) [yes, in ProteinTools] that claims to create a new Protein sequence based on the input parameters. Is this just a typo, or am I missing something? 2. createProtein(seqstring) returns a SymbolList based on an alphabet called PROTEIN-TERM (which is apparently a protein alphabet with terminator characters permitted). When you call getName() on this alphabet, it returns "PROTEIN-TERM", which is what BioSQLSequenceDB attempts to store in the Molecule field of the Biosequence table when storing a Sequence. The problem is that that field is only 10 characters wide in the BioSQL spec, so when you do a BioSQLSequenceDB.addSequence(..) with the new sequence, it fails. I'm not really sure who's in charge of that schema, but it'd be good if the default fields in Biojava were friendly with the default spec for BioSQL... Thanks! Mayank _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
