Hi - I have corrected the naming of the method in the CVS. It looks like someone did a copy and paste and forgot to rename the method. Everything else about it seems OK.
As to point2. Probably Thomas is the best person to deal with the interactions between biojava and BioSQL. My suggestion on this would be that the method that puts the sequence into biosql doesn't call the getName method on the alphabet but rather puts in "protein" or something valid. Another bigger issue is that a protein sequence (of the type you'd put in a DB) doesn't really have termination residues. I understand that the ProteinTAlphabet exists for translation purposes so you can make fancy six frame translations of a DNA seq in which case you need the termination symbols. Possibly splitting hairs here, what do others think? - Mark > -----Original Message----- > From: Mayank Thanawala [mailto:[EMAIL PROTECTED]] > Sent: Thursday, 26 September 2002 4:52 a.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] ProteinTools > > > 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 > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
