I would be strongly against it. Deprecating methods will always break people's code. I'm sure it would break some of mine. I find that I am often going between a String and a SymbolList since 1) I work with other peoples non-biojavaized code 2) I work with a database that stores its sequence as varchars or clobs - getting my sequence in requires putting it into a String 3) Sometimes I want to output my sequence in a form that is readable, and I find that a String is a generally useful means of displaying it ;)
I'm not sure why you would want to deprecate methods that are as obvious to have on a SymbolList. I agree that the Tokenization code is a great way to handle the intricacies of multiple alphabets. Yes it is possible to use this whenever you want to get a String, after all that is what AbstractSymbolList does! I would say that seqString() is as obviously necessary to an object representing a DNA or protein sequence, as toString() is to an Object. David > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]On > Behalf Of Matthew Pocock > Sent: Monday, July 15, 2002 8:53 AM > To: [EMAIL PROTECTED] > Subject: [Biojava-l] deprecating some SymbolList methods > > > Hi All, > > I hope you are all enjoying your summer holidays. I look forward to > seeing some of you at ISMB soon. > > I was wondering if anybody would object if the subStr and seqString > methods of SymbolList were deprecated with a message saying that you > should be using Thomas' excelent symbol tokenization code? I'm more than > willing to go with popular opinion on this one. > > Matthew > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
