Thank you for the suggestion. I made that work. Here is another related question: how can I make my own custom alphabet handle the ambiguity symbol X like what the predefined protein alphabet does? Thanks.
Zhen -----Original Message----- From: Thomas Down [mailto:[EMAIL PROTECTED]] Sent: Monday, December 09, 2002 3:16 PM To: Ren, Zhen Cc: [EMAIL PROTECTED] Subject: Re: [Biojava-l] SymbolParsers in Alphabet On Mon, Dec 09, 2002 at 02:07:51PM -0800, Ren, Zhen wrote: > Hi, there, > > The interface Alphabet has a method > public SymbolTokenization getTokenization(java.lang.String name) throws >BioException > > Every alphabet should have a SymbolParser under the name 'token' that uses the >symbol token characters to translate a string into a SymbolList. Likewise, there >should be a SymbolParser under the name 'name' that uses symbol names to identify >symbols. > > I'd like to know how I can have these two SymbolParsers under the names 'token' and >'name' incorporated into an alphabet I intend to create by myself. Hmmm, "SymbolParser" is an old interface name. Its functionality has been subsumed into SymbolTokenization, but a few references to it survived in the javadoc for a while. I think these are gone now, if you get the latest CVS version. Exactly how tokenizations are handled depends on the Alphabet implementation. If you write your own Alphabet, you can, of coure, write a getTokenization method yourself. If you're construction a SimpleAlphabet, getTokenization("name") is handled automatically for you. To add extra tokenizations, you can do something like: CharacterTokenization toke = new CharacterTokenization( myAlphabet, false ); toke.bindSymbol(symbol0, '0'); toke.bindSymbol(symbol1, '1'); myAlphabet.putTokenization("token", toke); Hope this helps, Thomas. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
