[Biojava-l] (no subject)

Dear Biojava-l I tried to recompile biojava under 1.4.1 , but found many warnings. Is is dangerous? ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/ma

Re: [Biojava-l] get all symbols in an alphabet

On Thu, Jan 09, 2003 at 11:26:13AM +1300, Schreiber, Mark wrote: > Hi - > > If the Alphabet is a FiniteAlphabet you can get an iterator over the > Alphabet or you can use AlphabetManager to generate an AlphabetIndex > which can be used to access each Symbol. > > The getSymbol method you describe

Re: [Biojava-l] anonymous cvs down?

Works for me testing right now - you might check your firewall settings? Has it worked in the past? In the future send system problems to [EMAIL PROTECTED] please. -jason On Wed, 8 Jan 2003, Russell Smithies wrote: > It looks like the anonymous cvs server may be down :-( > It doesn't work usin

RE: [Biojava-l] get all symbols in an alphabet

Hi - If the Alphabet is a FiniteAlphabet you can get an iterator over the Alphabet or you can use AlphabetManager to generate an AlphabetIndex which can be used to access each Symbol. The getSymbol method you describe generates an ambiguity symbol that uniquely describes the set of Symbols in the

[Biojava-l] anonymous cvs down?

It looks like the anonymous cvs server may be down :-( It doesn't work using the commands from the webpage: cvs -d :pserver:[EMAIL PROTECTED]:/home/repository/biojava login Can someone please try it or see what the problem is? It seems to timeout after asking for and receiving the password (cvs)

[Biojava-l] get all symbols in an alphabet

Hi, gang, How do I get all symbols in an alphabet? The Alphabet interface has a method: Symbol getSymbol(java.util.List rl); Can someone help me understand what symbol it really returns, a random one, the first one or what? How do I use this? Thanks so much. Zhen __

[Biojava-l] (no subject)

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Re: [Biojava-l] biojava cvs

Hiya, biojava-live is the module that contains what everybody thinks of as biojava. Everything else is either exciting or arcane code (read, it may or may work). bytecode contains a java bytecode generator that looks like a macro-assembler and is used to build new bytecode.jar files. Matthew --

Re: [Biojava-l] locating genes in a genomic sequence

Karin Lagesen wrote: On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote: Hi - If you already have the SimpleGene features constructed these will contain a Location object. However, I think you are saying how can I find a subsequence in my Genomic sequence and locate the gene that

Re: [Biojava-l] locating genes in a genomic sequence

On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote: > Hi - > > If you already have the SimpleGene features constructed these will > contain a Location object. However, I think you are saying how can I > find a subsequence in my Genomic sequence and locate the gene that way? > > To ra