Probably the best way (currently) to get a Distribution to emmit an ambiguity is to emit two symbols and merge them together. The getWeight(Symbol s) methods also work where s is an ambiguity (should return the summed weight of each). Could possibly put a method in DistributionTools but I'm not sure how you would parameterize the frequency of ambiguity.
Another possiblity would be to look at the phred sequence classes in org.biojava.bio.programs.phred, Sequences over this alphabet contain the concept of ambiguity. You could randomly generate symbols from this alphabet and then convert them to DNA using some quality threshold to decide when to use an ambiguity Symbol. The getToken method is obsolete, the SymbolTokenization is now used instead. - Mark > -----Original Message----- > From: David Huen [mailto:david.huen@;ntlworld.com] > Sent: Tuesday, 29 October 2002 11:29 a.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] Alphabets with ambiguity symbols included > > > How do I get an Alphabet that has all the ambiguity symbols > too? Do we have > one canned? > > I'm trying to get a Distribution to generate an almighty brew > of random > symbols to torture test the SymbolList implementations with a jUnit. > > Incidentally, in the Symbol interface blurb, it mentions a > getToken method > that doesn't seem to be there. Is that obsolete or has the > method been > inadvertently omitted? > > Regards, > David Huen > > _______________________________________________ > 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
