Matthew Pocock wrote: > We need to make this process much easier. Unfortunately, getAsChar() > doesn't realy work for us because we can have symbols for things that > don't have a single char representation, such as codons. However, you > shouldn't have to end up going through 20 function calls either. > > Is there a biojava in anger example of geting letters from symbols?
Nope, not that I could see. BTW, the BioJava in Anger is a very helpful document, I've been consulting it often :-). Sounds like this would make a good addition to the "how do I get between strings and symbols" section. On a related note, biojava seems to always use lowercase when writing out DNA sequences. Is there an officially endorsed method for switching to upper case? Should I modify my AlphabetManager.xml, or should I reregister a new CharacterTokenization with the name "token" so that it overrides the default one and gets picked by the various output formats? > > Parsing a BLAST output file was also easy, however, I had to use > > "lazy" mode to work with our files (from NCBI BLAST 2.2.1), and I have > > not yet figured out how to extract a) the length of the query > > sequence, and b) the frame of the hits. Any suggestions here? > > Is that information in the annotation attached to the > SeqSimilaritySearchSubHit or the SeqSimilritySearchResult? When I print out all the annotations (basically using the BIA example BlastParser.java, modified to include sub hit information), I see that the queryFrame is present, but the query length information is not. > Good luck with BioSQL and GFF. These are parts of the library that I use > daily. Oh, and for the GFF, start off by using GFFTools. I've written some sequences, annotated from GFF files to a mysql database using BioSQL, and it worked great! Does the BioJava code support writing taxonomy information to the database, so I can link my sequences to species? (I've moved this to biojava-l, since this seems more of a biojava-l question than biojava-dev question, although with open source class libraries, the line often seems to get blurred :-)) Cheers, Len. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
