Hi - I'm not too clear on what you are trying to do but you may find the Blast and Fasta tutorials on this page helpful http://www.biojava.org/docs/bj_in_anger/index.htm Much of the stuff that is from the blast tutorials is relevant to the Fasta parsers.
>From my understanding of your email you are not getting some of the information you want from the standard classes. You should know that the SearchContentAdapters provided with BioJava do not capture every detail of a search, only the bits we thought were most interesting. If you need to get more (or less) information you will need to make a custom SearchContentAdapter (usually you just extend the SearchContentAdapter and override some or all of the methods). Particularly you may want to look at http://www.biojava.org/docs/bj_in_anger/blastecho.htm which shows how to echo events from a BlastLikeSAXParser to STDOUT. It should be very easy to change this to echo for a FastaSearchSAXParser. Running this program will help you determine where the things you are looking for may end up and help you decide if and how you need to make a custom SearchContentAdapter to get the information you want. Hope this helps, Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Piroska Devay/PH/[EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 01/17/2005 11:53 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] (no subject) Dear All, I am new to biojava and unfortunately new to Java also. Parsing a Fasta output I could modify the FastaSearchSAX Parser to return the parsed data on the standard output. In the Fasta output the query-hit alignments are not returned, instead the query sequence and the subject sequence are returned separately. If the sequences were shifted by Fasta for matching, '-' symbols are inserted (-----------------------QVQLQQSGNELAKPGASMKMSCRASGYSFTSYWIHWLKQRPDQGLEWIGYIDPATAYTESNQKFKDKAILTADRS) I would like to align these sequence-strings. I simply would have 2 strings as an input or converted into SymbolLists. I don't seem to find the right class to do this. Could someone offer advice or refer me to some sample programs that I can browse through or a more detailed tutorial? Thanks very much, Piroska _______________________________________________ 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
