Hi Suman, If you are trying to determine the Alphabet of a BJ Sequence or SymbolList you would say something like seq.getAlphabet().getName() which will return "DNA" or RNA etc.
Unfortunately there is not a good (fool proof) way to guess the sequence type from a "flat file" unless that file specifically says the type. Often you can infer it (ie GenBank is DNA, SwissProt is protein) but for Fasta you often cannot unless it contains a symbol not found in the DNA alphabet (including ambiguities). - Mark -----Original Message----- From: Suman Kanuganti [mailto:[EMAIL PROTECTED] Sent: Thursday, 18 September 2003 9:20 a.m. To: [EMAIL PROTECTED] Subject: [Biojava-l] Detect seq? Ok; is there any best method to tell what is the seq type is in biojava? I mean is that a dna sequence or protein sequence etc. I have seen SeqAlignReadWrite.guessFileType but this is no approriate and does work, Thanks, Suman K ===== Suman K BioInformatics Associate, Genomics Research, University of Missouri - Columbia. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com _______________________________________________ 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
