You're almost right already - the sample code would be this: BufferedReader br = new BufferedReader(new FileReader(args[0])); Namespace ns = RichObjectFactory.getDefaultNamespace(); RichSequenceIterator iterator = RichSequence.IOTools.readFastaProtein(br,ns);
(No need to cast it - it's already a RichSequenceIterator). The namespace is a hangover from the object model being based on BioSQL, where all sequences belong to a namespace. If you don't care about namespaces (which is highly likely if you're not persisting to BioSQL) then a default one is provided to use as a placeholder, as shown above. cheers, Richard On 16 Dec 2009, at 09:10, Chris Cole wrote: > [ repost as the first attempt never got through ] > > Hi, > > I'm new to biojava and relatively new to Java, but not new to progamming in > general (perl and C). > > As a quick exercise I wanted to be able to read in a Fasta file, but this > code here (Solution 2): > http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ReadFasta > > Has deprecated warnings for SeqIOTools and fileToBioJava(). The code > currently works, but what's the non-deprecated way of going about it? > > I can see from Javadoc that RichSequence.IOTools from org.biojavax.bio.seq is > now the recommended class, but how does one implement it? > > I've tried this, but readFastaProtein() requires a namespace, which I've no > idea what that means. > BufferedReader br = new BufferedReader(new FileReader(args[0])); > RichSequenceIterator iter = > (RichSequenceIterator)RichSequence.IOTools.readFastaProtein(br); > > All pointers appreciated. > Cheers, > Chris > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
