[Biojava-l] Reading Fasta file problem (new to biojava)

[Chris Cole]

[ 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