[Biojava-l] Fasta parsing question

Andreas Prlic andreas at sdsc.edu
Wed Jun 17 05:04:04 UTC 2015

Hi Henk,

Do you want to share some code-snippets so we can help you debug?



On Mon, Jun 15, 2015 at 1:58 AM, Toorn, H.W.P. van den (Henk) <
h.w.p.vandentoorn at uu.nl> wrote:

> Dear List,
> I've just started using BioJava 4.0.0 in my projects, and wanted to ask a
> question about parsing large Fasta files. There is the option to read parts
> of the fasta file.
> FastaReader.process(number)
> The problem I have is that it's not documented what happens if the file is
> read in its entirety. I was expecting a null or an empty map, or even some
> exception, but none happened and the parser kept on producing (empty)
> sequences.
> Could anyone enlighten me? I'm probably missing the point here. Maybe
> there is a better way to do this (there used to be the SequenceIterator if
> I remember correctly, but I can't find that in version 4.0).
> Regards, Henk
> My setup: windows 7 64-bit, java 1.8.0_45 64 bit, BioJava 4.0.0 via Maven.
> --
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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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