[Biojava-l] Fasta parsing question

Toorn, H.W.P. van den (Henk) h.w.p.vandentoorn at uu.nl
Mon Jun 15 08:58:45 UTC 2015

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.


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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