[Biojava-l] BufferedReader and FastaFormat

[Matthew Pocock]

I was having the same trouble, but it went away when I changed line 138 
of FastaFormat to:

     char[] cache = new char[512];

Thomas - could this cache be auto-extended to avoid overflows?

Thomas Down wrote:
> On Tue, Mar 05, 2002 at 10:07:11AM +1300, Schreiber, Mark wrote:
> 
>>java.io.IOException: Mark invalid
>>	at java.io.BufferedReader.reset(BufferedReader.java:467)
>>	at
>>org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:164
>>)
>>	at
>>org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:121)
>>	at
>>org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100)
>>rethrown as org.biojava.bio.BioException: Could not read sequence
>>	at
>>org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103)
>>
> 
> I've heard a few problems with the mark/restore sytem
> on BufferedReader.  They can usually be fixed by setting
> the mark-validity a bit further ahead than you're actually
> planning to read.
> 
> I wonder if your file contains any DOS-type line endings
> (\r\n).  There was one case where someone was having trouble
> with EMBL parsing, and fixed it by stripping these out.
> 
> Alternatively, you could just try changing:
> 
>    r.mark(cache.length);
> 
> To:
> 
>    r.mark(cache.length + 50); // fudge factor.
> 
> It's not a particularly  satisfying solution until we understand
> exactly where the marks are falling out of scope, but I bet
> it will get your file parsing...
> 
>      Thomas.
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