[Biojava-dev] blast parser

[Mark Schreiber]

Hi -

There have been lots of emails on this in the past. Essentially you
need to set the BlastParser to lazy parsing.

I keep meaning to make lazy parsing the default but I don't have a
machine that can access CVS version at the moment to do the check in.
Could someone make this change before we switch to subversion??

Thanks,

- Mark

On Dec 16, 2007 9:53 AM, Michael Gang <michaelgang at gmail.com> wrote:
> Dear All,
>
> I have a problem when running the blast parser example from the
> cookbook (http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser)
> with my custom blast I get the following error.
> org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.16 is not
> supported by the biojava blast-like parsing framework
>         at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241)
>         at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
>         at parse.BlastParser.main(BlastParser.java:44)
>
> Does it mean that I just can use the parser for older versions of blast ?
>
> Furthermore, as I understand the parser first parses all the blast
> queries and then I can iterate on the results.
> Is there a blast parser available where it parses every time just the
> next hit (this would save lots of memory).
>
> I searched in google and in the biojava wiki and did not find answers
> on these questions.
>
> Can you please help me in this topic ?
>
> Best regards,
> Michael
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