[Biojava-l] Question about BioJava DASClient classes

[Patrick McConnell]

I also noticed an inconsistency with the numberOfIdentities and the
percentageIdentity of the HSPSummary element.  The identities are 0 but the
percentage identity is 100.  This seems strange to me.  Am I interpretting
the results incorrectly?

            <biojava:HSPSummary score="1036.8"
                                expectValue="4e-54"
                                numberOfIdentities="0"
                                alignmentSize="141"
                                percentageIdentity="100.0"
                                querySequenceType="protein"
                                hitSequenceType="protein">


-Patrick





Keith James <kdj@sanger.ac.uk> on 09/11/2002 05:30:46 PM

To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
cc:    biojava-l@biojava.org

Subject:    Re: [Biojava-l] Question about BioJava DASClient classes


>>>>> "Patrick" == Patrick McConnell <MCCon012@mc.duke.edu> writes:

    Patrick> Incidentally, it breaks on fasta34t10d3 - the error is:

    Patrick> org.biojava.utils.ParserException: Fasta parser failed to
    Patrick> recognise line type Parsing line: 37 ; pg_open-ext: -10
    Patrick> -2

Alrighty. That's an easy one - it's designed to break when it finds
new/unknown lines in the output and pg_open-ext is a new one.

When I get hold of the source for 34t10d3 (ftp site is down right now)
I'll add it to the supported versions & the test suite.

Keith

--

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -