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 <[EMAIL PROTECTED]> on 09/11/2002 05:30:46 PM
To: "Patrick McConnell" <[EMAIL PROTECTED]>
cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Question about BioJava DASClient classes
>>>>> "Patrick" == Patrick McConnell <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
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