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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2008-03-18 14:44:57 UTC
  • mfrom: (4 hardy)
  • mto: This revision was merged to the branch mainline in revision 6.
  • Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
http://bugs.debian.org/448890
* debian/control:
  - Removed MIA Matt Hope (dopey) from the Uploaders field.
    Thank you for your work, Matt. I hope you are doing well.
  - Downgraded some recommended package to the 'Suggests' priority,
    according to the following discussion on Upstream's mail list.
    http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
    (Closes: #448890)
* debian/copyright converted to machine-readable format.

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t/hmmer.t
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# -*-Perl-*-
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## Bioperl Test Harness Script for Modules
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##
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# $Id: hmmer.t,v 1.17 2003/12/15 17:36:11 jason Exp $
 
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# $Id: hmmer.t,v 1.18 2004/11/11 18:29:10 jason Exp $
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# Before `make install' is performed this script should be runnable with
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# `make test'. After `make install' it should work as `perl test.t'
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    ok($result->sequence_file, '/home/birney/src/wise2/example/road.pep');
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    ok($result->query_name, 'roa1_drome');
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    ok($result->query_description, '');
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    ok($result->num_hits(), 1);
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    while( my $hit = $result->next_model ) {
 
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    ok($result->num_hits(), 2);
 
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    my ($hsp,$hit);
 
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    if( $hit = $result->next_model ) {
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        ok($hit->name, 'SEED');
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        ok($hit->raw_score, '146.1');
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        ok($hit->significance, '6.3e-40');
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        ok(ref($hit), 'Bio::Search::Hit::HMMERHit');
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        ok($hit->num_hsps, 2);
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        my $hsp = $hit->next_domain;
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        if( defined $hsp ) {
 
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        ok($hit->num_hsps, 1);
 
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        if( defined( $hsp = $hit->next_domain ) ) {
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            ok($hsp->hit->start, 1);
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            ok($hsp->hit->end, 77);
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            ok($hsp->query->start, 33);
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            ok( length($hsp->homology_string), length($hsp->hit_string));
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            ok( length($hsp->query_string), length($hsp->homology_string));
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        }
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        $hsp = $hit->next_domain;
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        if( defined $hsp ) {
 
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    }
 
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    if( defined ($hit = $result->next_model) ) {
 
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        if( defined($hsp = $hit->next_domain) ) {
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            ok($hsp->hit->start, 1);
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            ok($hsp->hit->end, 77);
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            ok($hsp->query->start, 124);
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            ok( length($hsp->homology_string), length($hsp->hit_string));
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            ok( length($hsp->query_string), length($hsp->homology_string));
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        }
 
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        last;
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    }
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}
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$searchio = new Bio::SearchIO(-format => 'hmmer',