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Viewing changes to t/SeqFeature/SeqFeatAnnotated.t

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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t/SeqFeature/SeqFeatAnnotated.t
 
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# -*-Perl-*- Test Harness script for Bioperl
 
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# $Id: SeqFeatAnnotated.t 15112 2008-12-08 18:12:38Z sendu $
 
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use strict;
 
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BEGIN { 
 
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    use lib '.';
 
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    use Bio::Root::Test;
 
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    test_begin(-tests => 34, 
 
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               -requires_modules => [qw(URI::Escape Graph::Directed)],
 
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               -requires_networking => 1
 
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        );
 
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        use_ok('Bio::SeqFeature::Generic');
 
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        use_ok('Bio::SeqFeature::Annotated');
 
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}
 
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my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
 
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                                          -end => 5,
 
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                                          -strand => "+",
 
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                                          -frame => 2,
 
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                                          -type => 'nucleotide_motif',
 
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                                          -phase => 2,
 
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                                          -score => 12,
 
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                                          -source => 'program_b',
 
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                                          -display_name => 'test.annot',
 
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                                          -seq_id => 'test.displayname' );
 
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ok (defined $sfa);
 
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my $loc = $sfa->location;
 
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ok $loc->isa("Bio::Location::Simple");    
 
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ok $sfa->display_name eq 'test.annot';
 
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#test bsfa::from_feature
 
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my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
 
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                                          -end => 440,
 
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                                          -strand => 1,
 
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                                          -primary => 'nucleotide_motif',
 
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                                          -source  => 'program_a',
 
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                                          -tag => {
 
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                                          silly => 20,
 
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                                          new => 1
 
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                                          }
 
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                                          );
 
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my $sfa2;
 
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$sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
 
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is $sfa2->type->name,'nucleotide_motif';
 
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is $sfa2->primary_tag, 'nucleotide_motif';
 
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is $sfa2->source->display_text,'program_a';
 
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is $sfa2->source_tag,'program_a';
 
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is $sfa2->strand,1;
 
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is $sfa2->start,400;
 
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is $sfa2->end,440;
 
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is $sfa2->get_Annotations('silly')->value,20;
 
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is $sfa2->get_Annotations('new')->value,1;
 
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my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
 
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is $sfaa->type->name,'nucleotide_motif';
 
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is $sfaa->primary_tag, 'nucleotide_motif';
 
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is $sfaa->source->display_text,'program_b';
 
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is $sfaa->source_tag,'program_b';
 
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is $sfaa->strand,1;
 
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is $sfaa->start,1;
 
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is $sfaa->end,5;
 
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is $sfaa->score,12;
 
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my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
 
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                                        -end => 5,
 
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                                        -strand => "+",
 
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                                        -frame => 2,
 
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                                        -phase => 2,
 
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                                        -score => 12,
 
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                                        -display_name => 'test.annot',
 
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                                        -seq_id => 'test.displayname' );
 
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$sfa3->from_feature($sfg);
 
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is $sfa3->type->name,'nucleotide_motif', 'type->name';
 
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is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
 
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is $sfa3->source->display_text,'program_a';
 
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is $sfa3->source_tag,'program_a';
 
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is $sfa3->strand,1;
 
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is $sfa3->start,400;
 
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is $sfa3->end,440;
 
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is $sfa3->get_Annotations('silly')->value,20;
 
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is $sfa3->get_Annotations('new')->value,1;
 
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# Note there is an API conflict with SeqFeature::Generic, where score is a
 
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# simple scalar, and here it is a Bio::Annotation::SimpleValue
 
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# By popular vote there is no operator overloading, so this needs to be
 
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# resolved
 
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is $sfa3->score(), 12; 
 
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$sfa3->score(11);
 
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is $sfa3->score(), 11; 
 
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$sfa3->score(0);
 
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is $sfa3->score(), 0;   # test that setting to 0 no longer is overriddent to set score to '.' (fixed in Bio::SeqFeature::Annotated version 1.3.7)
 
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