← Back to branch summary

~ubuntu-branches/ubuntu/raring/bioperl/raring

« back to all changes in this revision

Viewing changes to t/AnnotationAdaptor.t

  • 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.

Show diffs side-by-side

added added

removed removed

Lines of Context:
t/AnnotationAdaptor.t
1
1
# -*-Perl-*-
2
2
## Bioperl Test Harness Script for Modules
3
 
## $Id: AnnotationAdaptor.t,v 1.1 2002/09/29 23:32:15 lapp Exp $
 
3
## $Id: AnnotationAdaptor.t,v 1.2 2004/11/24 02:14:06 allenday Exp $
4
4
 
5
5
# Before `make install' is performed this script should be runnable with
6
6
# `make test'. After `make install' it should work as `perl test.t'
15
15
        use lib 't';
16
16
    }
17
17
    use Test;
18
 
    plan tests => 21;
 
18
    plan tests => 19;
19
19
}
20
20
 
21
21
use Bio::SeqFeature::Generic;
32
32
$feat->add_tag_value("tag2", "some value for a tag");
33
33
 
34
34
my $link1 = new Bio::Annotation::DBLink(-database => 'TSC',
35
 
                                        -primary_id => 'TSC0000030',
36
 
                                        -tagname => "tag2"
37
 
                                        );
 
35
                                        -primary_id => 'TSC0000030',
 
36
                                        #cannot use "tag2", already claimed by Bio::Annotation::SimpleValue by above $feat->add_tag_value() call.
 
37
                                        -tagname => "tag3"
 
38
                                       );
38
39
$feat->annotation->add_Annotation($link1);
39
40
 
40
41
ok(1);
42
43
my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat);
43
44
 
44
45
ok ($anncoll->get_num_of_annotations(), 4);
45
 
ok (scalar($anncoll->get_all_annotation_keys()), 2);
 
46
ok (scalar($anncoll->get_all_annotation_keys()), 3);
46
47
 
47
48
my @anns = $anncoll->get_Annotations("tag1");
48
49
my @vals = $feat->each_tag_value("tag1");
 
50
 
49
51
ok (scalar(@anns), scalar(@vals));
50
52
for(my $i = 0; $i < @anns; $i++) {
51
 
    ok ($anns[$i]->value(), $vals[$i]);
 
53
  ok ($anns[$i]->value(), $vals[$i]);
52
54
}
53
55
 
54
 
@anns = $anncoll->get_Annotations("tag2");
55
 
my @fanns = $feat->annotation->get_Annotations("tag2");
56
 
@vals = $feat->each_tag_value("tag2");
 
56
@anns = $anncoll->get_Annotations("tag3");
 
57
my @fanns = $feat->annotation->get_Annotations("tag3");
 
58
@vals = $feat->each_tag_value("tag3");
57
59
 
58
60
ok (scalar(@fanns), 1);
59
 
ok (scalar(@anns), 2);
 
61
ok (scalar(@anns), 1);
60
62
ok (scalar(@vals), 1);
61
 
ok ($anns[0]->value(), $vals[0]);
62
 
ok ($anns[1]->primary_id(), $fanns[0]->primary_id());
 
63
ok ($anns[0]->primary_id(), $vals[0]);
 
64
 
 
65
ok ($anns[0]->primary_id(), $fanns[0]->primary_id());
63
66
 
64
67
my $comment = Bio::Annotation::Comment->new( '-text' => 'sometext');
65
68
$anncoll->add_Annotation('comment', $comment);
72
75
                                               -tagname => "tag2");
73
76
$anncoll->add_Annotation($tagval);
74
77
 
75
 
@anns = $anncoll->get_Annotations("tag2");
76
 
@fanns = $feat->annotation->get_Annotations("tag2");
77
 
@vals = $feat->each_tag_value("tag2");
 
78
@anns = $anncoll->get_Annotations("tag3");
 
79
@fanns = $feat->annotation->get_Annotations("tag3");
 
80
@vals = $feat->each_tag_value("tag3");
78
81
 
79
82
ok (scalar(@fanns), 1);
80
 
ok (scalar(@anns), 3);
81
 
ok (scalar(@vals), 2);
82
 
ok ($anns[0]->value(), $vals[0]);
83
 
ok ($anns[1]->value(), $vals[1]);
84
 
ok ($anns[2]->primary_id(), $fanns[0]->primary_id());
 
83
ok (scalar(@anns), 1);
 
84
ok (scalar(@vals), 1);
 
85
ok ($anns[0]->primary_id(), $vals[0]);
85
86
 
86
87
ok ($anncoll->get_num_of_annotations(), 6);
87
88