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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Annotation.t,v 1.11 2003/12/22 08:50:35 juguang Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 63;
}
use Bio::Annotation::Collection;
use Bio::Annotation::DBLink;
use Bio::Annotation::Comment;
use Bio::Annotation::Reference;
use Bio::Annotation::SimpleValue;
use Bio::Annotation::OntologyTerm;
use Bio::Annotation::StructuredValue;
use Bio::Seq;
use Bio::SeqFeature::Generic;
use Bio::Cluster::UniGene;
ok(1);
my $link1 = new Bio::Annotation::DBLink(-database => 'TSC',
-primary_id => 'TSC0000030'
);
ok $link1->isa('Bio::AnnotationI');
ok $link1->database(), 'TSC';
ok $link1->primary_id(), 'TSC0000030';
ok $link1->as_text, 'Direct database link to TSC0000030 in database TSC';
my $ac = Bio::Annotation::Collection->new();
ok $ac->isa('Bio::AnnotationCollectionI');
$ac->add_Annotation('dblink',$link1);
$ac->add_Annotation('dblink',
Bio::Annotation::DBLink->new(-database => 'TSC',
-primary_id => 'HUM_FABV'));
my $comment = Bio::Annotation::Comment->new( '-text' => 'sometext');
ok $comment->text, 'sometext';
ok $comment->as_text, 'Comment: sometext';
$ac->add_Annotation('comment', $comment);
my $ref = Bio::Annotation::Reference->new( '-authors' => 'author line',
'-title' => 'title line',
'-location'=> 'location line',
'-start' => 12);
ok $ref->authors, 'author line';
ok $ref->title, 'title line';
ok $ref->location, 'location line';
ok $ref->start, 12;
ok $ref->database, 'MEDLINE';
ok $ref->as_text, 'Reference: title line';
$ac->add_Annotation('reference', $ref);
my $n = 0;
foreach my $link ( $ac->get_Annotations('dblink') ) {
ok $link->database, 'TSC';
ok $link->tagname(), 'dblink';
$n++;
}
ok ($n, 2);
$n = 0;
my @keys = $ac->get_all_annotation_keys();
ok (scalar(@keys), 3);
foreach my $ann ( $ac->get_Annotations() ) {
shift(@keys) if ($n > 0) && ($ann->tagname ne $keys[0]);
ok $ann->tagname(), $keys[0];
$n++;
}
ok ($n, 4);
$ac->add_Annotation($link1);
$n = 0;
foreach my $link ( $ac->get_Annotations('dblink') ) {
ok $link->tagname(), 'dblink';
$n++;
}
ok ($n, 3);
# annotation of structured simple values (like swissprot''is GN line)
my $ann = Bio::Annotation::StructuredValue->new();
ok ($ann->isa("Bio::AnnotationI"));
$ann->add_value([-1], "val1");
ok ($ann->value(), "val1");
$ann->value("compat test");
ok ($ann->value(), "compat test");
$ann->add_value([-1], "val2");
ok ($ann->value(-joins => [" AND "]), "compat test AND val2");
$ann->add_value([0], "val1");
ok ($ann->value(-joins => [" AND "]), "val1 AND val2");
$ann->add_value([-1,-1], "val3", "val4");
$ann->add_value([-1,-1], "val5", "val6");
$ann->add_value([-1,-1], "val7");
ok ($ann->value(-joins => [" AND "]), "val1 AND val2 AND (val3 AND val4) AND (val5 AND val6) AND val7");
ok ($ann->value(-joins => [" AND ", " OR "]), "val1 AND val2 AND (val3 OR val4) AND (val5 OR val6) AND val7");
$n = 1;
foreach ($ann->get_all_values()) {
ok ($_, "val".$n++);
}
# nested collections
my $nested_ac = Bio::Annotation::Collection->new();
$nested_ac->add_Annotation('nested', $ac);
ok (scalar($nested_ac->get_Annotations()), 1);
($ac) = $nested_ac->get_Annotations();
ok $ac->isa("Bio::AnnotationCollectionI");
ok (scalar($nested_ac->get_all_Annotations()), 5);
$nested_ac->add_Annotation('gene names', $ann);
ok (scalar($nested_ac->get_Annotations()), 2);
ok (scalar($nested_ac->get_all_Annotations()), 6);
ok (scalar($nested_ac->get_Annotations('dblink')), 0);
my @anns = $nested_ac->get_Annotations('gene names');
ok $anns[0]->isa("Bio::Annotation::StructuredValue");
@anns = map { $_->get_Annotations('dblink');
} $nested_ac->get_Annotations('nested');
ok (scalar(@anns), 3);
ok (scalar($nested_ac->flatten_Annotations()), 2);
ok (scalar($nested_ac->get_Annotations()), 6);
ok (scalar($nested_ac->get_all_Annotations()), 6);
# OntologyTerm annotation
my $termann = Bio::Annotation::OntologyTerm->new(-label => 'test case',
-identifier => 'Ann:00001',
-ontology => 'dumpster');
ok ($termann->term);
ok ($termann->term->name, 'test case');
ok ($termann->term->identifier, 'Ann:00001');
ok ($termann->tagname, 'dumpster');
ok ($termann->ontology->name, 'dumpster');
ok ($termann->as_text, "dumpster|test case|Ann:00001");
# AnnotatableI
my $seq = Bio::Seq->new();
ok ($seq->isa("Bio::AnnotatableI"));
my $fea = Bio::SeqFeature::Generic->new();
ok ($fea->isa("Bio::AnnotatableI"));
my $clu = Bio::Cluster::UniGene->new();
ok ($clu->isa("Bio::AnnotatableI"));
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