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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Term.t,v 1.9 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 => 51;
}
use Bio::Ontology::Term;
use Bio::Ontology::TermFactory;
use Bio::Annotation::DBLink;
use Bio::Annotation::Reference;
my $obj = Bio::Ontology::Term->new();
ok( $obj->isa( "Bio::Ontology::TermI" ) );
ok( $obj->identifier( "0003947" ), "0003947" );
ok( $obj->identifier(), "0003947" );
ok( $obj->name( "N-acetylgalactosaminyltransferase" ), "N-acetylgalactosaminyltransferase" );
ok( $obj->name(), "N-acetylgalactosaminyltransferase" );
ok( $obj->definition( "Catalysis of ..." ), "Catalysis of ..." );
ok( $obj->definition(), "Catalysis of ..." );
ok( $obj->version( "666" ), "666" );
ok( $obj->version(), "666" );
ok( $obj->ontology( "category 1 name" ) );
ok( $obj->ontology()->name(), "category 1 name" );
my $ont = Bio::Ontology::Ontology->new();
ok( $ont->name( "category 2 name" ) );
ok( $obj->ontology( $ont ) );
ok( $obj->ontology()->name(), "category 2 name" );
ok( $obj->is_obsolete( 1 ), 1 );
ok( $obj->is_obsolete(), 1 );
ok( $obj->comment( "Consider the term ..." ), "Consider the term ..." );
ok( $obj->comment(), "Consider the term ..." );
ok( $obj->get_synonyms(), 0 );
$obj->add_synonym( ( "AA", "AB" ) );
my @al1 = $obj->get_synonyms();
ok( scalar(@al1), 2 );
ok( $al1[ 0 ], "AA" );
ok( $al1[ 1 ], "AB" );
my @al2 = $obj->remove_synonyms();
ok( $al2[ 0 ], "AA" );
ok( $al2[ 1 ], "AB" );
ok( $obj->get_synonyms(), 0 );
ok( $obj->remove_synonyms(), 0 );
$obj->add_synonyms( ( "AA", "AB" ) );
ok( $obj->identifier(undef), undef );
ok( $obj->name(undef), undef );
ok( $obj->definition(undef), undef );
ok( $obj->is_obsolete(0), 0 );
ok( $obj->comment(undef), undef );
$obj = Bio::Ontology::Term->new(
-identifier => "0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-version => "6.6.6",
-ontology => "cat",
-comment => "X",
-dblinks => [
Bio::Annotation::DBLink->new(-database => 'db1'),
Bio::Annotation::DBLink->new(-database => 'db2')
],
-references => []
);
ok( $obj->identifier(), "0016847" );
ok( $obj->name(), "1-aminocyclopropane-1-carboxylate synthase" );
ok( $obj->definition(), "Catalysis of ..." );
ok( $obj->is_obsolete(), 0);
ok( $obj->comment(), "X" );
ok( $obj->version(), "6.6.6" );
ok( $obj->ontology()->name(), "cat" );
ok( scalar($obj->get_dblinks), 2);
ok( scalar($obj->get_references), 0);
# test object factory for terms
my $fact = Bio::Ontology::TermFactory->new();
$obj = $fact->create_object(-name => "some ontology term");
ok $obj->isa("Bio::Ontology::TermI");
ok ($obj->name, "some ontology term");
$fact->type("Bio::Ontology::GOterm");
$obj = $fact->create_object(-name => "some ontology term",
-identifier => "GO:987654");
ok $obj->isa("Bio::Ontology::TermI");
ok (ref($obj), "Bio::Ontology::GOterm");
ok ($obj->name, "some ontology term");
ok ($obj->identifier, "GO:987654");
$fact->type("Bio::Annotation::OntologyTerm");
$obj = $fact->create_object(-name => "some ontology term",
-identifier => "GO:987654",
-ontology => "nonsense");
ok $obj->isa("Bio::Ontology::TermI");
ok $obj->isa("Bio::AnnotationI");
ok ($obj->name, "some ontology term");
ok ($obj->identifier, "GO:987654");
ok ($obj->tagname, "nonsense");
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