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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: GOterm.t,v 1.8 2003/05/27 22:13:41 lapp 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 => 59;
}
use Bio::Ontology::GOterm;
use Bio::Ontology::Ontology;
my $obj = Bio::Ontology::GOterm->new();
ok( $obj->isa( "Bio::Ontology::GOterm" ) );
$obj->init();
ok( $obj->to_string() );
ok( $obj->GO_id( "GO:0003947" ), "GO:0003947" );
ok( $obj->GO_id(), "GO:0003947" );
ok( $obj->get_dblinks(), 0 );
$obj->add_dblink( ( "dAA", "dAB" ) );
ok( scalar($obj->get_dblinks()), 2 );
my @df1 = $obj->get_dblinks();
ok( $df1[ 0 ], "dAA" );
ok( $df1[ 1 ], "dAB" );
ok( $obj->get_dblinks(), 2 );
my @df2 = $obj->remove_dblinks();
ok( $df2[ 0 ], "dAA" );
ok( $df2[ 1 ], "dAB" );
ok( $obj->get_dblinks(), 0 );
ok( $obj->remove_dblinks(), 0 );
ok( $obj->get_secondary_GO_ids(), 0 );
$obj->add_secondary_GO_id( ( "GO:0000000", "GO:1234567" ) );
ok( scalar($obj->get_secondary_GO_ids()), 2 );
my @si1 = $obj->get_secondary_GO_ids();
ok( $si1[ 0 ], "GO:0000000" );
ok( $si1[ 1 ], "GO:1234567" );
ok( $obj->get_secondary_GO_ids(), 2 );
my @si2 = $obj->remove_secondary_GO_ids();
ok( $si2[ 0 ], "GO:0000000" );
ok( $si2[ 1 ], "GO:1234567" );
ok( $obj->get_secondary_GO_ids(), 0 );
ok( $obj->remove_secondary_GO_ids(), 0 );
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_synonym( ( "AA", "AB" ) );
$obj->add_dblink( ( "dAA", "dAB" ) );
$obj->add_secondary_GO_id( ( "GO:1234567", "GO:1234567" ) );
$obj->init();
ok( $obj->identifier(), undef ); # don't make up identifiers
ok( $obj->name(), undef );
ok( $obj->definition(), undef );
ok( $obj->is_obsolete(), 0 );
ok( $obj->comment(), undef );
$obj = Bio::Ontology::GOterm->new( -go_id => "0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-version => "6.6.6",
-ontology => "cat",
-comment => "X" );
ok( $obj->identifier(), "GO: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" );
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