exon.t

# Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

use strict;
use warnings;

use Test::More;

use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::CoordSystem;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Exon;

our $verbose = 0; #set to 1 to turn on debug printouts

my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();

ok(1);



my $db = $multi->get_DBAdaptor( 'core' );

ok($db);


# Exon specific tests

my $exonad = $db->get_ExonAdaptor();
my $slice_adaptor = $db->get_SliceAdaptor();

my $slice = $slice_adaptor->fetch_by_region('chromosome', '20',
                                            30_811_000,
                                            32_000_000);
ok($exonad);

my $exon = Bio::EnsEMBL::Exon->new();


$exon->start(1000);
ok(&test_getter_setter($exon, 'start', 200));

$exon->end(1400);
ok(&test_getter_setter($exon, 'end', 400));

$exon->strand(1);
ok(&test_getter_setter($exon, 'strand', -1));

$exon->phase(0);
ok(&test_getter_setter($exon, 'phase', -1));

$exon->slice( $slice );
ok(&test_getter_setter($exon, 'slice', $slice));

# should try to store (!)
$exon->end_phase( -1 );