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use strict;
use lib 't';
use TestUtils qw(test_getter_setter debug);
BEGIN { $| = 1;
use Test;
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}
use MultiTestDB;
use Bio::EnsEMBL::AssemblyExceptionFeature;
our $verbose = 0;
my $multi = MultiTestDB->new;
# get a core DBAdaptor
#
my $dba = $multi->get_DBAdaptor("core");
my $aefa = $dba->get_AssemblyExceptionFeatureAdaptor();
ok($aefa);
#
# 1 create a new AssemblyExceptionFeature
#
my $aef = new Bio::EnsEMBL::AssemblyExceptionFeature;
ok($aef);
#
# test the basic getter and setters
#
# start
ok(test_getter_setter($aef,'start',10));
# end
ok(test_getter_setter($aef,'end',14));
# type
ok(test_getter_setter($aef,'type', 'HAP'));
# check adaptor attaching
$aef->adaptor($aefa);
ok($aef->adaptor->isa('Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor'));
# fetch all
my $chr_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome',
'20_HAP1');
my @features = @{$aefa->fetch_all_by_Slice($chr_slice)};
ok(@features);
foreach my $f (@features) {
debug( "Feature: " . $f->slice->seq_region_name . " " .
$f->start . " " . $f->end . " " . $f->type);
my $as = $f->alternate_slice();
debug(" Alternate slice: " . $as->seq_region_name . " " .
$as->start . " " . $as->end);
}
my ($f) = @features;
ok($f->display_id eq $f->alternate_slice->seq_region_name);
my $feat = $aefa->fetch_by_dbID(1);
ok($feat->dbID() == 1);