dbEntries.t

use strict;
use warnings;

BEGIN { $| = 1;
	use Test;
	plan tests => 42;
}

use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;

use Bio::EnsEMBL::DBEntry;

# switch on the debug prints

our $verbose = 0;

debug( "Startup test" );
#
# 1 Test started
#
ok(1);

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

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

debug( "Test database instatiated" );

#
# 2 Database instatiated
#
ok( $db );

# some retrievals
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();


my $sth = $db->dbc->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
$sth->execute();

my ( $xref_count )  = $sth->fetchrow_array();
my $db_entry_count = 0;
my $goxref_count = 0;
my $ident_count = 0;

$sth->finish();

my $ga = $db->get_GeneAdaptor();

my $all_gene_ids = $ga->list_dbIDs();
for my $gene_id ( @$all_gene_ids ) {
  my $gene = $ga->fetch_by_dbID( $gene_id );

  for my $tr ( @{$gene->get_all_Transcripts()} ) {
    my $tl = $tr->translation();
    my $dbentries = $dbEntryAdaptor->fetch_all_by_Translation( $tl );
    $db_entry_count += scalar( @{$dbentries});
    $goxref_count += grep { $_->isa( "Bio::EnsEMBL::GoXref" )} @$dbentries;
    $ident_count += grep {$_->isa( "Bio::EnsEMBL::IdentityXref" )} @$dbentries;
  }
}

debug( "Found $xref_count xrefs and $db_entry_count dblinks." );
debug( " $goxref_count GoXrefs, $ident_count identityXrefs." );

#
# 3 as many dblinks as entries in object_xref
#
ok( $db_entry_count == $xref_count );