modules/t/ditag.t

modules/t/ditagAdaptor.t

@@ -51,7 +51,7 @@ ok($ditag_adaptor->store(\@ditags));
 
 #test fetch_all_by_name
 
-my $ditags = $ditag_adaptor->fetch_by_name($name);
+my $ditags = $ditag_adaptor->fetch_all_by_name($name);
 #if feature was stored it has a dbID now
 ok(scalar(@$ditags) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
 ok($ditags->[0]->name eq $name);
@@ -70,11 +70,11 @@ ok($ditags->[0]->type eq $type);
 # 7-8 #
 #######
 
-#test fetch_all_by_name_and_type
+#test fetch_by_name_and_type
 
-$ditags = $ditag_adaptor->fetch_all_by_name_and_type($name, $type);
-ok(scalar(@$ditags) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
-ok($ditags->[0]->type eq $type && $ditags->[0]->name eq $name);
+my $ditag = $ditag_adaptor->fetch_by_name_and_type($name, $type);
+ok($ditag && $ditag->isa('Bio::EnsEMBL::Map::Ditag'));
+ok($ditag->type eq $type && $ditag->name eq $name);
 
 ######
 # 9  #
@@ -91,8 +91,8 @@ $multi->restore('core', 'ditag');
 # 10 #
 ######
 
-#test fetch_with_limit
-$ditags = $ditag_adaptor->fetch_with_limit($type, 5, 0);
+#test fetch_all_with_limit
+$ditags = $ditag_adaptor->fetch_all_with_limit($type, 5, 0);
 ok((scalar(@$ditags) == 5) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
 
 ######

modules/t/ditagFeature.t

@@ -62,7 +62,7 @@ ok($feature && $feature->isa('Bio::EnsEMBL::Map::DitagFeature'));
 # hit_strand, cigar_line, start, end, strand,
 # dbID, sequence, slice, ditag_pair_id
 
-my $ditagFeatures = $dfa->fetch_by_ditagID($ditag_id);
+my $ditagFeatures = $dfa->fetch_all_by_ditagID($ditag_id);
 my $ditagFeature  = $ditagFeatures->[0];
 
 ok(defined $ditagFeature && $ditagFeature->isa('Bio::EnsEMBL::Map::DitagFeature'));

modules/t/ditagFeatureAdaptor.t

@@ -2,7 +2,7 @@ use strict;
 
 BEGIN { $| = 1;  
 	use Test ;
-	plan tests => 12;
+	plan tests => 14;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -14,25 +14,24 @@ use Bio::EnsEMBL::Analysis;
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
 my $db    = $multi->get_DBAdaptor( 'core' );
 
-my $region        = 11;
+my $region        = '11';
 my $ditag_id      = 1;
-my $qstart        = 120635196;
-my $qend          = 120635214;
-my $qstrand       = 1;
+my $qstart        = 83225874;
+my $qend          = 83236347;
+my $qstrand       = -1;
 my $tstart        = 3;
 my $tend          = 19;
 my $tstrand       = 1;
 my $ditag_side    = 'L';
 my $ditag_pair_id = 1;
 my $cigar_line    = '17M',
-my $type          = "ZZ13";
-
+my $tag_library   = 'ZZ13';
+my $logic_name    = 'DitagAlign';
 my $dbID          = 4828567;
 my $other_ditag   = 3278337;
-#469273
 
 my $slice         = $db->get_SliceAdaptor->fetch_by_region('chromosome', $region);
-my $analysis      = $db->get_AnalysisAdaptor->fetch_by_logic_name('DitagAlign' );
+my $analysis      = $db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
 
 ######
 # 1  #
@@ -85,7 +84,7 @@ ok($testfeature && $testfeature->isa('Bio::EnsEMBL::Map::DitagFeature'));
 $multi->restore('core', 'ditag_feature');
 
 ########
-# 5-11 #
+# 5-13 #
 ########
 
 #test fetch methods
@@ -99,28 +98,37 @@ my $df = $dfa->fetch_by_dbID($dbID);
 ok($df && $df->isa('Bio::EnsEMBL::Map::DitagFeature') && $df->dbID == $dbID);
 
 #test fetch by ditagID
-$dfs = $dfa->fetch_by_ditagID($other_ditag);
+$dfs = $dfa->fetch_all_by_ditagID($other_ditag);
 ok((scalar @$dfs == 2) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature')
 	&& $dfs->[0]->ditag_id == $other_ditag);
 
 #test fetch by type
-$dfs = $dfa->fetch_all_by_type($type);
+$dfs = $dfa->fetch_all_by_type($tag_library);
 ok((scalar @$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature')
-	&& $dfs->[0]->fetch_ditag->type eq $type);
+	&& $dfs->[0]->fetch_ditag->type eq $tag_library);
 
 # test fetch all by slice
 $slice = $db->get_SliceAdaptor->fetch_by_region('chromosome', $region,
                                                 $qstart, $qend);
+#use slice only
 $dfs = $dfa->fetch_all_by_Slice($slice);
 ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
 
+#use tag-library
+$dfs = $dfa->fetch_all_by_Slice($slice, $tag_library);
+ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
+
+#use logic-name
+$dfs = $dfa->fetch_all_by_Slice($slice, '', $logic_name);
+ok(1);#scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
+
 #test fetch_grouped
-$dfs = $dfa->fetch_grouped('', $type);
+$dfs = $dfa->fetch_grouped('', $tag_library);
 ok(scalar @$dfs);
 ok($dfs->[0]->{'ditag_id'} && $dfs->[0]->{'start'} && $dfs->[0]->{'end'});
 
 ######
-# 12 #
+# 14 #
 ######
 
 #test list_dbIDs