tests for new maps/marker schema/API

modules/t/mapLocation.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;  
+	use Test ;
+	plan tests => 11
+}
+
+use Bio::EnsEMBL::Map::MapLocation;
+use Bio::EnsEMBL::Chromosome;
+use MultiTestDB;
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+
+my $multi = MultiTestDB->new();
+my $db = $multi->get_DBAdaptor( 'core' );
+
+
+######
+# 1  #
+######
+
+#test constructor
+my $mapname = 'genethon';
+my $name = 'DS1234';
+my $chr = $db->get_ChromosomeAdaptor->fetch_by_chr_name('X');
+my $pos = '12.5';
+my $lod = 0.23;
+
+my $mloc = 
+  Bio::EnsEMBL::Map::MapLocation->new($name, $mapname, $chr, $pos, $lod);
+
+ok($mloc && ref $mloc && $mloc->isa('Bio::EnsEMBL::Map::MapLocation'));
+
+
+
+#######
+# 2-3 #
+#######
+
+#test map_name
+
+ok($mapname eq $mloc->map_name);
+ok(&test_getter_setter($mloc, 'map_name', 'marshfield'));
+
+#######
+# 4-5 #
+#######
+
+#test chromosome
+ok($chr == $mloc->chromosome);
+ok(&test_getter_setter($mloc, 'chromosome', undef));
+
+#######
+# 6-7 #
+#######
+
+#test name
+ok($name eq $mloc->name);
+ok(&test_getter_setter($mloc, 'name', 'Z123213')); 
+
+
+#######
+# 8-9 #
+#######
+
+#test position
+ok($pos eq $mloc->position);
+ok(&test_getter_setter($mloc, 'position', 'q13.1'));
+
+########
+# 10-11#
+########
+
+#test lod_score
+
+ok($lod == $mloc->lod_score);
+ok(&test_getter_setter($mloc, 'lod_score', 0.03 ));
+
+

modules/t/marker.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;  
+	use Test ;
+	plan tests => 23;
+}
+
+use MultiTestDB;
+use Bio::EnsEMBL::Map::Marker;
+use Bio::EnsEMBL::Map::MarkerSynonym;
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+my $multi = MultiTestDB->new();
+my $db = $multi->get_DBAdaptor( 'core' );
+
+my $dbID = 1;
+my $marker_adaptor = $db->get_MarkerAdaptor;
+
+my $left_primer = 'ACCTGTTG';
+my $right_primer = 'CCCCTTTGGG';
+my $min_primer_dist = 75;
+my $max_primer_dist = 100;
+my $priority = 80;
+
+
+
+######
+# 1  #
+######
+
+#test the constructor
+my $marker = Bio::EnsEMBL::Map::Marker->new
+  ($dbID, $marker_adaptor, $left_primer, $right_primer, $min_primer_dist, 
+   $max_primer_dist, $priority);
+
+ok($marker && ref $marker && $marker->isa('Bio::EnsEMBL::Map::Marker'));
+
+
+#######
+# 2-3 #
+#######
+
+#test dbID
+ok($marker->dbID == $dbID);
+ok(&test_getter_setter($marker, 'dbID', 123));
+
+#######
+# 4-5 #
+#######
+
+#test adaptor
+ok($marker->adaptor == $marker_adaptor);
+ok(&test_getter_setter($marker, 'adaptor', undef));
+
+#######
+# 6-7 #
+#######
+
+#test left primer
+ok($marker->left_primer eq $left_primer);
+ok(&test_getter_setter($marker, 'left_primer', 'ACCCTTTGGG'));
+
+#######
+# 8-9 #
+#######
+ 
+#test right primer
+ok($marker->right_primer eq $right_primer);
+ok(&test_getter_setter($marker, 'right_primer', 'CCTTGGGTTTT'));
+
+#########
+# 10-11 #
+#########
+
+#test min primer dist
+ok($marker->min_primer_dist == $min_primer_dist);
+ok(&test_getter_setter($marker, 'min_primer_dist', 130));
+
+##########
+# 12-13  #
+##########
+
+#test max primer dist
+ok($marker->max_primer_dist == $max_primer_dist);
+ok(&test_getter_setter($marker, 'max_primer_dist', 180));
+
+#########
+# 14-15 #
+#########
+
+#test priority
+ok($marker->priority == $priority);
+ok(&test_getter_setter($marker, 'priority', 50));
+
+
+#######
+# 16 #
+######
+
+#test add_MarkerSynonyms & get_all_MarkerSynonyms
+my $ms = Bio::EnsEMBL::Map::MarkerSynonym->new(123, 'genbank', 'Z123456');
+
+$marker->add_MarkerSynonyms($ms);
+ok($marker->get_all_MarkerSynonyms->[0] == $ms);
+
+######
+# 17 #
+######
+
+# test flush markerSynonyms & get_all_MarkerSynonyms
+$marker->flush_MarkerSynonyms;
+
+#expect lazy loaded synonyms
+debug("got " . scalar(@{$marker->get_all_MarkerSynonyms}) . 
+      "synonyms, expected 9");
+ok(scalar(@{$marker->get_all_MarkerSynonyms}) == 9);
+
+######
+# 18 #
+######
+
+#test display marker synonym
+ok(&test_getter_setter($marker, 'display_MarkerSynonym', $ms));
+
+######
+# 19 #
+######
+
+#test add_MapLocations
+my $ml = Bio::EnsEMBL::Map::MapLocation->new('genethon', 1, 12.3, 0.05);
+
+$marker->flush_MapLocations;
+$marker->add_MapLocations($ml);
+
+ok($marker->get_all_MapLocations->[0] == $ml);
+
+######
+# 20 #
+######
+
+#test flush_MapLocations & get_all_MapLocations
+$marker->flush_MapLocations;
+debug("got " . scalar(@{$marker->get_all_MapLocations}) . 
+      " locations, expected 2");
+#expect lazy-loaded map locations
+ok(scalar @{$marker->get_all_MapLocations} == 2 );
+
+
+######
+# 21 #
+######
+
+#test get_MapLocation
+ok($marker->get_MapLocation('genethon') && 
+   $marker->get_MapLocation('marshfield'));
+
+#########
+# 22-23 #
+#########
+
+#test get_MarkerFeatures
+my @mfs = @{$marker->get_all_MarkerFeatures};
+
+ok(scalar(@mfs) == 1);
+my $mf = shift @mfs;
+ok($mf->start == 5769 && $mf->end == 5959);

modules/t/markerAdaptor.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;  
+	use Test ;
+	plan tests => 6;
+}
+
+use MultiTestDB;
+
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+my $multi = MultiTestDB->new();
+my $db = $multi->get_DBAdaptor( 'core' );
+
+
+######
+# 1  #
+######
+
+#test get_MarkerAdaptor
+my $marker_adaptor = $db->get_MarkerAdaptor;
+ok($marker_adaptor && ref $marker_adaptor);
+
+#####
+# 2 #
+#####
+
+#test fetch_by_dbID
+my $marker = $marker_adaptor->fetch_by_dbID(1);
+
+ok($marker->dbID == 1 && 
+   $marker->left_primer && 
+   $marker->right_primer &&
+   $marker->min_primer_dist &&
+   $marker->max_primer_dist);
+
+
+#######
+# 3-5 #
+#######
+
+#test fetch_all_by_synonym
+
+my $markers = $marker_adaptor->fetch_all_by_synonym('D1S243');
+ok(scalar(@$markers) == 1 && 
+   $markers->[0]->dbID == 1 &&
+   $markers->[0]->left_primer == $marker->left_primer);
+
+$markers = $marker_adaptor->fetch_all_by_synonym('Z16979', 'genbank');
+ok(scalar(@$markers == 1));
+
+$markers = $marker_adaptor->fetch_all_by_synonym('Z16979', 'other');
+ok(scalar(@$markers == 0));
+
+#####
+# 6 #
+#####
+
+$marker_adaptor->fetch_attributes($marker);
+ok(scalar(@{$marker->get_all_MarkerSynonyms}) == 9 &&
+   scalar(@{$marker->get_all_MapLocations}) == 2);

modules/t/markerFeature.t

 use lib 't';
-use TestUtils qw(test_getter_setter);
+use strict;
 
 BEGIN { $| = 1;  
-	use Test;
-	plan tests => 2;
+	use Test ;
+	plan tests => 11
 }
 
-use Bio::EnsEMBL::MarkerFeature;
+use MultiTestDB;
+use Bio::EnsEMBL::Map::MarkerFeature;
+use Bio::EnsEMBL::RawContig;
+use Bio::EnsEMBL::Analysis;
+use TestUtils qw(debug test_getter_setter);
 
-#
-# 1 create a new Simplefeature
-#
-$mf = new Bio::EnsEMBL::MarkerFeature;
-ok($mf);
+our $verbose = 0; #set to 1 to turn on debug printouts
 
+my $multi = MultiTestDB->new();
+my $db = $multi->get_DBAdaptor( 'core' );
 
-#
-# 2 test the only method getter and setters
-#
+######
+# 1  #
+######
 
-ok(test_getter_setter($mf,'marker_name','dummy_marker'));
+#test constructor
 
+my $adaptor = $db->get_MarkerFeatureAdaptor;
+my $dbID = 111;
+my $start = 100;
+my $end   = 10;
+my $contig = Bio::EnsEMBL::RawContig->new;
+my $strand = -1;
+my $analysis = Bio::EnsEMBL::Analysis->new;
+my $marker_id = 1;
+my $mapweight = 1;
+
+
+#####
+# 1 #
+#####
+
+#test construction
+my $mf = Bio::EnsEMBL::Map::MarkerFeature->new
+  ($dbID, $adaptor, $start, $end, $strand, $contig, $analysis, $marker_id, 
+   $mapweight);
+
+ok($mf && ref $mf && $mf->isa('Bio::EnsEMBL::Map::MarkerFeature'));
+
+
+#######
+# 2-3 #
+#######
+
+#test dbID
+ok($dbID == $mf->dbID);
+ok(&test_getter_setter($mf, 'dbID', undef));
+
+#######
+# 4-5 #
+#######
+
+#test adaptor
+ok($adaptor == $mf->adaptor);
+ok(&test_getter_setter($mf, 'adaptor', undef));
+
+#######
+# 6   #
+#######
+
+#test marker lazy-loading
+
+my $marker = $mf->marker;
+ok($marker->dbID == $marker_id);
+
+#######
+# 7-10#
+#######
+
+#test contig, start, end, strand (inherited)
+
+ok($contig == $mf->contig);
+ok($start == $mf->start);
+ok($end == $mf->end);
+ok($strand == $mf->strand);
+
+#######
+#  11 #
+#######
+
+ok($mapweight == $mf->map_weight);

modules/t/markerFeatureAdaptor.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;  
+	use Test ;
+	plan tests => 5
+}
+
+use MultiTestDB;
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 1; #set to 1 to turn on debug printouts
+
+my $multi = MultiTestDB->new();
+my $db = $multi->get_DBAdaptor( 'core' );
+
+######
+# 1  #
+######
+
+#test get_MarkerFeatureAdaptor
+
+my $mfa = $db->get_MarkerFeatureAdaptor;
+
+ok($mfa && ref $mfa);
+
+#######
+# 2-3 #
+#######
+
+#test fetch by dbID
+
+my $mf = $mfa->fetch_by_dbID(1);
+
+ok($mf && ref $mf && $mf->isa('Bio::EnsEMBL::Map::MarkerFeature'));
+
+ok($mf->contig->dbID == 339816 && 
+   $mf->analysis->dbID == 10 &&
+   $mf->start == 5769 &&
+   $mf->end == 5959 &&
+   $mf->strand == 1 &&
+   $mf->map_weight == 1);
+
+
+#####
+# 4 #
+#####
+
+
+# test fetch all by slice
+
+my $slice = $db->get_SliceAdaptor->fetch_by_chr_start_end('20',
+							  '30249935', 
+							  '31254640');
+
+my $feats = $mfa->fetch_all_by_Slice($slice);
+
+debug("got " . scalar(@$feats) . " markerfeatures from slice");
+
+ok(scalar(@$feats) == 97);
+
+if($verbose) {
+  foreach my $f (@$feats) {
+    my $marker = $f->marker;
+    print $f->start."-".$f->end ."(". $f->strand.") [".$mf->dbID ."]\n";
+    foreach my $ms (@{$marker->get_all_MarkerSynonyms}) {
+      print "\t" . $ms->name ."\n";
+    }
+  }
+}
+
+#####
+# 5 #
+#####
+
+#test fetch_all_by_Marker
+
+my $marker = $db->get_MarkerAdaptor->fetch_by_dbID(2);
+
+$feats = $mfa->fetch_all_by_Marker($marker); 
+
+ok(scalar(@$feats) == 1 && $feats->[0]->start==12671 &&
+   $feats->[0]->dbID() == 2);
+
+

modules/t/markerSynonym.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;  
+	use Test ;
+	plan tests => 7
+}
+
+use Bio::EnsEMBL::Map::MarkerSynonym;
+
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+
+######
+# 1  #
+######
+
+#test constructor
+my $source = 'genbank';
+my $name = 'DS1234';
+my $dbID = 10;
+
+
+my $ms = Bio::EnsEMBL::Map::MarkerSynonym->new($dbID, $source, $name);
+
+ok($ms && ref $ms && $ms->isa('Bio::EnsEMBL::Map::MarkerSynonym'));
+
+#######
+# 2-3 #
+#######
+
+#test source
+
+ok($source eq $ms->source);
+ok(&test_getter_setter($ms, 'source', 'uniSTS'));
+
+#######
+# 4-5 #
+#######
+
+#test name
+ok($name eq $ms->name);
+ok(&test_getter_setter($ms, 'name', 'new_name'));
+
+
+#######
+# 6-7 #
+#######
+
+#test dbID
+ok($dbID == $ms->dbID);
+ok(&test_getter_setter($ms, 'dbID', 123)); 
+