updated tests for new toplevel implementation

modules/t/coordSystem.t

@@ -10,16 +10,17 @@ our $verbose = 0;
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 8;
+	plan tests => 12;
 }
 
 
 my $name    = 'chromosome';
 my $version = 'NCBI33';
 my $dbID    = 1;
-my $top_level = 1;
+my $top_level = 0;
 my $sequence_level = 0;
 my $default = 1;
+my $rank    = 1;
 
 #
 # Test constructor
@@ -29,6 +30,7 @@ my $coord_system = Bio::EnsEMBL::CoordSystem->new
    -VERSION => $version,
    -DBID    => $dbID,
    -TOP_LEVEL => $top_level,
+   -RANK    => $rank,
    -SEQUENCE_LEVEL => $sequence_level,
    -DEFAULT => 1);
 
@@ -49,7 +51,7 @@ ok($coord_system->version() eq $version);
 #
 # Test is_top_level()
 #
-ok($coord_system->is_top_level());
+ok(!$coord_system->is_top_level());
 
 #
 # Test is_sequence_level()
@@ -61,6 +63,10 @@ ok(!$coord_system->is_sequence_level());
 #
 ok($coord_system->is_default());
 
+#
+# Test rank()
+#
+ok($coord_system->rank() == $rank);
 
 #
 # Test equals()
@@ -70,6 +76,7 @@ my $coord_system2 = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => $name,
    -VERSION => $version,
    -DBID    => 123,
+   -RANK    => $rank,
    -TOP_LEVEL => $top_level);
 
 ok($coord_system->equals($coord_system2));
@@ -78,10 +85,24 @@ $coord_system2 = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => 'chromosome',
    -VERSION => 'NCBI34',
    -DBID    => 123,
+   -RANK    => $rank,
    -TOP_LEVEL => $top_level);
 
 ok(!$coord_system->equals($coord_system2));
 
+#
+# test creation of toplevel system
+#
+$name    = 'toplevel';
+$top_level = 1;
 
+#
+# Test constructor
+#
+$coord_system = Bio::EnsEMBL::CoordSystem->new
+  (-NAME    => $name,
+   -TOP_LEVEL => $top_level);
 
-
+ok($coord_system->name() eq $name);
+ok($coord_system->is_top_level());
+ok($coord_system->rank() == 0);

modules/t/coordSystemAdaptor.t

@@ -3,7 +3,7 @@ use strict;
 
 BEGIN { $| = 1;
 	use Test ;
-	plan tests => 25;
+	plan tests => 32;
 }
 
 use MultiTestDB;
@@ -33,7 +33,7 @@ my $cs = $csa->fetch_by_name('chromosome');
 ok($cs->name eq 'chromosome');
 ok($cs->dbID());
 ok($cs->version eq 'NCBI33');
-ok($cs->is_top_level());
+ok(!$cs->is_top_level());
 ok(!$cs->is_sequence_level());
 ok($cs->is_default());
 
@@ -48,6 +48,7 @@ ok(@cs_list == 1);
 ok($cs_list[0]->equals($cs));
 
 
+
 #
 # Test fetch_by_dbID()
 #
@@ -59,22 +60,26 @@ ok($cs->version() eq '');
 
 
 #
-# 11 Test fetch_top_level
+# Test fetch_top_level
 #
 $cs = $csa->fetch_top_level();
 
-ok($cs->name eq 'chromosome');
+ok($cs->name eq 'toplevel');
+ok($cs->is_top_level());
+ok($cs->rank == 0);
 
 #
-# 12 Test fetch_all_top_level
+# Test fetch_by_rank
 #
-($cs) = @{$csa->fetch_all_top_level()};
+$cs = $csa->fetch_by_rank(1);
+ok($cs->name() eq 'chromosome' && $cs->rank() == 1);
 
-ok($cs->name eq 'chromosome');
+$cs = $csa->fetch_by_rank(0);
+ok($cs->name() eq 'toplevel' && $cs->rank() == 0);
 
 
 #
-# 13-14 Test fetch_sequence_level
+# Test fetch_sequence_level
 #
 $cs = $csa->fetch_sequence_level();
 
@@ -83,7 +88,22 @@ ok($cs->is_sequence_level());
 
 
 #
-# 15-16 Test get_mapping_path
+# Test fetch_all
+#
+@cs_list = @{$csa->fetch_all()};
+my $prev_cs;
+
+#make sure that they are ordered by rank
+foreach my $cs (@cs_list) {
+  if($prev_cs) {
+    ok($prev_cs->rank < $cs->rank);
+  }
+  $prev_cs = $cs;
+}
+
+
+#
+# Test get_mapping_path
 #
 
 my $ctg_cs = $csa->fetch_by_name('contig');
@@ -116,11 +136,11 @@ ok(@$path == 3 &&
 $multi->save('core', 'coord_system');
 
 $cs = Bio::EnsEMBL::CoordSystem->new
-  (-NAME            => 'chromosome',
+  (-NAME            => 'newsystem',
    -VERSION         => 'NCBI35',
-   -DEFAULT         => 0,
+   -DEFAULT         => 1,
    -SEQUENCE_LEVEL  => 0,
-   -TOP_LEVEL        => 1);
+   -RANK            => 10);
 
 $csa->store($cs);
 
@@ -128,19 +148,20 @@ ok($cs->adaptor == $csa);
 ok($cs->dbID());
 
 #now make sure we can retrieve this
-$cs = $csa->fetch_by_name('chromosome', 'NCBI35');
-ok($cs->name eq 'chromosome');
+$cs = $csa->fetch_by_name('newsystem', 'NCBI35');
+ok($cs->name eq 'newsystem');
 ok($cs->version eq 'NCBI35');
-ok(!$cs->is_default);
+ok($cs->is_default);
 ok(!$cs->is_sequence_level);
-ok($cs->is_top_level);
+ok(!$cs->is_top_level);
+ok($cs->rank() == 10);
 
 my $sth = $db->prepare('SELECT attrib FROM coord_system ' .
                        'WHERE  name = ? and version = ?');
-$sth->execute('chromosome', 'NCBI35');
+$sth->execute('newsystem', 'NCBI35');
 
 my ($attrib) = $sth->fetchrow_array();
-ok($attrib eq 'top_level');
+ok($attrib eq 'default_version');
 $sth->finish();
 
 $multi->restore('core', 'coord_system');

modules/t/feature.t

@@ -5,7 +5,7 @@ use lib 't';
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 92;
+	plan tests => 97;
 }
 
 use TestUtils qw( debug test_getter_setter );
@@ -26,7 +26,7 @@ my $coord_system = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => 'chromosome',
    -VERSION => 'NCBI34',
    -DBID    => 123,
-   -TOP_LEVEL => 1);
+   -RANK => 1);
 
 my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
 
@@ -158,6 +158,8 @@ ok($feature->slice->seq_region_name() eq 'AL359765.6.1.13780');
 ok($feature->slice->coord_system->name() eq 'contig');
 
 
+
+
 #
 # Test Transform contig -> clone
 #
@@ -176,6 +178,30 @@ ok($feature->slice->seq_region_name() eq 'AL359765.6');
 ok($feature->slice->coord_system->name() eq 'clone');
 
 
+
+#
+# Test transform clone -> toplevel
+#
+
+$feature = $feature->transform('toplevel');
+
+debug("\nclone -> toplevel");
+debug("start  = " . $feature->start());
+debug("end    = " . $feature->end());
+debug("strand = " . $feature->strand());
+debug("seq_region = " . $feature->slice->seq_region_name());
+
+
+ok($feature->start() == 300 + $slice->start() - 1);
+ok($feature->end()   == 500 + $slice->start() - 1);
+ok($feature->strand() == 1);
+ok($feature->slice->coord_system->name() eq 'chromosome');
+ok($feature->slice->seq_region_name() eq '20');
+
+#put back to clone
+$feature = $feature->transform('clone');
+
+
 #
 # Test transform to into gap
 #

modules/t/featurePair.t

@@ -22,7 +22,7 @@ my $coord_system = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => 'chromosome',
    -VERSION => 'NCBI34',
    -DBID    => 123,
-   -TOP_LEVEL => 1);
+   -RANK    => 1);
 
 my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
 

modules/t/gene.t

@@ -361,7 +361,7 @@ debug( "checking external references" );
 $multi->restore();
 
 $slice = $db->get_SliceAdaptor()->fetch_by_region
-  ( "toplevel", "20", 30_252_000, 31_252_001 );
+  ( "chromosome", "20", 30_252_000, 31_252_001 );
 
 my $known = 0;
 my $unknown = 0;

modules/t/karyotypeBand.t

@@ -22,7 +22,7 @@ my $coord_system = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => 'chromosome',
    -VERSION => 'NCBI34',
    -DBID    => 123,
-   -TOP_LEVEL => 1);
+   -RANK => 1);
 
 
 my $slice = Bio::EnsEMBL::Slice->new(-COORD_SYSTEM    => $coord_system,

modules/t/repeatFeature.t

@@ -24,7 +24,7 @@ my $coord_system = Bio::EnsEMBL::CoordSystem->new
   (-NAME    => 'chromosome',
    -VERSION => 'NCBI34',
    -DBID    => 123,
-   -TOP_LEVEL => 1);
+   -RANK    => 1);
 
 my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
 

modules/t/slice.t

@@ -47,7 +47,7 @@ ok($slice->adaptor == $slice_adaptor);
 #
 #TEST - Slice::new
 #
-my $coord_system = $csa->fetch_by_name('toplevel');
+my $coord_system = $csa->fetch_by_name('chromosome');
 
 $slice = new Bio::EnsEMBL::Slice
   (-seq_region_name   => $CHR,

modules/t/sliceAdaptor.t

@@ -36,7 +36,7 @@ ok($slice_adaptor->db);
 #
 # fetch_by_region
 #
-my $slice = $slice_adaptor->fetch_by_region('toplevel',$CHR, $START, $END);
+my $slice = $slice_adaptor->fetch_by_region('chromosome',$CHR, $START, $END);
 ok($slice->seq_region_name eq $CHR);
 ok($slice->start == $START);
 ok($slice->end   == $END);

modules/t/topLevelAssemblyMapper.t

+use lib 't';
+use strict;
+
+BEGIN { $| = 1;
+	use Test ;
+	plan tests => 7;
+}
+
+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' );
+
+
+my $asma = $db->get_AssemblyMapperAdaptor();
+
+#
+# Test fetch_by_CoordSystems
+#
+
+my $csa = $db->get_CoordSystemAdaptor();
+my $toplevel_cs = $csa->fetch_by_name('toplevel');
+my $cln_cs    = $csa->fetch_by_name('clone');
+my $superctg_cs = $csa->fetch_by_name('supercontig');
+
+my $cln_toplevel_mapper =
+  $asma->fetch_by_CoordSystems($toplevel_cs, $cln_cs);
+my $superctg_toplevel_mapper =
+  $asma->fetch_by_CoordSystems($toplevel_cs, $superctg_cs);
+
+ok($cln_toplevel_mapper && 
+   $cln_toplevel_mapper->isa('Bio::EnsEMBL::TopLevelAssemblyMapper'));
+
+
+#
+# test db has chr 20  (50KB -> 62MB)
+#
+
+#
+# Test map
+#
+
+debug("MAP 'AL359765.6'->toplevel");
+my @coords = $cln_toplevel_mapper->map('AL359765.6', 1, 13780, 1, $cln_cs);
+print_coords(@coords);
+ok(@coords);
+
+
+debug("MAP NT_028392->toplevel");
+@coords = $superctg_toplevel_mapper->map('NT_028392', 600_000, 1e6, 1, 
+                                         $superctg_cs);
+print_coords(@coords);
+ok(@coords);
+
+
+
+#
+# Test list_seq_regions
+#
+
+my @seq_regions =
+  $cln_toplevel_mapper->list_seq_regions('AL359765.6', 1, 13780, $cln_cs);
+my $str = join("\n", "----------", @seq_regions);
+debug("$str\n");
+ok(@seq_regions == 1 && $seq_regions[0] eq '20');
+
+
+@seq_regions = $superctg_toplevel_mapper->list_seq_regions('NT_028392',
+                                                           6e5, 1e6,
+                                                           $superctg_cs);
+
+$str = join("\n", "----------", @seq_regions);
+debug("$str\n");
+ok(@seq_regions == 1 && $seq_regions[0] eq '20');
+
+
+#
+# Test list_seq_ids
+#
+
+my @ids =
+  $cln_toplevel_mapper->list_ids('AL359765.6', 1, 13780, $cln_cs);
+$str = join("\n", "----------", @ids);
+debug("$str\n");
+ok(@ids == 1 && $ids[0] == 469283);
+
+@ids = $superctg_toplevel_mapper->list_ids('NT_028392',
+                                                   6e5, 1e6,
+                                                   $superctg_cs);
+$str = join("\n", "----------", @ids);
+debug("$str\n");
+ok(@ids == 1 && $ids[0] == 469283);
+
+sub print_coords {
+  my @coord_list = @_;
+
+  return if(!$verbose);
+
+  foreach my $coord (@coord_list) {
+    if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
+      debug("GAP");
+      next;
+    }
+    my $cs = $coord->coord_system();
+    my $cs_str = ($cs) ? $cs->name() . $cs->version() : '';
+    debug($coord->id()."\t". $coord->start()."-".$coord->end().
+          " (".$coord->strand.") [$cs_str]");
+  }
+}