[ENSCORESW-635]. Code now supports karyotype retrieval and display.

SliceAdaptor has been changed to bring back the karyotype rank and
the karyotype boolean when retriving karyoptype slices. The Slice object
now caches the rank locally. AssemblyAdaptor now adds the list of
karyotype regions for the rest API.

modules/Bio/EnsEMBL/DBSQL/AssemblyAdaptor.pm

@@ -109,27 +109,26 @@ sub fetch_info {
       $assembly_info{'schema_build'} = $schema_build;
   }
   
- #fetch available coordinate systems
-
+  #fetch available coordinate systems
   my $csa = $self->db()->get_adaptor('CoordSystem');
-  my %versions;
-  foreach my $cs (@{$csa->fetch_all()}) {
-    $versions{$cs->version()} = 1;
-  }
-  my @coord_system_versions = keys %versions;
-
-  $assembly_info{'coord_system_versions'} = \@coord_system_versions;
+  my $coord_systems = $csa->fetch_all();
+  my %versions = map { $_->version(), 1 } @{$coord_systems};
+  $assembly_info{'coord_system_versions'} = [keys %versions];
+  my ($default_assembly) = @{$coord_systems};
+  $assembly_info{default_coord_system_version} = $default_assembly->version();
 
   #fetch top level seq_region names
 
   my $sa = $self->db()->get_adaptor('Slice');
 
   my $slices = $sa->fetch_all('toplevel');
-  
   my %unique = map { $_->seq_region_name(), 0 } @{$slices};
   my $names = [sort { $a cmp $b } keys %unique];
   $assembly_info{'top_level_seq_region_names'} = $names;
 
+  my $karyotype = $sa->fetch_all_karyotype();
+  $assembly_info{karyotype} = [ map { $_->seq_region_name() } @{$karyotype}];
+
   return \%assembly_info;
 }
 

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -1147,18 +1147,18 @@ sub fetch_all_karyotype {
 
   my $sth = 
     $self->prepare( 'SELECT sr.seq_region_id, sr.name, '
-                      . 'sr.length, sr.coord_system_id '
+                      . 'sr.length, sr.coord_system_id, sra.value '
                       . 'FROM seq_region sr, seq_region_attrib sra, '
                       . 'attrib_type at, coord_system cs '
                       . 'WHERE at.code = "karyotype_rank" '
                       . 'AND at.attrib_type_id = sra.attrib_type_id '
                       . 'AND sra.seq_region_id = sr.seq_region_id '
                       . 'AND sr.coord_system_id = cs.coord_system_id '
-                      . 'AND cs.species_id = ?' );
+                      . 'AND cs.species_id = ?');
   $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
   $sth->execute();
-  my ( $seq_region_id, $name, $length, $cs_id );
-  $sth->bind_columns( \( $seq_region_id, $name, $length, $cs_id ) );
+  my ( $seq_region_id, $name, $length, $cs_id, $rank );
+  $sth->bind_columns( \( $seq_region_id, $name, $length, $cs_id, $rank ) );
 
   my @out;
   while($sth->fetch()) {
@@ -1166,17 +1166,22 @@ sub fetch_all_karyotype {
 
     my $slice = Bio::EnsEMBL::Slice->new_fast({
           'start'           => 1,
-          'end'             => $length,
+          'end'             => ($length+0),
           'strand'          => 1,
          'seq_region_name'  => $name,
-         'seq_region_length'=> $length,
+         'seq_region_length'=> ($length+0),
          'coord_system'     => $cs,
-         'adaptor'          => $self});
+         'adaptor'          => $self,
+         'karyotype'        => 1,
+         'karyotype_rank'   => ($rank+0),
+         });
 
     push @out, $slice;
-
   }
 
+  #Sort using Perl as value in MySQL is a text field and not portable
+  @out = sort { $a->{karyotype_rank} <=> $b->{karyotype_rank} } @out;
+
   return \@out;
 }
 

modules/Bio/EnsEMBL/Slice.pm

@@ -551,6 +551,24 @@ sub has_karyotype {
   return $self->{'karyotype'};
 }
 
+=head2 karyotype_rank
+  Arg        : none
+  Example    : my $rank = $slice->karyotype_rank()
+  Description: Returns the numeric ranking in the karyotype. Otherwise 0 is returned
+  Returntype : int
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub karyotype_rank {
+  my ($self) = @_;
+  if(! defined( $self->{karyotype_rank})) {
+    my $rank = $self->adaptor()->get_karyotype_rank($self->get_seq_region_id());
+    $self->{karyotype_rank} = $rank if $rank;
+  }
+  return $self->{karyotype_rank} || 0;
+}
 
 =head2 is_circular
   Arg        : none