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

Code has been altered to support new REST requirements.

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