slices from chromosomes, chromosome adaptor caches on name, tests in a second

modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm

@@ -80,6 +80,7 @@ sub fetch_by_dbID {
 
   unless(defined $self->{'_chr_cache'} ) {
     $self->{'_chr_cache'} = {};
+    $self->{'_chr_name_cache'} = {};
   }
 
   #
@@ -90,8 +91,8 @@ sub fetch_by_dbID {
     my $sth = $self->prepare( "SELECT name, known_genes, unknown_genes, 
                                       snps, length
                                FROM chromosome
-                               WHERE chromosome_id = $id" );
-    $sth->execute();
+                               WHERE chromosome_id = ?" );
+    $sth->execute( $id );
     
     my($name, $known_genes, $unknown_genes, $snps, $length);
     $sth->bind_columns(\$name,\$known_genes,\$unknown_genes,\$snps,\$length); 
@@ -108,14 +109,16 @@ sub fetch_by_dbID {
     }
 
     $chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
+                                         -dbID => $id,
 					 -chr_name => $name,
-					 -chromosome_id => $id,
 					 -known_genes => $known_genes,
 					 -unknown_genes => $unknown_genes,
 					 -snps => $snps,
 					 '-length' => $length );
 
     $self->{'_chr_cache'}->{$id} = $chr;
+    $self->{'_chr_name_cache'}->{$name} = $chr;
+    
   }
 
   return $chr;
@@ -137,15 +140,46 @@ sub fetch_by_dbID {
 sub fetch_by_chr_name{
    my ($self,$chr_name) = @_;
 
-   #Convert the name to the dbID
-   my $dbID = $self->get_dbID_by_chr_name($chr_name);
+  my $chr = (); 
 
-   unless(defined $dbID) {
-     $self->warn("chromosome with name $chr_name not in database");
-     return undef;
-   } 
-   
-   return $self->fetch_by_dbID($dbID);
+  unless(defined $chr_name) {
+    $self->throw("Chromosome name argument required\n");
+  }
+
+  unless(defined $self->{'_chr_cache'} ) {
+    $self->{'_chr_cache'} = {};
+    $self->{'_chr_name_cache'} = {};
+  }
+
+  #
+  # If there is not already a cached version of this chromosome pull it
+  # from the database and add it to the cache.
+  #
+  unless($chr = $self->{'_chr_name_cache'}->{$chr_name}) {
+    my $sth = $self->prepare( "SELECT chromosome_id, known_genes, unknown_genes, 
+                                      snps, length
+                               FROM chromosome
+                               WHERE name = ?" );
+    $sth->execute( $chr_name );
+    
+    my($dbID, $known_genes, $unknown_genes, $snps, $length);
+    $sth->bind_columns(\$dbID,\$known_genes,\$unknown_genes,\$snps,\$length); 
+    $sth->fetch();
+
+    $chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
+					 -dbID => $dbID,
+					 -chr_name => $chr_name,
+					 -known_genes => $known_genes,
+					 -unknown_genes => $unknown_genes,
+					 -snps => $snps,
+					 '-length' => $length );
+
+    $self->{'_chr_cache'}->{$dbID} = $chr;
+    $self->{'_chr_name_cache'}->{$chr_name} = $chr;
+    
+  }
+
+  return $chr;
 }
 
 
@@ -179,13 +213,14 @@ sub fetch_all {
    
     my $chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
 					 -chr_name => $name,
-					 -chromosome_id => $chromosome_id,
+					 -dbID => $chromosome_id,
 					 -known_genes => $known_genes,
 					 -unknown_genes => $unknown_genes,
 					 -snps => $snps,
 					 '-length' => $length );
 
     $self->{'_chr_cache'}->{$chromosome_id} = $chr;
+    $self->{'_chr_name_cache'}->{$name} = $chr;
     push @chrs, $chr;
   }
 

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -734,7 +734,6 @@ sub assembly_type{
       $obj->{'assembly'} = $value;
     }
     if (! defined $obj->{'assembly'}) {
-      print STDERR "DBAdaptor.pm: using default assembly type\n";
       my $ass;
       eval {
         $ass = $obj->get_MetaContainer()->get_default_assembly();

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -123,6 +123,8 @@ sub list_stable_geneIds {
 
   Arg [1]    : int $geneId 
                the unique internal database id of the Gene to be retrieved
+  Arg [2]    : int $chromosomal_coordinates (optional)
+               if defined, try to return chromosomal coordinates.
   Example    : $gene = $gene_adaptor->fetch_by_dbID
   Description: Retrieves a gene object from the database using its unique
                internal identifier.
@@ -133,7 +135,7 @@ sub list_stable_geneIds {
 =cut
 
 sub fetch_by_dbID {
-  my ( $self, $geneId ) = @_;
+  my ( $self, $geneId, $chr_coordinates ) = @_;
 
   my $exonAdaptor = $self->db->get_ExonAdaptor();
   my @exons = @{$exonAdaptor->fetch_all_by_gene_id( $geneId )};
@@ -223,6 +225,18 @@ sub fetch_by_dbID {
     $gene->add_Transcript( $transcript );
   }
   
+  # if chromosomal coordinates are needed, transform with empty slice
+
+  if( defined $chr_coordinates ) {
+    my $sa = $self->db->get_SliceAdaptor();
+    my $empty_slice = Bio::EnsEMBL::Slice->new
+      ( 
+       -empty => 1,
+       -adaptor => $sa 
+      );
+    $gene->transform( $empty_slice );
+  }
+
   return $gene;
 }
 

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -106,7 +106,7 @@ sub fetch_by_chr_start_end {
           -chr_start     => $start,
           -chr_end       => $end,
           -assembly_type => $type,
-          -adaptor       => $self->db->get_SliceAdaptor()
+          -adaptor       => $self
 	 );
 
     return $slice;
@@ -177,8 +177,14 @@ sub fetch_by_fpc_name {
 
     my $slice;
 
-    $slice = new Bio::EnsEMBL::Slice($chr,$slice_start,$slice_end,
-                                     $strand,$type);
+    $slice = new Bio::EnsEMBL::Slice
+      (
+       -chr_name => $chr,
+       -chr_start =>$slice_start,
+       -chr_end => $slice_end,
+       -strand => $strand,
+       -assembly_type => $type
+      );
 
     return $slice;
 }
@@ -394,7 +400,18 @@ sub fetch_by_chr_name{
    my $chromosome = $ca->fetch_by_chr_name($chr_name);
    my $chr_end = $chromosome->length();
 
-   return $self->fetch_by_chr_start_end($chr_name, $chr_start, $chr_end);
+   my $type = $self->db->assembly_type();
+
+   my $slice = Bio::EnsEMBL::Slice->new
+     (
+      -chr_name      => $chr_name,
+      -chr_start     => 1,
+      -chr_end       => $chr_end,
+      -assembly_type => $type,
+      -adaptor       => $self
+     );
+
+   return $slice;
 }