Container now updates its symbol table on the fly when AUTOLOAD is called (as...

Container now updates its symbol table on the fly when AUTOLOAD is called (as suggested by Jim Stalker)

modules/Bio/EnsEMBL/Container.pm

@@ -132,24 +132,17 @@ sub AUTOLOAD {
 
   $method =~ s/.*:://;
 
-  unless($self->_obj->can($method)) {
-    #the object doesn't have method of this name but this may be ok
-    #if the something sneaky has been done with an AUTOLOAD
-    #to be safe use a (slow) eval
-    my $ret_val;
-
-    eval { 
-      $ret_val = $self->_obj->$method(@args);
+  #update the symbol table so AUTOLOAD is not needed the next time
+  #this method is called (faster this way)
+  no strict 'refs';
+  *{$AUTOLOAD} = 
+    sub {
+      my $self = shift;    
+      return $self->_obj->$method(@args);
     };
-
-    if($@) {
-      $self->throw("Could not invoke requested method on contained object:\n" .
-		   "$@");
-    }
-
-    return $ret_val;
-  }
-
+  use strict 'refs';
+  
+  #call the method on the contained object
   return $self->_obj->$method(@args);
 }
 

modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm

@@ -154,4 +154,23 @@ sub AUTOLOAD {
   return undef;
 }
 
+
+=head2 DELETE
+
+  Arg [1]    : none
+  Example    : none
+  Description: Called automatically by garbage collector. This method does not
+               actually do anything, but if it was not defined, then the 
+               AUTOLOAD method would be called during destruction by the 
+               garbage collector instead.
+  Returntype : none
+  Exceptions : none
+  Caller     : automatic
+
+=cut
+
+sub DELETE {
+  #do nothing
+}
+
   

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -60,16 +60,22 @@ use Bio::EnsEMBL::DBSQL::DBAdaptor;
 # new is inherited from BaseAdaptor
 
 
-=head2 fetch_by_chr_start_end
 
- Title   : fetch_by_chr_start_end
- Usage   :
- Function: create a Slice based on a segment of a chromosome and
-           start/end
- Example :
- Returns : A Slice
- Args    : chromosome, start, end (in Chromosome coordinates)
+=head2 fetch_by_chr_start_end
 
+  Arg [1]    : string $chr
+               the name of the chromosome to obtain a slice for
+  Arg [2]    : int $start
+               the start basepair of the slice to obtain in chromosomal 
+               coordinates
+  Arg [3]    : int $end 
+               the end basepair of the slice to obtain in chromosomal 
+               coordinates
+  Example    : $slice = $slice_adaptor->fetch_by_chr_start_end();
+  Description: Creates a slice object on the given chromosome and coordinates.
+  Returntype : Bio::EnsEMBL::Slice
+  Exceptions : none
+  Caller     : general
 
 =cut