blast fixes and moveing new_fast from ???DnaA... to BaseAlignFeature

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -132,6 +132,29 @@ sub new {
 }
 
 
+=head2 new_fast
+
+  Arg [1]    : hashref $hashref
+               A hashref which will be blessed into a PepDnaAlignFeature.
+  Example    : none
+  Description: This allows for very fast object creation when a large number
+               of PepDnaAlignFeatures needs to be created.  This is a bit of
+               a hack but necessary when thousands of features need to be
+               generated within a couple of seconds for web display. It is
+               not recommended that this method be called unless you know what
+               you are doing.  It requires knowledge of the internals of this
+               class and its superclasses.
+  Returntype : Bio::EnsEMBL::BaseAlignFeature
+  Exceptions : none
+  Caller     : none currently
+
+=cut
+
+sub new_fast {
+  my ($class, $hashref) = @_;
+
+  return bless $hashref, $class;
+}
 
 =head2 cigar_string
 

modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm

@@ -26,31 +26,6 @@ use strict;
 
 @ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
 
-=head2 new_fast
-
-  Arg [1]    : hashref $hashref
-               A hashref which will be blessed into a DnaDnaAlignFeature. 
-  Example    : none
-  Description: This allows for very fast object creation when a large number 
-               of DnaAlignFeatures needs to be created.  This is a bit of 
-               a hack but necessary when thousands of features need to be
-               generated within a couple of seconds for web display. It is
-               not recommended that this method be called unless you know what
-               you are doing.  It requires knowledge of the internals of this
-               class and its superclasses.  
-  Returntype : Bio::EnsEMBL::DnaDnaAlignFeature
-  Exceptions : none
-  Caller     : Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor
-
-=cut
-
-sub new_fast {
-  my ($class, $hashref) = @_;
-
-  return bless $hashref, $class;
-}
-
-
 =head2 restrict_between_positions
 
   Arg  1     : int $start

modules/Bio/EnsEMBL/External/BlastAdaptor.pm

@@ -64,8 +64,8 @@ WHERE  ticket = ? );
 AND    chr_name = ? );
 
    my $RANGE_SQL = qq(
-AND    chr_start >= ?
-AND    chr_end   <= ? );
+AND    chr_start <= ?
+AND    chr_end   >= ? );
 
    my $q = $SQL;
    my @binded = ( $ticket );
@@ -76,9 +76,11 @@ AND    chr_end   <= ? );
 
      if( $chr_start && $chr_end ){
        $q .= $RANGE_SQL;
-       push @binded, $chr_start, $chr_end;
+       push @binded, $chr_end, $chr_start;
      }
    }
+   warn( "$q: ", join( ', ',@binded ) ); 
+
    my $sth = $self->db->db_handle->prepare($q);
    my $rv = $sth->execute( @binded ) || $self->throw( $sth->errstr );
 

modules/Bio/EnsEMBL/PepDnaAlignFeature.pm

@@ -24,32 +24,6 @@ use strict;
 
 @ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
 
-
-=head2 new_fast
-
-  Arg [1]    : hashref $hashref
-               A hashref which will be blessed into a PepDnaAlignFeature. 
-  Example    : none
-  Description: This allows for very fast object creation when a large number 
-               of PepDnaAlignFeatures needs to be created.  This is a bit of 
-               a hack but necessary when thousands of features need to be
-               generated within a couple of seconds for web display. It is
-               not recommended that this method be called unless you know what
-               you are doing.  It requires knowledge of the internals of this
-               class and its superclasses.  
-  Returntype : Bio::EnsEMBL::PepDnaAlignFeature
-  Exceptions : none
-  Caller     : none currently
-
-=cut
-
-sub new_fast {
-  my ($class, $hashref) = @_;
-
-  return bless $hashref, $class;
-}
-
-
 sub transform {
   my $self = shift;
 

modules/Bio/EnsEMBL/Slice.pm

@@ -1049,11 +1049,10 @@ sub get_all_SearchFeatures {
     my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
 
     my $offset = $self->chr_start-1;
-    warn $sfa,"--",$ticket;
-    my $features = $sfa ? $sfa->get_all_SearchFeatures($ticket) : [];#, $self->chr_name, $self->chr_start, $self->chr_end) : [];
 
+    my $features = $sfa ? $sfa->get_all_SearchFeatures($ticket, $self->chr_name, $self->chr_start, $self->chr_end) : [];
+    warn join(', ', @$features );
     foreach( @$features ) { 
-      warn ( $_ );
       $_->start( $_->start-$offset );
       $_->end(   $_->end-$offset );
     };