removed restrict_between_positions method, confusing and apparently never used

modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm

@@ -15,7 +15,7 @@ package Bio::EnsEMBL::DnaDnaAlignFeature;
 
   See BaseAlignFeature
 
-=cut 
+=cut
 
 
 use Bio::EnsEMBL::BaseAlignFeature;
@@ -26,109 +26,6 @@ use strict;
 
 @ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
 
-=head2 restrict_between_positions
-
-  Arg  1     : int $start
-  Arg  2     : int $end
-  Arg  3     : string $sequence_name
-               The Feature can either be restricted on Ensembl coords
-               or on hit coords. The sequence_name decides which one. 
-  Example    : none
-  Description: Makes a new AlignFeature that sits in the new coords
-  Returntype : DnaDnaAlignFeature
-  Exceptions : returns undef if it cant do the job
-  Caller     : general
-
-=cut
-
-sub restrict_between_positions {
-  my ($self,$start,$end,$seqref) = @_;
-  
-  unless (defined $start && $start =~ /^\d+$/) {
-    $self->throw("The first argument is not defined or is not an integer");
-  }
-  unless (defined $end && $end =~ /^\d+$/) {
-    $self->throw("The second argument is not defined or is not an integer");
-  }
-  unless (defined $seqref && 
-	  ($seqref eq "seqname" || $seqref eq "hseqname")) {
-    $self->throw("The third argument is not defined or is not equal to 'seqname' or 'hseqname'");
-  }
-
-# symbolic method references should be forbidden!
-
-  my ($start_method1,$end_method1,$strand_method1,$start_method2,$end_method2,$strand_method2) =
-    qw(start end strand hstart hend hstrand);
-
-  if ($seqref eq "hseqname") {
-    ($start_method1,$end_method1,$strand_method1,$start_method2,$end_method2,$strand_method2) =
-    qw(hstart hend hstrand start end strand);
-  }
-  
-  my @restricted_features;
-  
-  foreach my $ungapped_feature ($self->ungapped_features) {
-
-    if ($ungapped_feature->$start_method1() > $end ||
-	$ungapped_feature->$end_method1() < $start) {
-      
-      next;
-      
-    } elsif ($ungapped_feature->$end_method1() <= $end &&
-	     $ungapped_feature->$start_method1() >= $start) {
-      
-      push @restricted_features, $ungapped_feature;
-      
-    } else {
-      
-      if ($ungapped_feature->$strand_method1() eq $ungapped_feature->$strand_method2()) {
-
-	if ($ungapped_feature->$start_method1() < $start) {
-	  
-	  my $offset = $start - $ungapped_feature->$start_method1();
-	  $ungapped_feature->$start_method1($start);
-	  $ungapped_feature->$start_method2($ungapped_feature->$start_method2() + $offset);
-	  
-	}
-	if ($ungapped_feature->$end_method1() > $end) {
-	  
-	  my $offset = $ungapped_feature->$end_method1() - $end;
-	  $ungapped_feature->$end_method1($end);
-	  $ungapped_feature->$end_method2($ungapped_feature->$end_method2() - $offset);
-	  
-	}
-      } else {
-	
-	if ($ungapped_feature->$start_method1() < $start) {
-	  
-	  my $offset = $start - $ungapped_feature->$start_method1();
-	  $ungapped_feature->$start_method1($start);
-	  $ungapped_feature->$end_method2($ungapped_feature->$end_method2() - $offset);
-	  
-	}
-	if ($ungapped_feature->$end_method1() > $end) {
-	  
-	  my $offset = $ungapped_feature->$end_method1() - $end;
-	  $ungapped_feature->$end_method1($end);
-	  $ungapped_feature->$start_method2($ungapped_feature->$start_method2() + $offset);
-	  
-	}
-      }
-      
-      push @restricted_features, $ungapped_feature;
-      
-    }
-  }
-
-  if (scalar @restricted_features) {
-    my $DnaDnaAlignFeature = new Bio::EnsEMBL::DnaDnaAlignFeature('-features' =>\@restricted_features);
-    return $DnaDnaAlignFeature;
-  } else {
-    return undef;
-  }
-}
-
-
 
 =head2 _hit_unit