[Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.17, 1.18

[Lincoln Stein]

Update of /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature
In directory dev.open-bio.org:/tmp/cvs-serv21183/Bio/DB/SeqFeature

Modified Files:
	NormalizedFeature.pm 
Log Message:
output of gff3_string() method now matches input to GFF3 loader

Index: NormalizedFeature.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/NormalizedFeature.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** NormalizedFeature.pm	1 Oct 2006 17:15:30 -0000	1.17
--- NormalizedFeature.pm	2 Oct 2006 00:09:57 -0000	1.18
***************
*** 456,464 ****
      }
      if ($min_tstart < $tstart or $max_tend > $tend) {
!       $self->{attributes}{Target}[0] = join "\t",($seqid,$min_tstart,$max_tend,$strand||'');
      }
    }
  }
  
  sub _create_subfeatures {
    my $self = shift;
--- 456,487 ----
      }
      if ($min_tstart < $tstart or $max_tend > $tend) {
!       $self->{attributes}{Target}[0] = join ' ',($seqid,$min_tstart,$max_tend,$strand||'');
      }
    }
  }
  
+ # undo the load_id and Target hacks on the way out
+ sub format_attributes {
+   my $self   = shift;
+   my $parent = shift;
+   my $load_id   = $self->load_id || '';
+   my ($target)  = split /\s+/,($self->attributes('Target'))[0];
+   $target ||= '';
+   my @tags = $self->all_tags;
+   my @result;
+   for my $t (@tags) {
+     my @values = $self->each_tag_value($t);
+     @values = grep {$_ ne $load_id && $_ ne $target} @values if $t eq 'Alias';
+     next if defined($load_id) && $t eq 'load_id';
+     push @result,join '=',$self->escape($t),$self->escape($_) foreach @values;
+   }
+   my $id   = $self->load_id || $self->primary_id;
+   my $name = $self->display_name;
+   push @result,"ID=".$self->escape($id)                     if defined $id;
+   push @result,"Parent=".$self->escape($parent->primary_id) if defined $parent;
+   push @result,"Name=".$self->escape($name)                 if defined $name;
+   return join ';', at result;
+ }
+ 
  sub _create_subfeatures {
    my $self = shift;