fixed 3030462 bug related to not finding features with square bracket…

…s in their names

Changes

@@ -22,6 +22,8 @@
        by calling renderer() method.
      * Fixed regression in which database option wasn't propagating from base track to semantic 
        zoom tracks.
+     * Fixed SequenceDumper behavior on GFF dumping.
+     * Removed brackets from list of naughty search characters to fix bug 3030462
 
 2.15 Mon Sep 13 11:22:40 EDT 2010
      * Set the "DNA accessor" for databases to the default database. Assuming that the backend supports

conf/plugins/SequenceDumper.pm

@@ -72,7 +72,7 @@ my @FORMATS = ( 'fasta'   => ['Fasta',        undef],
 		'raw'     => ['Raw sequence', undef],
 		'game'    => ['GAME (XML)',   'xml'],
 		'bsml'    => ['BSML (XML)',   'xml'],
-		'gff'     => ['GFF',          undef],
+		'gff'     => ['GFF3',          undef],
 	      );
 
 # initialize @ORDER using the even-numbered elements of the array
@@ -91,7 +91,7 @@ unshift @ORDER,'gff';
 my %FORMATS = @FORMATS;
 my %LABELS  = map { $_ => $FORMATS{$_}[0] } keys %FORMATS;
 
-$VERSION = '0.12';
+$VERSION = '0.13';
 
 @ISA = qw(Bio::Graphics::Browser2::Plugin);
 
@@ -268,7 +268,7 @@ sub gff_dump {
   print start_html($segment) if $html;
 
   print h1($segment),start_pre() if $html;
-  print "##gff-version 2\n";
+  print "##gff-version 3\n";
   print "##date $date\n";
   print "##sequence-region ",join(' ',$segment->ref,$segment->start,$segment->stop),"\n";
   print "##source gbrowse SequenceDumper\n";
@@ -278,11 +278,12 @@ sub gff_dump {
   $segment->absolute(0);
   my $iterator = $segment->get_seq_stream(-types => \@feature_types) or return;
   while (my $f = $iterator->next_seq) {
-    print $f->gff_string,"\n";
-    for my $s ($f->sub_SeqFeature) {
-      print $s->gff_string,"\n";
-    }
+      eval{$f->version(3)};
+      my $s =$f->gff_string(1);
+      chomp($s);
+      print $s,"\n";
   }
+
   print end_pre() if $html;
   print end_html() if $html;
 }

lib/Bio/Graphics/Browser2/Region.pm

@@ -200,7 +200,7 @@ sub search_db {
   my $args = shift;
   my ($features);
   if (my $name = $args->{-search_term}) {
-      $name =~ tr/a-zA-Z0-9.'"_*?: ;+-\/\#//cd;  # remove rude characters
+      $name =~ tr/a-zA-Z0-9.'"_*?: ;+-\/\#\[\]//cd;  # remove rude characters
       my ($ref,$start,$stop,$class,$id) = $self->parse_feature_name($name);
       $features =  $self->lookup_features($ref,$start,$stop,$class,$name,$id);
   }

lib/Bio/Graphics/Browser2/RegionSearch.pm

@@ -93,7 +93,6 @@ sub init_databases {
 
     my $source = $self->source;
     my $labels = $track_labels || [$source->labels];
-#    my $labels = $track_labels || [$source->dbs];
 
     my $renderfarm = $self->source->global_setting('renderfarm');