support for placing cap on number of features to display per track; n…

…eed bio::graphics 1.97 or higher

Changes

@@ -1,4 +1,5 @@
 1.996   * Add "feature limit" option to keep very populous tracks under control.
+	* Attempt to fix problem of FastCGI processes hanging around even after apache restarted.
 1.995	* Install to an alternate location (e.g. home directory) by using --install_base argument when
 	  calling perl Build.PL.
 	* Don't overwrite user's configuration files when doing an upgrade install!

cgi-bin/gb2/gbrowse

@@ -20,7 +20,6 @@ if ($fcgi) {
     };
 
     while (!$FCGI_DONE && ($fcgi->Accept >= 0)) {
-	print STDERR "accepted request\n";
 	my $globals = Bio::Graphics::Browser->open_globals;
 	CGI->initialize_globals();
 	Bio::Graphics::Browser::Render::HTML->new($globals)->run();

conf/languages/POSIX.pm

@@ -245,6 +245,8 @@ END
 
    NO_TRACKS    => '*none*',
 
+   FEATURES_CLIPPED => 'Showing %s of %s features',
+
    FILE_INFO    => 'Last modified %s.  Annotated landmarks: %s',
 
    FOOTER_1     => <<END,
@@ -318,7 +320,7 @@ END
 
    FORMAT => 'Format',
 
-   LIMIT  => 'Limit',
+   LIMIT  => 'Max. features to show',
 
    ADJUST_ORDER => 'Adjust Order',
 
@@ -426,6 +428,8 @@ END
 
  LINEWIDTH        => 'Line width',
 
+ STRANDED         => 'Show strand',
+
  DEFAULT          => '(default)',
 
  DYNAMIC_VALUE    => 'Dynamically calculated',

conf/languages/en.pm

@@ -237,6 +237,8 @@ END
 
    NO_TRACKS    => '*none*',
 
+   FEATURES_CLIPPED => 'Showing %s of %s features',
+
    FILE_INFO    => 'Last modified %s.  Annotated landmarks: %s',
 
    FOOTER_1     => <<END,
@@ -310,7 +312,7 @@ END
 
    FORMAT => 'Format',
 
-   LIMIT  => 'Limit',
+   LIMIT  => 'Max. features to show',
 
    ADJUST_ORDER => 'Adjust Order',
 
@@ -420,6 +422,8 @@ END
 
  LINEWIDTH        => 'Line width',
 
+ STRANDED         => 'Show strand',
+
  DEFAULT          => '(default)',
 
  DYNAMIC_VALUE    => 'Dynamically calculated',

lib/Bio/Graphics/Browser/Render.pm

@@ -1970,15 +1970,17 @@ sub reconfigure_track {
     my $self  = shift;
     my $label = shift;
     my $state = $self->state();
-    $state->{features}{$label}{visible}  = param('show_track') ? 1 : 0;
-    $state->{features}{$label}{options}  = param('format_option');
-    $state->{features}{$label}{limit}    = param('limit');
+    $state->{features}{$label}{visible}          = param('show_track') ? 1 : 0;
+    $state->{features}{$label}{options}          = param('format_option');
+    $state->{features}{$label}{limit}            = param('limit');
     my $dynamic = $self->tr('DYNAMIC_VALUE');
     for my $s ( 'bgcolor', 'fgcolor', 'height', 'glyph', 'linewidth' ) {
         my $value = param($s);
-        delete $state->{features}{$label}{override_settings}{$s}, next
-            if $value eq $dynamic;
-        $state->{features}{$label}{override_settings}{$s} = $value;
+	if ($value eq $dynamic) {
+	    delete $state->{features}{$label}{override_settings}{$s};
+	} else {
+	    $state->{features}{$label}{override_settings}{$s} = $value;
+	}
     }
     $state->{features}{$label}{override_settings}{stranded} = param('stranded') || 0;
 }

lib/Bio/Graphics/Browser/Render/HTML.pm

@@ -1620,6 +1620,7 @@ sub track_config {
 
     if ( param('track_defaults') ) {
         $state->{features}{$label}{override_settings} = {};
+	$state->{features}{$label}{limit} = $data_source->fallback_setting( $label => 'feature_limit');
     }
 
     my $override = $state->{features}{$label}{override_settings}||{};
@@ -1634,12 +1635,14 @@ sub track_config {
     my $width    = $data_source->fallback_setting( $label => 'linewidth' ) || 1;
     my $glyph    = $data_source->fallback_setting( $label => 'glyph' )     || 'box';
     my $stranded = $data_source->fallback_setting( $label => 'stranded');
+    my $dynamic = $self->tr('DYNAMIC_VALUE');
+
     my @glyph_select = shellwords(
         $data_source->fallback_setting( $label => 'glyph select' ) );
     @glyph_select
-        = qw(arrow anchored_arrow box crossbox dashed_line diamond dna dot dumbbell ellipse
+        = ($dynamic,qw(arrow anchored_arrow box crossbox dashed_line diamond dna dot dumbbell ellipse
         ex line primers saw_teeth segments span splice_site translation triangle
-        two_bolts wave) unless @glyph_select;
+        two_bolts wave)) unless @glyph_select;
     my %glyphs = map { $_ => 1 } ( $glyph, @glyph_select );
 
     my $url = url( -absolute => 1, -path => 1 );
@@ -1736,12 +1739,12 @@ END
             )
         ),
         TR( th( { -align => 'right' }, $self->tr('Limit') ),
-            td( popup_menu(
-                    -name   => 'limit',
-                    -values => [ 0, 5, 10, 25, 100 ],
+            td( $picker->popup_menu(
+                    -name     => 'limit',
+                    -values   => [ 0, 5, 10, 25, 50, 100, 200, 500, 1000 ],
                     -labels   => { 0 => $self->tr('No_limit') },
                     -override => 1,
-                    -default => $state->{features}{$label}{limit}
+                    -default  => $state->{features}{$label}{limit},
                 )
             )
         ),

lib/Bio/Graphics/Browser/RenderPanels.pm

@@ -1333,10 +1333,15 @@ sub add_features_to_track {
 
   my (%iterators,%iterator2dbid);
   for my $db (keys %db2db) {
-      my @types_in_this_db = map { $source->label2type($_,$length) } keys %{$db2label{$db}};
+      my @labels           = keys %{$db2label{$db}};
+      my @types_in_this_db = map { $source->label2type($_,$length) } @labels;
       next unless @types_in_this_db;
-      my $iterator  = $self->get_iterator($db2db{$db},$segment,\@types_in_this_db)
+
+      my $iterator  = $self->get_iterator($db2db{$db},
+					  $segment,
+					  \@types_in_this_db)
 	  or next;
+
       $iterators{$iterator}     = $iterator;
       $iterator2dbid{$iterator} = $source->db2id($db);
   }
@@ -1346,7 +1351,7 @@ sub add_features_to_track {
   # The effect of this loop is to fetch a feature from each iterator in turn
   # using a queueing scheme. This allows streaming iterators to parallelize a
   # bit. This may not be worth the effort.
-  my (%feature2dbid,%classes,%max_features,%limit_hit);
+  my (%feature2dbid,%classes);
 
   while (keys %iterators) {
     for my $iterator (values %iterators) {
@@ -1368,19 +1373,8 @@ sub add_features_to_track {
 
 	  my $track = $tracks->{$l}  or next;
 
-
-	  $max_features{$l} = $source->fallback_setting($l => 'feature limit') || 0
-	      unless exists $max_features{$l};
-
 	  $filters->{$l}->($feature) or next if $filters->{$l};
 	  $feature_count{$l}++;
-
-	  if ($max_features{$l}
-	      && $feature_count{$l} 
-	      && $feature_count{$l} >= $max_features{$l}) {
-	      $limit_hit{$l}++;
-	      next;
-	  }
 
 	  # -----------------------------------------------------------------------------
 	  # GROUP CODE
@@ -1472,12 +1466,15 @@ sub add_features_to_track {
 			     -description => $do_description,
 			      );
     $tracks->{$l}->configure(-connector  => 'none') if !$do_bump;
-    $tracks->{$l}->configure(-bump_limit => $limit)
+    $tracks->{$l}->configure(-bump_limit    => $limit,
+			     -feature_limit => $limit)
       if $limit && $limit > 0;
 
-    if ($limit_hit{$l}) {
+    if (eval{$tracks->{$l}->features_clipped}) { # may not be present in older Bio::Graphics
+	my $max   = $tracks->{$l}->feature_limit;
+	my $count = $tracks->{$l}->feature_count;
 	$tracks->{$l}->panel->key_style('between');
-	$tracks->{$l}->configure(-key => "Showing $max_features{$l} of $feature_count{$l} features");
+	$tracks->{$l}->configure(-key => $self->language->tr('FEATURES_CLIPPED',$max,$count));
     }
   }
 }
@@ -1516,7 +1513,7 @@ sub load_external_sources {
 
 sub get_iterator {
   my $self = shift;
-  my ($db,$segment,$feature_types) = @_;
+  my ($db,$segment,$feature_types,$max) = @_;
 
   # The Bio::DB::SeqFeature::Store database supports correct
   # semantics for directly retrieving features that overlap
@@ -1528,7 +1525,9 @@ sub get_iterator {
       my @args = (-type   => $feature_types,
 		  -seq_id => $segment->seq_id,
 		  -start  => $segment->start,
-		  -end    => $segment->end);
+		  -end    => $segment->end,
+		  -max_features => $max,  # some adaptors allow this
+	  );
       return $db->get_seq_stream(@args);
   }
 
@@ -1719,6 +1718,8 @@ sub create_track_args {
   my $override        = $self->settings->{features}{$label}{override_settings} || {};   # user-set override settings for tracks
   my @override        = map {'-'.$_ => $override->{$_}} keys %$override;
 
+  push @override,(-feature_limit => $self->settings->{features}{$label}{limit}||0);
+
   my $hilite_callback = $args->{hilite_callback};
 
   my $length = $segment->length;
@@ -1755,6 +1756,7 @@ sub create_track_args {
 	     @override,
 	    );
   }
+
   return @args;
 }