* Fixed "no overloaded magic in Bio::DAS::Segment" error.

* Made Menus and tabbed section labels larger (if you don't like, 
    edit htdocs/css/dropdown/default-theme.css).

* Moved track table into its own tabbed section.

* TrackFinder plugin now hilights the matches in the track table.

Changes

@@ -5,6 +5,10 @@
         * Fixed various bugs in the processing of SAM and BAM files.
 	* BAM parser now creates BigWig indexes if library is available.
 	* Fixed "no overloaded magic in Bio::DAS::Segment" error.
+	* Made Menus and tabbed section labels larger (if you don't like, 
+	  edit htdocs/css/dropdown/default-theme.css).
+	* Moved track table into its own tabbed section.
+	* TrackFinder plugin now hilights the matches in the track table.
 
 2.08 Thu May 20 22:46:13 EDT 2010
 	* Added the ability to control the toggle state of each category and subcategory at

TODO

@@ -1,12 +1,13 @@
-* Fix all /gbrowse2 hard-coded instances.
 * Document the REST API; in particular the action=list and action=scan commands.
 * DAS Server support.
-* Download underlying track data via single click on track title.
 * Bring internationalization support up to date.
-* Support for BigWig and remote BAM files.
 * Share tracks via a LOCAL link rather than through gff3 bottleneck.
 * Automatically load datasource .conf files from a special directory
 * Turn off show/hide toggles for any section.
+* Rewrite subtrack selection to allow subtracks to appear as a
+  separate selectable/sortable table.
+* Introduce the idea of a sort order among subtracks.
+* Put track selection table into a separate tab.
 
 $Id: TODO,v 1.15 2006-12-02 21:34:26 lstein Exp $
 

conf/languages/POSIX.pm

@@ -149,6 +149,8 @@ END
 
    TRACKS   => 'Tracks',
 
+   SELECT_TRACKS   => 'Select Tracks',
+
    TRACK_SELECT   => 'Search for Specific Tracks',
 
    TRACK_NAME     => 'Track name',

conf/plugins/TrackFinder.pm

@@ -83,6 +83,13 @@ sub filter_tracks {
   return @result;
 }
 
+sub hilite_terms {
+    my $self = shift;
+  my $config  = $self->configuration;
+    my @keywords = map {quotemeta($_)} shellwords $config->{keywords};    
+    return @keywords;
+}
+
 1;
 
 __END__

htdocs/css/dropdown/default_theme.css

@@ -64,7 +64,7 @@ ul.dropdown {
 	 border-color: #f0f0f0 #666 #666 #f0f0f0;
 	 background-color: #fff;
 	 font-weight: bold;
-	 font-size: 12px;
+	 font-size: 14px;
 	}
 
 		ul.dropdown ul li {
@@ -79,6 +79,7 @@ ul.dropdown {
 
 
 ul.dropdown *.dir {
+ font-size: 14px;
  padding-right: 25px;
  background-image: url(images/nav-arrow-down.png);
  background-position: 95% 50%;

htdocs/css/gbrowse_warm.css

@@ -41,7 +41,7 @@ BODY              { background-color: #F7FBFF;
 .tabmenu_active   { cursor: pointer;
 			color: black;
 			background-color: beige;
-			font-size: 10pt;
+			font-size: 11pt;
 			font-weight: bold;
                         font-family: sans-serif;
 			padding-top: 5px;
@@ -56,7 +56,7 @@ BODY              { background-color: #F7FBFF;
 		      }
 .tabmenu_inactive { cursor: pointer;
 			color: blue;
-			font-size: 10pt;
+			font-size: 11pt;
 			background-color: transparent;
 			font-weight: bold;
                         font-family: sans-serif;

htdocs/js/controller.js

@@ -982,7 +982,7 @@ var Controller = new GBrowseController; // singleton
 function initialize_page() {
 
   // These statements initialize the tabbing
-  Controller.tabs = new TabbedSection(['main_page','custom_tracks_page','settings_page']);
+  Controller.tabs = new TabbedSection(['main_page','track_page','custom_tracks_page','settings_page']);
 
   //event handlers
     [page_title_id,visible_span_id,galaxy_form_id,search_form_objects_id].each(function(el) {

lib/Bio/Graphics/Browser2/Plugin.pm

@@ -601,6 +601,10 @@ configuration form methods with calls to the javascript routine
 doPluginUpdate(). This causes GBrowse to update the plugin's
 configuration and refresh the tracks table as a side effect.
 
+=item @terms = $plugin->hilite_terms
+
+Returns a list of terms to hilight in the tracks table, or empty if none.
+
 =back
 
 =head2 METHODS TO BE IMPLEMENTED IN FEATURE HILITERS
@@ -907,6 +911,11 @@ sub filter_tracks {
     return @$tracks;  # pass 'em all through
 }
 
+sub hilite_terms {
+    my $self = shift;
+    return;
+}
+
 sub pkg {
   my $self  = shift;
   my $class = ref $self or return;

lib/Bio/Graphics/Browser2/Render.pm

@@ -706,24 +706,23 @@ sub render_body {
 
   if ($region->feature_count > 1) {
       $main_page .= $self->render_multiple_choices($features,$self->state->{name});
-      $main_page .= $self->render_toggle_track_table;
+      $main_page .= $self->render_select_track_link;
   }
 
   elsif (my $seg = $region->seg) {
       $main_page .= $self->render_panels($seg,{overview   => $source->show_section('overview'),
 					       regionview => $source->show_section('region'),
 					       detailview => $source->show_section('detail')});
-      $main_page .= $self->render_toggle_track_table;
       $main_page .= $self->render_galaxy_form($seg);
-  }
-  else {
-      $main_page .= $self->render_toggle_track_table;
+  } else {
+      $main_page .= $self->render_select_track_link;
   }
 
+  my $tracks        = $self->render_tracks_section;
   my $upload_share  = $self->render_upload_share_section;
   my $global_config = $self->render_global_config;
 
-  $output .= $self->render_tabbed_pages($main_page,$upload_share,$global_config);
+  $output .= $self->render_tabbed_pages($main_page,$tracks,$upload_share,$global_config);
   $output .= $self->render_bottom($features);
 
   $output .= $self->render_login_section;
@@ -754,6 +753,15 @@ sub render_login_section {
     return $output;
 }
 
+sub render_select_track_link {
+    croak "implement in subclass";
+}
+
+sub render_tracks_section {
+    my $self = shift;
+    return $self->render_toggle_track_table;
+}
+
 sub render_upload_share_section {
     croak "implement in subclass";
 }
@@ -898,9 +906,12 @@ sub render_panels {
 			  div({ -id => 'detail_panels', -class => 'track'},
 			      $details_msg,
 			      $scale_bar_html, 
-			      $panels_html
+			      $panels_html,
+			  ),
+			  div({-style=>'text-align:center'},
+			      $clear_hilites,
+			      $self->render_select_track_link
 			  ),
-			  div({-style=>'text-align:right'},$clear_hilites),
 			  div($self->html_frag('html4',$self->state))
             )
 	    ) . $drag_script;

lib/Bio/Graphics/Browser2/Render/HTML.pm

@@ -74,19 +74,22 @@ sub render_error_div {
 
 sub render_tabbed_pages {
     my $self = shift;
-    my ($main_html,$custom_tracks_html,$settings_html) = @_;
+    my ($main_html,$tracks_html,$custom_tracks_html,$settings_html) = @_;
     my $main_title          = $self->tr('MAIN_PAGE');
+    my $tracks_title        = $self->tr('SELECT_TRACKS');
     my $custom_tracks_title = $self->tr('CUSTOM_TRACKS_PAGE');
     my $settings_title      = $self->tr('SETTINGS_PAGE');
 
     my $html = '';
     $html   .= div({-id=>'tabbed_section', -class=>'tabbed'},
 		   div({-id=>'tabbed_menu',-class=>'tabmenu'},
-		       span({id=>'main_page_select'},    $main_title),
+		       span({id=>'main_page_select'},         $main_title),
+		       span({id=>'track_page_select'},        $tracks_title),
 		       span({id=>'custom_tracks_page_select'},$custom_tracks_title),
-		       span({id=>'settings_page_select'},$settings_title)
+		       span({id=>'settings_page_select'},     $settings_title)
 		   ),
 		   div({-id=>'main_page',         -class=>'tabbody'}, $main_html),
+		   div({-id=>'track_page',        -class=>'tabbody'}, $tracks_html),
 		   div({-id=>'custom_tracks_page',-class=>'tabbody'}, $custom_tracks_html),
 		   div({-id=>'settings_page',     -class=>'tabbody'}, $settings_html)
 	);
@@ -777,11 +780,14 @@ sub render_toggle_track_table {
   my $self     = shift;
   my $html;
 
+  $html .= div({-style=>'font-weight:bold'},'<<',$self->render_select_browser_link('link'));
+
   if (my $filter = $self->track_filter_plugin) {
       $html .= $self->toggle({tight=>1},'track_select',div({class=>'searchtitle',
 							    style=>"text-indent:2em;padding-top:8px"},$self->render_track_filter($filter)));
   }
   $html .= $self->toggle('Tracks',$self->render_track_table);
+  $html .= div({-style=>'text-align:center'},$self->render_select_browser_link('button'));
 
   return $html;
 }
@@ -803,6 +809,14 @@ sub render_track_table {
 
   warn "potential tracks = @labels" if DEBUG;
 
+  my ($filter_active,@hilite);
+  if (my $filter = $self->track_filter_plugin) {
+      $filter_active++;
+      eval {@labels    = $filter->filter_tracks(\@labels,$source)};
+      eval {@hilite    = $filter->hilite_terms};
+      warn $@ if $@;
+  }
+
   # add citation link and markup
   my %labels;
   for my $label (@labels) {
@@ -811,42 +825,41 @@ sub render_track_table {
    if ($label =~ /^plugin:/) {
        $labels{$label} = $key;
        next;
-       }
+   }
    elsif ($label =~ /^file:/){
        $link = "?Download%20File=$key";
-       }
+   }
    else {
        $link = "?display_citation=$label";#;source=" . $settings->{source};
        my $cit_txt = citation( $source, $label, $self->language ) || '';
        if ( length $cit_txt > 100) {
-   	$cit_txt =~ s/\<[^\>]+\>//g;     # truncate and strip tags for preview
-   	$cit_txt =~ s/(.{100}).+/$1/; 
-   	$cit_txt =~ s/\s+\S+$//; 
-   	$cit_txt =~ s/\'/\&\#39;/g;
-   	$cit_txt =~ s/\"/\&\#34;/g;
-        $cit_txt .= '... <i>Click for more</i>';
-        }
-        $mouseover = "<b>$key</b>";
-        $mouseover .= ": $cit_txt"                           if $cit_txt;
-        }
+	   $cit_txt =~ s/\<[^\>]+\>//g;     # truncate and strip tags for preview
+	   $cit_txt =~ s/(.{100}).+/$1/; 
+	   $cit_txt =~ s/\s+\S+$//; 
+	   $cit_txt =~ s/\'/\&\#39;/g;
+	   $cit_txt =~ s/\"/\&\#34;/g;
+	   $cit_txt .= '... <i>Click for more</i>';
+       }
+       $mouseover = "<b>$key</b>";
+       $mouseover .= ": $cit_txt"                           if $cit_txt;
+   }
 
-  my $balloon = $source->setting('balloon style') || 'GBubble';
+   my $balloon = $source->setting('balloon style') || 'GBubble';
 
-  my @args = ( -href => $link, -target => 'citation');
-      push @args, -style => 'Font-style: italic' if $label =~ /^(http|ftp|file):/;
-      push @args, -onmouseover => "$balloon.showTooltip(event,'$mouseover')" if $mouseover;
+   my @args = ( -href => $link, -target => 'citation');
+   push @args, -style => 'Font-style: italic' if $label =~ /^(http|ftp|file):/;
+   push @args, -onmouseover => "$balloon.showTooltip(event,'$mouseover')" if $mouseover;
+
+   # add hilighting if requested
+   for my $h (@hilite) {
+       $key =~ s!($h)!<span style="background-color:yellow">$1</span>!gi;
+   }
 
-  $labels{$label} = a({@args},$key);
+   $labels{$label} = a({@args},$key);
   }
 
-  #my %labels     = map {$_ => $self->label2key($_)}              @labels;
   my @defaults   = grep {$settings->{features}{$_}{visible}  }   @labels;
 
-  if (my $filter = $self->track_filter_plugin) {
-      eval {@labels    = $filter->filter_tracks(\@labels,$source)};
-      warn $@ if $@;
-  }
-
   # Sort the tracks into categories:
   # Overview tracks
   # Region tracks
@@ -916,8 +929,10 @@ sub render_track_table {
 				      -override   => 1,
 				     );
       $table = $self->tableize(\@checkboxes,$category);
-      my $visible = exists $settings->{section_visible}{$id} 
-                    ? $settings->{section_visible}{$id} : $c_default;
+      my $visible =  $filter_active ? 1
+                   : exists $settings->{section_visible}{$id} 
+                        ? $settings->{section_visible}{$id} 
+                        : $c_default;
 
       my ($control,$section)=$self->toggle_section({on=>$visible,nodiv => 1},
 						   $id,
@@ -1192,6 +1207,32 @@ sub clear_highlights {
 		 $self->tr('CLEAR_HIGHLIGHTING'));
 }
 
+sub render_select_track_link {
+    my $self  = shift;
+    my $title = $self->tr('SELECT_TRACKS');
+    return button({-name=>$title,
+		   -onClick => "Controller.select_tab('track_page')"
+		  }
+	);
+
+}
+sub render_select_browser_link {
+    my $self  = shift;
+    my $style  = shift || 'button';
+
+    my $title = $self->tr('BACK_TO_BROWSER');
+    if ($style eq 'button') {
+	return button({-name=>$title,
+		       -onClick => "Controller.select_tab('main_page')"
+		      }
+	    );
+    } elsif ($style eq 'link') {
+	return a({-href=>'javascript:void(0)',
+		  -onClick => "Controller.select_tab('main_page')"},
+		 $title);
+    }
+}
+
 sub render_upload_share_section {
     my $self = shift;
     return $self->is_admin