added fmini's, small refresh fix

bin/gbrowse_create_account.pl

@@ -79,10 +79,10 @@ END
 unless ($uid) {
 # this creates a new session for the admin user
     my $session     = $globals->session;
-    my $favoritetable = $globals->favorites;
+
     my $sessionid   = $session->id;
     my $uploadsid   = $session->uploadsid;
-    my @favorites_list = $favoritetable->favorites;
+
     $session->flush();
 
     my ($status,undef,$message) = 

htdocs/js/controller.js

@@ -1141,6 +1141,57 @@ var GBrowseController = Class.create({
      }
   },
 
+  saveSession:
+  function(/*settings_json*/){
+//     var settings = settings_json.evalJSON();
+
+
+alert('hello');
+
+
+ new Ajax.Request(document.URL, {
+  	          method: 'POST',
+  		  asynchronous:true,
+  		  parameters: {
+  		        action:    'save_session',
+  			name:  'snapshot_test',
+
+  	          }});
+
+   /* 
+    for (var o in settings){
+    alert(o+" : "+settings[o]);
+    }*/
+  },
+
+
+  setSession:
+  function(/*settings_json*/){
+//     var settings = settings_json.evalJSON();
+
+
+
+alert('hello');
+
+
+ new Ajax.Request(document.URL, {
+  	          method: 'POST',
+  		  asynchronous:true,
+  		  parameters: {
+  		        action: 'set_session',
+  			name: 'hello',
+
+  	          }});
+
+
+
+
+   /* 
+    for (var o in settings){
+    alert(o+" : "+settings[o]);
+    }*/
+  },
+
   wait_for_initialization:
   function (html, callback) {
       $('main').setOpacity(0.2);

htdocs/js/toggle.js

@@ -237,7 +237,11 @@ function togglestars(event,imgID, txtID, favorites,cellid)
   var fileNameMainSpilt = fileName.split("_"); // check for a spilt on '_'
   var imgName ='';
   var show;     
-
+     var miniID = 'fav_'+imgID;
+
+  var browserstarTag = document.getElementById(miniID);
+    var blank_min_src =fullFilePath+"fmini.png";
+    var coloured_min_src = fullFilePath+"fmini_2.png";
 
 
   var stars = getElementsByClassName("star");  
@@ -302,10 +306,7 @@ function togglestars(event,imgID, txtID, favorites,cellid)
   			label:   imgID,
  			favorite:show,
   	          }});
-     var miniID = 'fav_'+imgID;
-  var browserstarTag = $(miniID);
-    var blank_min_src =fullFilePath+"fmini.png";
-    var coloured_min_src = fullFilePath+"fmini_2.png";
+
 
 if (event.shiftKey) {
 
@@ -352,9 +353,11 @@ new Ajax.Request(document.URL, {
        }
     }
 
-  
+
 // (favorite == true) ? fullFilePath+'fmini_2.png' : fullFilePath+'fmini.png';
+   if(browserstarTag){
    browserstarTag.src = (favorite == true) ? coloured_min_src : blank_min_src;
+   };
 //    alert(browserstarTag.src);
 //   alert(blank_min_src);
 //   alert(coloured_min_src);
@@ -662,6 +665,7 @@ new Ajax.Request(
 
 e.show();
 
+Controller.update_sections(new Array(track_listing_id),'',1,false)
 
 
 

htdocs/js/track.js

@@ -23,7 +23,7 @@ var GBrowseTrack = Class.create({
     this.track_image_id  = track_id + "_image";
     this.last_update_key = 0;
     this.expired_count   = 0;
-
+//  alert(track_section);
     if (track_type == 'scale_bar') {
       this.standard_track  = false;
     }
@@ -36,6 +36,7 @@ var GBrowseTrack = Class.create({
   set_last_update_key:
   function (time_key) {
     this.last_update_key = time_key;
+
   },
 
   get_last_update_key:

lib/Bio/Graphics/Browser2/Action.pm

@@ -299,6 +299,8 @@ sub ACTION_set_favorite {
 }
 
 
+
+
 #
 # parameters:
 #       method: 'post',
@@ -330,6 +332,40 @@ sub ACTION_clear_favorites {
     return (204,'text/plain',undef);
 }
 
+
+# sub ACTION_set_session {
+# 
+# }
+
+
+sub ACTION_save_session {
+    my $self = shift;
+    my $q     = shift;
+    my $name = $q->param('name');
+    my $settings = $self->state;
+# 
+# 
+#    %snapshot = %$settings;
+#     delete(%snapshot{snapshots});
+# 
+# 
+#     $settings->{snapshots}->{$name} = %snapshot;
+# #     warn "settings = $settings";
+# # warn "$self";
+# 
+# 
+#   my %temsess = %{$settings->{snapshots}}; 
+#  while ( (my $key, my $value) = each %temsess)
+#  {
+#    warn "key: $key, value: $temsess{$key}\n";
+#  };
+
+
+    $self->session->flush;
+    return (204,'text/plain',undef);
+}
+
+
 sub ACTION_reconfigure_plugin {
     my $self   = shift;
     my $q      = shift;

lib/Bio/Graphics/Browser2/Render.pm

@@ -100,13 +100,15 @@ sub session {
     my $self = shift;
     my $d = $self->{session};
     $self->{session} = shift if @_;
+    warn "d= $d" if DEBUG;
+    warn "self->session= $self->{session}" if DEBUG;
     $d;
 }
 
 sub state {
   my $self = shift;
   my $d = $self->{state};
-  $STATE = $self->{state} = shift if @_;
+  $STATE = $self->{state}= shift if @_;
   $d;
 }
 
@@ -2047,7 +2049,7 @@ sub track_visible {
 sub update_state_from_cgi {
   my $self  = shift;
   my $state = $self->state;
-warn "state = $state";
+warn "state = $state" if DEBUG;
   $self->update_options($state);
   $self->update_coordinates($state);
   $self->update_region($state);

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

@@ -179,7 +179,10 @@ sub render_navbar {
   my $source_form = div({-id=>'source_form'},$self->source_form());
 
   my $sliderform  = div({-id=>'slider_form'},$self->sliderform($segment));
-
+
+# my $sessionButton = div({-id=>'sessionbutton'},$self->render_select_saveSession());
+# 
+# my $setSession = div({-id=>'sessionbutton'},$self->render_select_setSession());
   return $self->toggle('Search',
 		       div({-class=>'searchbody'},
 			   table({-border=>0,-width=>'100%'},
@@ -189,7 +192,14 @@ sub render_navbar {
 				    ),
 				    td({-align=>'left'},
 				       $sliderform || ' '
-				    )
+				    ),
+# 				     td({-align=>'left'},
+# 				       $sessionButton || ' '
+# 				    ),
+# ,
+# 				     td({-align=>'left'},
+# 				       $setSession || ' '
+# 				    )
 				 )
 			   ),
 			   $self->html_frag('html3',$self->state)
@@ -975,7 +985,7 @@ my $checkid = "notselectedcheck_${label}";
 
 my $showicon;
 my $name =  $self->{$category_table_labels}->{label};
-warn "section = $name";
+warn "section = $name" if DEBUG;
 #if the track has already been favorited, the image source is made into the yellow star
  if($settings->{favorites}{$label}){
 
@@ -1516,6 +1526,40 @@ sub render_select_favorites_link {
 }
 
 
+sub render_select_saveSession {
+my $self = shift;
+my $title = 'Save Session';
+
+ return button({-name=>$title,
+		           -onClick => "Controller.saveSession()",
+
+# 		   "Controller.update_section('range');"
+		          },
+
+	        );
+}
+
+sub render_select_setSession {
+my $self = shift;
+my $title = 'Set Session';
+
+ return button({-name=>$title,
+		           -onClick => "Controller.setSession()",
+
+# 		   "Controller.update_section('range');"
+		          },
+
+	        );
+}
+
+
+# sub save_session{
+# my $self = shift;
+# warn "self = $self";
+# warn "hello";
+# }
+
+
 # Render Select Browser Link - Returns the HTML for the "Back to Browser" button/link.
 sub render_select_browser_link {
     my $self  = shift;
@@ -3576,4 +3620,3 @@ sub format_upload_autocomplete {
     return $html;
 }
 1;
-

lib/Bio/Graphics/Browser2/RenderPanels.pm

@@ -13,6 +13,7 @@ use Bio::Graphics::Browser2::Util qw[shellwords url_label];
 use Bio::Graphics::Browser2::Render::Slave::Status;
 use IO::File;
 use Time::HiRes 'sleep','time';
+use Data::Dumper;
 use POSIX 'WNOHANG','setsid';
 use CGI qw(:standard param escape unescape);
 
@@ -269,6 +270,7 @@ sub make_requests {
 
 	my $format_option = $settings->{features}{$label}{options};
 
+
 	my $filter     = $settings->{features}{$label}{filter};
 	@filter_args   = %{$filter->{values}} if $filter->{values};
 	@subtrack_args = @{$settings->{subtracks}{$label}} 
@@ -293,6 +295,7 @@ sub make_requests {
 				     $format_option, 
 				     $label ],
 		    );
+
 		my $msg = eval {$args->{remotes}->error($track)};
 		$cache_object->flag_error($msg || "Could not fetch data for $track");
 		$d{$track} = $cache_object;
@@ -323,7 +326,7 @@ sub make_requests {
 			     $label ],
 	    -cache_time => $cache_time
         );
-
+#       warn "object= $format_option";
         $d{$label} = $cache_object;
     }
 
@@ -391,6 +394,7 @@ sub render_tracks {
     }
 
     return \%result;
+
 }
 
 # Returns the HMTL to show a track with controls, title, arrows, etc.
@@ -582,7 +586,7 @@ sub wrap_rendered_track {
 	); 
 
 
-use Data::Dumper;
+
    my $ipad_collapse = $collapsed ? 'Expand':'Collapse';
 
   my $cancel_ipad = 'Turn off';
@@ -594,7 +598,7 @@ use Data::Dumper;
 
 #    $settings->{favorites} = {};
 #    print Dumper($settings->{favorites}{$label});
-  my $bookmark;  
+my $bookmark = 'Favorite'; 
 #  = ($HTMLPAGE->{favorites}{$label}) ? 'Favorite' : 'Unfavorite';
     my $menuicon = img ({-src => $menu, 
 			 -style => 'padding-right:15px;',},),
@@ -2086,6 +2090,15 @@ sub create_track_args {
   my $is_summary      = $source->show_summary($label,$self->vis_length,$self->settings);
 
   my $state            = $self->settings;
+
+#    my %temp = %$state;
+# 
+# foreach my $k (keys %temp) {
+#        warn "$k: $temp{$k}\n";
+#     }
+
+
+
   my ($semantic_override) = sort {$b<=>$a} grep {$_ < $length} 
                     keys %{$state->{features}{$label}{semantic_override}};
   $semantic_override ||= 0;