get name searches to show the relevant track if necessary again

GMOD · Jan 16, 2013 · 9726c76 · 9726c76
1 parent e56d13d
commit 9726c76
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Showing 5 changed files with 14 additions and 9 deletions.
diff --git a/bin/generate-names.pl b/bin/generate-names.pl
@@ -211,7 +211,7 @@ =head1 OPTIONS
 }
 
 # store the list of tracks that have names
-$nameStore->set( 'JBROWSE_TRACKS_WITH_NAMES', \@tracksWithNames );
+$nameStore->{meta}{track_names} = \@tracksWithNames;
 
 # set up the name store in the trackList.json
 $gdb->modifyTrackList( sub {

diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -1290,6 +1290,11 @@ Browser.prototype.showRegion = function( location ) {
                                start: location.start - flank,
                                end: location.end + flank
                              });
+
+    // if the location has a track associated with it, show it
+    if( location.tracks ) {
+        this.showTracks( location.tracks );
+    }
 };
 
 /**
@@ -1398,7 +1403,7 @@ Browser.prototype.navigateToLocation = function( location ) {
  * view location to any that match.
  */
 Browser.prototype.searchNames = function( /**String*/ loc ) {
-    var brwsr = this;
+    var thisB = this;
     this.nameStore.query({ name: loc })
         .then( function( nameMatches ) {
 
@@ -1435,16 +1440,13 @@ Browser.prototype.searchNames = function( /**String*/ loc ) {
             if( goingTo.location ) {
 
                 //go to location, with some flanking region
-                brwsr.showRegion( goingTo.location );
-
-                // var tracks = (brwsr.names.extra||{})[goingTo][ post1_4 ? 1 : 0 ]];
-                // brwsr.showTracks(brwsr.names.extra[goingTo][ post1_4 ? 1 : 0 ]]);
+                thisB.showRegion( goingTo.location );
             }
             // otherwise, pop up a dialog with a list of the locations to choose from
             else if( goingTo.multipleLocations ) {
                 new LocationChoiceDialog(
                     {
-                        browser: brwsr,
+                        browser: thisB,
                         locationChoices: goingTo.multipleLocations,
                         title: 'Choose '+goingTo.name+' location',
                         prompt: '"'+goingTo.name+'" is found in multiple locations.  Please choose a location to view.'

diff --git a/src/JBrowse/Model/Location.js b/src/JBrowse/Model/Location.js
@@ -13,6 +13,7 @@ return Util.fastDeclare(
             this.start = args.start;
             this.end = args.end;
             this.strand = args.strand;
+            this.tracks = args.tracks;
         }
     },
     toString: function() {

diff --git a/src/JBrowse/Store/Names/Hash.js b/src/JBrowse/Store/Names/Hash.js
@@ -52,7 +52,8 @@ return declare( HashStore,
                 item.location = new Location({
                     ref: nameRecord[3],
                     start: parseInt( nameRecord[4] ),
-                    end: parseInt( nameRecord[5] )
+                    end: parseInt( nameRecord[5] ),
+                    tracks: [ (this.track_names||{})[ nameRecord[1] ] ]
                 });
             } else {
                 item.name = nameRecord;

diff --git a/src/perl5/Bio/JBrowse/HashStore.pm b/src/perl5/Bio/JBrowse/HashStore.pm
@@ -76,7 +76,8 @@ sub DESTROY {
     CORE::open my $out, '>', $meta_path or die "$! writing $meta_path";
     $out->print( JSON::to_json(
         {
-            hash_bits => $self->{hash_bits}
+            hash_bits => $self->{hash_bits},
+            %{ $self->{meta} || {} }
         }
         )) or die "$! writing $meta_path";
 }