Merge branch 'master' of https://github.com/GMOD/jbrowse

bin/add-track-json.pl

@@ -2,6 +2,10 @@
 use strict;
 use warnings;
 
+use FindBin qw($RealBin);
+use lib "$RealBin/../src/perl5";
+use JBlibs;
+
 use Pod::Usage;
 
 use JSON 2;

main.css

@@ -11,6 +11,10 @@ html, body {
     color: #aaa;
 }
 
+.dijitDialogPaneActionBar {
+    text-align: right;
+}
+
 .nav {
     vertical-align: middle;
     z-index: 10;
@@ -268,6 +272,11 @@ div.track-label, div.tracklist-label {
 /* NOTE: browsers that don't support rgba colors will fall back to all
    track labels being #bcbcbc */
 
+.notfound-dialog .message {
+    margin: 1em;
+    text-align: center;
+}
+
 div.track-label {
     color: black;
     margin: 5px 0 0 3px;

release-notes.txt

@@ -1,5 +1,24 @@
 {{$NEXT}}
 
+ * Fixed "Can't locate JSON.pm" errors with add-track-json.pl.
+
+ * Added a reference-sequence-selection dropdown box, similar to the
+   old one, that is on by default if fewer than 30 reference
+   sequences, otherwise it's off unless `refSeqDropdown: true` is set
+   in the configuration (issue #138).
+
+ * Fixed bug in which popup dialog boxes showing other websites showed
+   the website in only the top portion of the dialog box.  Only
+   present in some browsers (issue #149).
+
+ * Fix coordinate display bug in feature detail popups.  The feature's
+   position was being displayed in interbase coordinates, but should
+   be displayed in 1-based coordinates.  Thanks to Steffi Geisen for
+   pointing this out.
+
+ * Added a `style.height` option to Wiggle tracks to control the
+   track's height in pixels (issue #131). (Erik Derohanian)
+
  * Added support for a `style.trackLabelCss` configuration variable to
    allow customizing the appearance of the label for a particular
    track (issue #4).

src/JBrowse/Browser.js

@@ -3,11 +3,14 @@ var _gaq = _gaq || []; // global task queue for Google Analytics
 define( [
             'dojo/_base/lang',
             'dojo/topic',
+            'dojo/aspect',
+            'dojo/_base/array',
             'dijit/layout/ContentPane',
             'dijit/layout/BorderContainer',
             'dijit/Dialog',
             'dijit/form/ComboBox',
             'dijit/form/Button',
+            'dijit/form/Select',
             'JBrowse/Util',
             'JBrowse/Store/LazyTrie',
             'JBrowse/Store/Autocomplete',
@@ -18,11 +21,14 @@ define( [
         function(
             lang,
             topic,
+            aspect,
+            array,
             dijitContentPane,
             dijitBorderContainer,
             dijitDialog,
             dijitComboBox,
             dijitButton,
+            dijitSelectBox,
             Util,
             LazyTrie,
             AutocompleteStore,
@@ -729,9 +735,11 @@ Browser.prototype.navigateTo = function(loc) {
             } catch (x) {}
             if( oldLoc ) {
                 this.navigateToLocation( oldLoc );
+                return;
             } else {
                 // if we don't just go to the middle 80% of that refseq
                 this.navigateToLocation({ref: ref.name, start: ref.end*0.1, end: ref.end*0.9 });
+                return;
             }
         }
 
@@ -816,7 +824,27 @@ Browser.prototype.searchNames = function( /**String*/ loc ) {
                              + ":" + (startbp - flank)
                              + ".." + (endbp + flank));
             brwsr.showTracks(brwsr.names.extra[nameMatches[0][ post1_4 ? 1 : 0 ]]);
-        });
+        },
+        // if no match for the name is found, show a popup dialog saying this.
+        function() {
+            var d =  dijitDialog({ title: 'Not found', className: 'notfound-dialog' });
+
+            var content = dojo.create('div', {
+                className: 'message',
+                innerHTML: 'Not found: <span class="locString">'+loc+'</span>'
+            });
+
+            var actionBar = dojo.create( 'div', { className: 'dijitDialogPaneActionBar' });
+            new dijitButton({label: 'OK', onClick: dojo.hitch(d,'hide')}).placeAt(actionBar);
+
+            d.set('content',[content,actionBar]);
+
+            // clean up this dialog completely when it's hidden
+            aspect.after(d, 'hide', function() { d.destroyRecursive(); });
+
+            d.show();
+        }
+   );
 };
 
 
@@ -1299,6 +1327,22 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
 
     navbox.appendChild(document.createTextNode( four_nbsp ));
 
+    // if we have fewer than 30 ref seqs, or `refSeqDropdown: true` is
+    // set in the config, then put in a dropdown box for selecting
+    // reference sequences
+    if( this.refSeqOrder.length && this.refSeqOrder.length < 30 || this.config.refSeqDropdown ) {
+        this.refSeqSelectBox = new dijitSelectBox({
+            name: 'refseq',
+            options: array.map( this.refSeqOrder || [],
+                                function( refseqName ) {
+                return { label: refseqName, value: refseqName };
+            }),
+            onChange: dojo.hitch(this, function( newRefName ) {
+                this.navigateToLocation({ ref: newRefName });
+            })
+        }).placeAt( navbox );
+    }
+
     // make the location box
     this.locationBox = new dijitComboBox(
         {

src/JBrowse/Store/LazyTrie.js

@@ -138,26 +138,36 @@ return declare('JBrowse.Store.LazyTrie', null,
         return results;
     },
 
-    exactMatch: function(key, callback) {
+    exactMatch: function(key, callback, notfoundCallback ) {
+        notfoundCallback = notfoundCallback || function() {};
+
         var trie = this;
-        this.findNode(key, function(prefix, node) {
+        this.findNode(key,
+                      function(prefix, node) {
                           if ((prefix.toLowerCase() == key.toLowerCase()) && node[1])
                               callback(node[1]);
-                      });
+                      },
+                      notfoundCallback
+                     );
     },
 
-    findNode: function(query, callback) {
+    findNode: function(query, foundCallback, notfoundCallback ) {
+        notfoundCallback = notfoundCallback || function() {};
+
         var trie = this;
         this.findPath(query, function(path) {
                           var node = trie.root;
-                          for (i = 0; i < path.length; i++)
+                          for (var i = 0; i < path.length; i++)
                               node = node[path[i]];
                           var foundPrefix = trie.pathToPrefix(path);
-                          callback(foundPrefix, node);
-                      });
+                          foundCallback(foundPrefix, node);
+                      }, notfoundCallback);
     },
 
-    findPath: function(query, callback) {
+    findPath: function(query, foundCallback, notfoundCallback) {
+
+        notfoundCallback = notfoundCallback || function() {};
+
         if (!this.root) {
             this.deferred = arguments;
             return;
@@ -171,7 +181,10 @@ return declare('JBrowse.Store.LazyTrie', null,
 
         while(true) {
             childIndex = this.binarySearch(node, query.charAt(qStart));
-            if (childIndex < 0) return;
+            if (childIndex < 0) {
+                notfoundCallback();
+                return;
+            }
             path.push(childIndex);
 
             if ("number" == typeof node[childIndex][0]) {
@@ -181,7 +194,7 @@ return declare('JBrowse.Store.LazyTrie', null,
                              handleAs: "json",
                              load: function(o) {
                                  node[childIndex] = o;
-                                 trie.findPath(query, callback);
+                                 trie.findPath(query, foundCallback);
                              }
                             });
                 return;
@@ -194,14 +207,16 @@ return declare('JBrowse.Store.LazyTrie', null,
             // match
             if (query.substr(qStart, node[0].length)
                 != node[0].substr(0, Math.min(node[0].length,
-                                              query.length - qStart)))
+                                              query.length - qStart))) {
+                notfoundCallback();
                 return;
+            }
 
             qStart += node[0].length;
             if (qStart >= query.length) {
                 // we've reached the end of the query string, and we
                 // have some matches
-                callback(path);
+                foundCallback(path);
                 return;
             }
         }

src/JBrowse/View/Track/HTMLFeatures.js

@@ -144,7 +144,7 @@ var HTMLFeatures = declare( BlockBased,
         container.innerHTML += fmt( 'Name', f.get('name') );
         container.innerHTML += fmt( 'Type', f.get('type') );
         container.innerHTML += fmt( 'Description', f.get('note') );
-        container.innerHTML += fmt( 'Position', this.refSeq.name+':'+f.get('start')+'..'+f.get('end') );
+        container.innerHTML += fmt( 'Position', Util.assembleLocString({ start: f.get('start'), end: f.get('end'), ref: this.refSeq.name }));
         container.innerHTML += fmt( 'Strand', {'1':'+', '-1': '-', 0: undefined }[f.get('strand')] || f.get('strand') );
 
         var additionalTags = array.filter( f.tags(), function(t) { return ! {name:1,start:1,end:1,strand:1,note:1,subfeatures:1,type:1}[t.toLowerCase()]; });
@@ -972,16 +972,18 @@ var HTMLFeatures = declare( BlockBased,
                              onclick: dojo.hitch(dialog,'hide'),
                              innerHTML: spec.url
                          }, dialog.titleBar );
-            aspect.after( dialog, 'layout', function() {
-                              // hitch a ride on the dialog box's
-                              // layout function, which is called on
-                              // initial display, and when the window
-                              // is resized, to keep the iframe
-                              // sized to fit exactly in it.
-                              var cDims = domGeom.getMarginBox( dialog.domNode );
-                              iframe.width  = cDims.w;
-                              iframe.height = iframe.height = cDims.h - domGeom.getMarginBox(dialog.titleBar).h - 2;
-                          });
+            var updateIframeSize = function() {
+                // hitch a ride on the dialog box's
+                // layout function, which is called on
+                // initial display, and when the window
+                // is resized, to keep the iframe
+                // sized to fit exactly in it.
+                var cDims = domGeom.getMarginBox( dialog.domNode );
+                iframe.width  = cDims.w;
+                iframe.height = cDims.h - domGeom.getMarginBox(dialog.titleBar).h - 2;
+            };
+            aspect.after( dialog, 'layout', updateIframeSize );
+            aspect.after( dialog, 'show', updateIframeSize );
         }
 
         aspect.after( dialog, 'hide', function() { dialog.destroyRecursive(); });

src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm

@@ -18,7 +18,8 @@ use File::Path 'mkpath';
 
 use POSIX;
 
-use JsonGenerator;
+use JSON 2;
+use JsonFileStorage;
 use FastaDatabase;
 
 sub option_defaults {(
@@ -46,6 +47,8 @@ sub run {
     my $refs = $self->opt('refs');
     my $compress = $self->opt('compress');
 
+    $self->{storage} = JsonFileStorage->new( $self->opt('out'), $self->opt('compress'), { pretty => 0 } );
+
     pod2usage( 'must provide either a --fasta, --gff, or --conf option' )
         unless defined $self->opt('gff') || $self->opt('conf') || $self->opt('fasta');
 
@@ -102,7 +105,11 @@ sub run {
             $refs = join (",", $db->seq_ids);
         }
     } elsif ( $self->opt('conf') ) {
-        my $config = JsonGenerator::readJSON( $self->opt('conf') );
+        my $config = decode_json( do {
+            local $/;
+            open my $f, '<', $self->opt('conf') or die "$! reading ".$self->opt('conf');
+            scalar <$f>
+        });
 
         eval "require $config->{db_adaptor}; 1" or die $@;
 
@@ -189,7 +196,7 @@ sub run {
         exit;
     }
 
-    JsonGenerator::modifyJsonFile( catfile( $self->opt('out'), 'seq', 'refSeqs.json' ),
+    $self->{storage}->modify( 'seq/refSeqs.json',
                                    sub {
                                        #add new ref seqs while keeping the order
                                        #of the existing ref seqs
@@ -219,7 +226,7 @@ sub run {
     }
 
     unless( $self->opt('noseq') ) {
-        JsonGenerator::modifyJsonFile( catfile( $self->opt('out'), "trackList.json" ),
+    $self->{storage}->modify( 'trackList.json',
                                        sub {
                                            my $trackList = shift;
                                            unless (defined($trackList)) {

src/perl5/JsonFileStorage.pm

@@ -30,6 +30,8 @@ use IO::File;
 use Fcntl ":flock";
 use PerlIO::gzip;
 
+use constant DEFAULT_MAX_JSON_DEPTH => 2048;
+
 =head2 new( $outDir, $compress, \%opts )
 
 Constructor.  Takes the directory to work with, boolean flag of
@@ -44,7 +46,7 @@ sub new {
     my ($class, $outDir, $compress, $opts) = @_;
 
     # create JSON object
-    my $json = JSON->new->relaxed;
+    my $json = JSON->new->relaxed->max_depth( DEFAULT_MAX_JSON_DEPTH );
     # set opts
     if (defined($opts) and ref($opts) eq 'HASH') {
         for my $method (keys %$opts) {