Merge branch 'jbrowse_1.7' of github.com:berkeleybop/jbrowse into jbr…

…owse_1.7
GMOD · Nov 16, 2012 · e1ff062 · e1ff062
2 parents c486515 + 7bc7fcc
commit e1ff062
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Showing 6 changed files with 162 additions and 110 deletions.
diff --git a/genome.css b/genome.css
@@ -3,6 +3,7 @@
 @import url("src/dojo/resources/dojo.css");
 
 @import url("main.css");
+@import url("menubar.css");
 @import url("icons.css");
 
 /* CSS styles for the various types of feature glyphs */

diff --git a/main.css b/main.css
@@ -28,105 +28,6 @@ fieldset > legend {
     color: #aaa;
 }
 
-/* styles for the top menu bar */
-div.menuBar {
-    padding: 1px 0;
-    height: 25px;
-}
-.tundra .menuBar {
-    background: #396494;
-    text-align: right;
-}
-.tundra .menuBar a {
-    color: white;
-}
-div.topLink {
-    position: absolute;
-    right: 0;
-    top: 0;
-    z-index: 50;
-    background: white;
-    border: 1px solid #888;
-    border-width: 0 0 1px 1px;
-}
-div.menuBar a, .topLink a {
-    padding: 0 0.8ex;
-    text-decoration: none;
-}
-.menuBar .powered_by {
-    float: left;
-    font-size: 125%;
-    font-family: 'Helvetica Neue', Arial, Helvetica, 'Nimbus Sans L', sans-serif;
-    font-weight: bold;
-    line-height: 25px; /* note this line-height should be the same as the fixed height of the menuBar */
-}
-
-.share .icon {
-    height: 8px;
-    width: 19px;
-    display: inline;
-    display: inline-block;
-    background: url("img/glyphs_white.png") no-repeat -149px -91px;
-    margin-right: 2px;
-    margin-top: -2px;
-}
-a.topLink, a.topLink * {
-    cursor: pointer;
-}
-.topLink .powered_by {
-    padding: 0 0.5em;
-    color: black;
-    text-decoration: none;
-}
-.help .icon {
-    height: 14px;
-    width: 8px;
-    display: inline-block;
-    margin-top: -4px;
-    margin-right: 1px;
-    background: url("img/glyphs_white.png") no-repeat -174px -3px;
-}
-.tundra .menuBar * {
-    outline: none;
-}
-
-.tundra .menuBar .dijitButtonNode {
-    background: transparent;
-}
-
-.menuBar .topLink,
-.tundra .menuBar .dijitButtonNode {
-    border: 2px outset rgba( 120, 120, 120, 0.2 );
-}
-.menuBar .topLink:hover,
-.tundra .menuBar .dijitButtonHover .dijitButtonNode,
-.tundra .menuBar .dijitDropDownButtonHover .dijitButtonNode {
-    background: rgba( 255, 255, 255, 0.07 );
-}
-.menuBar .topLink:active,
-.tundra .menuBar .dijitButtonActive .dijitButtonNode,
-.tundra .menuBar .dijitDropDownButtonActive .dijitButtonNode {
-    border: 2px inset rgba( 120, 120, 120, 0.2 );
-}
-
-.menuBar .dijitButtonNode {
-    padding: 0 1em;
-}
-
-.menuBar .dijitButtonNode * {
-    color: white;
-}
-.menuBar .config .icon {
-    height: 16px;
-    width: 16px;
-    margin-right: 2px;
-    margin-top: -2px;
-    display: inline;
-    display: inline-block;
-    background: url("img/glyphs_white.png") no-repeat -168px -27px;
-}
-
-
 .tundra .dijitDialogCloseIcon {
     height: 25px;
     width:  25px;

diff --git a/menubar.css b/menubar.css
@@ -0,0 +1,124 @@
+/* styles for the top menu bar */
+div.menuBar {
+    padding: 1px 0;
+    height: 25px;
+}
+.tundra .menuBar {
+    background: #396494;
+    text-align: right;
+}
+.tundra .menuBar a {
+    color: white;
+}
+div.topLink {
+    position: absolute;
+    right: 0;
+    top: 0;
+    z-index: 50;
+    background: white;
+    border: 1px solid #888;
+    border-width: 0 0 1px 1px;
+}
+div.menuBar a, .topLink a {
+    padding: 0 0.8ex;
+    text-decoration: none;
+}
+.menuBar .powered_by {
+    float: left;
+    font-size: 125%;
+    font-family: 'Helvetica Neue', Arial, Helvetica, 'Nimbus Sans L', sans-serif;
+    font-weight: bold;
+    line-height: 25px; /* note this line-height should be the same as the fixed height of the menuBar */
+}
+
+.share .icon {
+    height: 8px;
+    width: 19px;
+    display: inline;
+    display: inline-block;
+    background: url("img/glyphs_white.png") no-repeat -149px -91px;
+    margin-right: 2px;
+    margin-top: -2px;
+}
+a.topLink, a.topLink * {
+    cursor: pointer;
+}
+.topLink .powered_by {
+    padding: 0 0.5em;
+    color: black;
+    text-decoration: none;
+}
+.help .icon {
+    height: 14px;
+    width: 8px;
+    display: inline-block;
+    margin-top: -4px;
+    margin-right: 1px;
+    background: url("img/glyphs_white.png") no-repeat -174px -3px;
+}
+.menuBar * {
+    outline: none;
+}
+.tundra .menuBar .dijitButtonNode {
+    background: transparent;
+}
+
+.tundra .menuBar .dijitButtonNode {
+    border: 2px outset rgba( 120, 120, 120, 0.2 );
+}
+.tundra .menuBar .dijitButtonHover .dijitButtonNode,
+.tundra .menuBar .dijitDropDownButtonHover .dijitButtonNode {
+    background: rgba( 255, 255, 255, 0.07 );
+}
+.tundra .menuBar .dijitButtonActive .dijitButtonNode,
+.tundra .menuBar .dijitDropDownButtonActive .dijitButtonNode {
+    border: 2px inset rgba( 120, 120, 120, 0.2 );
+}
+
+.menuBar .dijitButtonNode {
+    padding: 0 1em;
+}
+
+.menuBar .dijitButtonNode * {
+    color: white;
+}
+.menuBar .config .icon {
+    height: 16px;
+    width: 16px;
+    margin-right: 2px;
+    margin-top: -2px;
+    display: inline;
+    display: inline-block;
+    background: url("img/glyphs_white.png") no-repeat -168px -27px;
+
+}
+
+
+.menuBar > .menu {
+    float: left;
+    font-size: 120%;
+}
+.tundra .globalMenu .dijitMenuItem td {
+    padding: 0.5em 2px 0.5em 5px;
+}
+
+.tundra .menuBar > .menu .dijitButtonNode {
+    border: none;
+}
+.tundra .menuBar > .menu.dijitDropDownButton,
+.tundra .menuBar > .menu.dijitDropDownButton * {
+    margin: 0;
+    padding: 0;
+    line-height: 25px;
+}
+.tundra .menuBar > .menu.dijitDropDownButton .dijitButtonNode {
+    padding: 0 1em 0 0.7em;
+    text-align: left;
+}
+
+.tundra .menuBar > .menu .dijitDropDownButtonHover .dijitButtonNode {
+    background: rgba( 255, 255, 255, 0.07 );
+}
+.tundra .menuBar > .menu .dijitDropDownButtonActive .dijitButtonNode {
+    border: none;
+}
diff --git a/plugins/WebApollo/js/main.js b/plugins/WebApollo/js/main.js
@@ -38,7 +38,7 @@ return declare( JBPlugin,
                     }
                 });
 
-        browser.addGlobalConfigMenuItem( cds_frame_toggle );
+        browser.addGlobalMenuItem( 'options', cds_frame_toggle );
     }
 });
 

diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -15,6 +15,7 @@ define( [
             'dijit/form/Select',
             'dijit/form/DropDownButton',
             'dijit/DropDownMenu',
+            'dijit/MenuItem',
             'JBrowse/Util',
             'JBrowse/Store/LazyTrie',
             'JBrowse/Store/Autocomplete',
@@ -38,6 +39,7 @@ define( [
             dijitSelectBox,
             dijitDropDownButton,
             dijitDropDownMenu,
+            dijitMenuItem,
             Util,
             LazyTrie,
             AutocompleteStore,
@@ -324,18 +326,36 @@ Browser.prototype.initView = function() {
      }, menuBar );
 
     if( this.config.show_nav ) {
-        var configMenu = this.makeGlobalConfigMenu();
+
+        // this.addGlobalMenuItem( 'file',
+        //                         new dijitMenuItem(
+        //                             {
+        //                                 label: 'Open',
+        //                                 onClick: function() { alert('open sesame!'); }
+        //                             })
+        //                       );
+        // var fileMenu = this.makeGlobalMenu('file');
+        // if( fileMenu ) {
+        //     var fileButton = new dijitDropDownButton(
+        //         { className: 'file',
+        //           innerHTML: 'File',
+        //           //title: '',
+        //           dropDown: fileMenu
+        //         });
+        //     dojo.addClass( fileButton.domNode, 'menu' );
+        //     menuBar.appendChild( fileButton.domNode );
+        // }
+
+        var configMenu = this.makeGlobalMenu('options');
         if( configMenu ) {
             var configLink = new dijitDropDownButton(
                 { className: 'config',
-                  innerHTML: '<span class="icon"></span> Config',
+                  innerHTML: '<span class="icon"></span> Options',
                   title: 'configure JBrowse',
                   dropDown: configMenu
                 });
             menuBar.appendChild( configLink.domNode );
-
-
-        }
+       }
     }
 
     if( this.config.show_nav && this.config.show_tracklist && this.config.show_overview )
@@ -422,22 +442,26 @@ Browser.prototype.initView = function() {
 };
 
 
-Browser.prototype.makeGlobalConfigMenu = function( item ) {
-    var items = this._globalConfigMenuItems || [];
+Browser.prototype.makeGlobalMenu = function( menuName ) {
+    var items = ( this._globalMenuItems || {} )[menuName] || [];
     if( ! items.length )
         return null;
 
     var menu = new dijitDropDownMenu({ leftClickToOpen: true });
     dojo.forEach( items, function( item ) {
         menu.addChild( item );
     });
+    dojo.addClass( menu.domNode, 'globalMenu' );
     menu.startup();
     return menu;
 };
 
-Browser.prototype.addGlobalConfigMenuItem = function( item ) {
-    this._globalConfigMenuItems = this._globalConfigMenuItems || [];
-    this._globalConfigMenuItems.push( item );
+Browser.prototype.addGlobalMenuItem = function( menuName, item ) {
+    if( ! this._globalMenuItems )
+        this._globalMenuItems = {};
+    if( ! this._globalMenuItems[ menuName ] )
+        this._globalMenuItems[ menuName ] = [];
+    this._globalMenuItems[ menuName ].push( item );
 };
 
 /**

diff --git a/src/JBrowse/View/Export/GFF3.js b/src/JBrowse/View/Export/GFF3.js
@@ -166,6 +166,8 @@ return declare( ExportBase,
             var valtype = typeof val;
             if( valtype == 'boolean' )
                 val = val ? 1 : 0;
+            else if( valtype == 'undefined' )
+                return;
             tag = this._gff3_reserved_attribute(tag) || this._ensure_non_reserved( tag );
             attrs[tag] = val;
         },this);