Merge c57fcce into 4fc0649

apollo

@@ -7,13 +7,13 @@ function usage(){
     echo "Production Commands:";
     echo "";
     echo "deploy:           Builds war file (no processing of javascript) into the target directory.";
-    echo "install-tools:    Installs JBrowse tools in the ./bin directory if not preset."
+    echo "jbrowse-tools:    Installs JBrowse tools in the ./bin directory if not preset."
     echo "run-local <port>: Runs from current directory, but not in dev-mode. ";
     echo "help:             This message.";
     echo "";
     echo "Development Commands:";
     echo "devmode:          Runs from current directory debug mode (non-minimized javascript).";
-    echo "jbrowse:          Installs updated client/apollo files and JBrowse.";
+    echo "jbrowse:          Installs updated client/apollo files and JBrowse for the web.";
     echo "run-app   <port>: Runs from current directory, but does not compile annotator panel (you have to run run-local once first).";
     echo "test:             Runs test-suite.";
     echo "debug:            Runs from cuurent directory in debug mode (non-minimized javascript).";
@@ -207,10 +207,11 @@ if [[ $1 == "devmode" ]];then
     check_configs
     $gradle_executable installJBrowseWebOnly devmode &
     $grails_executable -reloading run-app
-elif [[ $1 == "install-tools" ]];then
+elif [[ $1 == "jbrowse-tools" ]];then
     check_configs
-    check_perldependencies
-    $gradle_executable installJBrowseLocal
+	$gradle_executable installJBrowseWebOnly
+	rm -rf bin
+	ln -s jbrowse/bin bin
 elif [[ $1 == "run-local" ]];then
     check_configs
     if [[ $# == 2 ]]; then

build.gradle

@@ -128,13 +128,6 @@ task cloneRepo3(dependsOn: evaluateJBrowseConfigs) {
     }
 }
 
-task installJBrowseLocal(type: Exec) {
-    doLast{
-        workingDir = '.'
-        commandLine './install_jbrowse.sh'
-    }
-}
-
 //task copyResourcesDev(dependsOn: installJBrowse) {
 task copyResourcesDev() {
     doLast {

client/apollo/js/TrackConfigTransformer.js

@@ -13,10 +13,19 @@ constructor: function( args )  {
     this.transformers=[];
     var browser=args.browser;
     this.overridePlugins=browser.config.overridePlugins;
+    this.transformers["NeatHTMLFeatures/View/Track/NeatFeatures"] = function(trackConfig) {
+        trackConfig.type = "WebApollo/View/Track/DraggableNeatHTMLFeatures";
+    };
+    this.transformers["NeatCanvasFeatures/View/Track/NeatFeatures"] = function(trackConfig) {
+        trackConfig.type = "WebApollo/View/Track/WebApolloNeatCanvasFeatures";
+    };
+    // have to set this explicitly if you want undecorated features
+    // and configure the jbrowse plugin off
     this.transformers["JBrowse/View/Track/HTMLFeatures"] = function(trackConfig) {
         trackConfig.type = "WebApollo/View/Track/DraggableHTMLFeatures";
     };
 
+    // trackConfig.type = "WebApollo/View/Track/WebApolloCanvasFeatures";
     this.transformers["JBrowse/View/Track/CanvasFeatures"] = function(trackConfig) {
         trackConfig.type = "WebApollo/View/Track/WebApolloCanvasFeatures";
     };

client/apollo/js/View/Track/AnnotTrack.js

@@ -5633,7 +5633,7 @@ define([
 
                     // if feature-render annot-render ,
                     // remove and add: gray-center-10pct
-                    if(div.className.indexOf("feature-render")>=0 &&  div.className.indexOf("annot-render")>=0 ){
+                    if(div.className && div.className.indexOf("feature-render")>=0 &&  div.className.indexOf("annot-render")>=0 ){
                         div.className = "gray-center-10pct";
                     }
 // annot_context_menu.unBindDomNode(div);

client/apollo/js/View/Track/DraggableNeatHTMLFeatures.js

@@ -0,0 +1,22 @@
+
+define( [
+            'dojo/_base/declare',
+            'dojo/_base/array',
+            'NeatHTMLFeatures/View/Track/NeatFeatures',
+            'WebApollo/View/Track/DraggableHTMLFeatures'
+        ],
+    function( declare,
+        array,
+        NeatFeatureTrack,
+        HTMLFeatureTrack
+        ) {
+
+
+var draggableTrack = declare( [NeatFeatureTrack,HTMLFeatureTrack],{
+    constructor: function(args)  {  }
+
+});
+
+    return draggableTrack;
+});
+

client/apollo/js/View/Track/WebApolloNeatCanvasFeatures.js

@@ -0,0 +1,24 @@
+define( [
+            'dojo/_base/declare',
+            'dojo/_base/array',
+            'NeatCanvasFeatures/View/Track/NeatFeatures',
+            'WebApollo/View/Track/WebApolloCanvasFeatures'
+        ],
+        function( declare,
+            array,
+            NeatFeatureTrack,
+            CanvasFeaturesTrack
+        )
+{
+
+return declare( [NeatFeatureTrack,CanvasFeaturesTrack], {
+    constructor: function() {
+        this.browser.getPlugin( 'WebApollo', dojo.hitch( this, function(p) {
+            this.webapollo = p;
+        }));
+    }
+});
+
+
+});
+

docs/Configure.md

@@ -90,7 +90,11 @@ or ```git```, which can include a ```tag``` or ```branch``` as above.
 
 Options for ```alwaysRecheck``` and ```alwaysRepull``` always check the branch and tag and always pull respectiviely. 
 
-__Warning:__ The ```NeatHTMLFeatures``` and ```NeatCanvasFeatures``` plugins work very well in JBrowse instances.  We are still in the process of testing and improving their performance in combination with the Apollo plugin. Until we finalize this process, we strongly advise caution if enabling them for use in your Apollo instances.
+##### NeatFeatures
+
+__Warning:__ The ```NeatHTMLFeatures``` and ```NeatCanvasFeatures``` plugins work very well in JBrowse instances.  
+
+However, there are some outstanding issues with them, so proceed with caution.
 
 ```
 jbrowse {
@@ -132,6 +136,20 @@ jbrowse {
 }
 ```
 
+To use `NeatFeatures` in the tracks you need to specify:
+
+```
+trackType: NeatHTMLFeatures/View/Track/NeatFeatures
+```
+
+or 
+
+```
+trackType: NeatCanvasFeatures/View/Track/NeatFeatures
+```
+
+In the `AnnotTrack.json` code you will have to change `WebApollo/View/Track/DraggableHTMLFeatures` to `WebApollo/View/Track/DraggableNeatHTMLFeatures`.
+
 
 ### Translation tables
 

grails-app/controllers/org/bbop/apollo/JbrowseController.groovy

@@ -460,6 +460,9 @@ class JbrowseController {
             // add core plugin: https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Browser.js#L244
 //            pluginKeys.add("RegexSequenceSearch")
             pluginKeys.add("WebApollo")
+            // see https://github.com/GMOD/jbrowse/issues/897
+            // https://github.com/GMOD/Apollo/issues/2014
+            jsonObject.plugins.add("stub")
             for (plugin in plugins) {
                 if (!pluginKeys.contains(plugin.key)) {
                     pluginKeys.add(plugin.key)