Merge branch 'require-js'

Gruntfile.js

@@ -1,27 +1,39 @@
 SOURCE_FILES = [
-  'src/core.js',
+  'src/buffer-allocators.js',
+  'src/color.js',
   'src/geom.js',
-  'src/trace.js',
-  'src/symmetry.js',
-  'src/mol.js',
+  'src/gfx/animation.js',
+  'src/gfx/base-geom.js',
+  'src/gfx/cam.js',
+  'src/gfx/chain-data.js',
+  'src/gfx/custom-mesh.js',
+  'src/gfx/framebuffer.js',
+  'src/gfx/geom-builders.js',
+  'src/gfx/indexed-vertex-array.js',
+  'src/gfx/label.js',
+  'src/gfx/line-geom.js',
+  'src/gfx/mesh-geom.js',
+  'src/gfx/render.js',
+  'src/gfx/scene-node.js',
+  'src/gfx/shaders.js',
+  'src/gfx/vert-assoc.js',
+  'src/gfx/vertex-array-base.js',
+  'src/gfx/vertex-array.js',
   'src/io.js',
-  'src/vert-assoc.js',
-  'src/buffer-allocators.js',
-  'src/vertex-array-base.js',
-  'src/indexed-vertex-array.js',
-  'src/vertex-array.js',
-  'src/chain-data.js',
-  'src/geom-builders.js',
-  'src/scene.js',
-  'src/render.js',
-  'src/shade.js',
-  'src/cam.js',
-  'src/shaders.js',
-  'src/framebuffer.js',
+  'src/mol/all.js',
+  'src/mol/atom.js',
+  'src/mol/bond.js',
+  'src/mol/chain.js',
+  'src/mol/mol.js',
+  'src/mol/residue.js',
+  'src/mol/select.js',
+  'src/mol/trace.js',
+  'src/mol/symmetry.js',
+  'src/pv.js',
   'src/slab.js',
-  'src/animation.js',
   'src/touch.js',
-  'src/custom-mesh.js',
+  'src/unique-object-id-pool.js',
+  'src/utils.js',
   'src/viewer.js',
   'src/viewpoint.js'
 ];
@@ -33,6 +45,30 @@ var browserify = require("browserify");
 var fs = require("fs");
 var mkdirp = require("mkdirp");
 
+var START_SNIPPET="\n\
+(function (root, factory) {\n\
+    if (typeof define === 'function' && define.amd) {\n\
+        define([], factory);\n\
+    } else {\n\
+        var pv = factory();\n\
+        root.pv = pv;\n\
+        root.io = pv.io;\n\
+        root.mol = pv.mol;\n\
+        root.color = pv.color;\n\
+        root.rgb = pv.rgb;\n\
+        root.viewpoint = pv.viewpoint;\n\
+        root.vec3 = pv.vec3;\n\
+        root.vec4 = pv.vec4;\n\
+        root.mat3 = pv.mat3;\n\
+        root.mat4 = pv.mat4;\n\
+        root.quat = pv.quat;\n\
+    }\n\
+}(this, function () {\n\
+    // modules will be inlined here\n\
+";
+
+var END_SNIPPET='return pv; }));';
+
 module.exports = function(grunt) {
 
   // Project configuration.
@@ -61,23 +97,46 @@ module.exports = function(grunt) {
         latedef : true,
         // would love to use, but current project structure does not allow 
         // for it.
-        /* undef : true, */
+        undef : true,
+        browser : true,
+        devel : true,
+        predef : [ 'define' ],
         unused : true
       },
       all : SOURCE_FILES
     },
 
-    concat: {
-      dist: {
-        src: ALL_FILES,
-        dest: 'js/pv.dbg.js'
-      }
-    },
     removelogging : {
       dist :  {
         src : 'js/pv.dbg.js',
         dest : 'js/pv.rel.js',
       }
+    },
+    requirejs: {
+      js : { options : {
+        findNestedDependencies : true,
+        baseUrl : 'src',
+        optimize: 'none',
+        skipModuleInsertion : true,
+        include: ['pv'],
+        out : 'js/pv.dbg.js',
+        onModuleBundleComplete : function(data) {
+          var fs = require('fs'),
+          amdclean = require('amdclean'),
+          outputFile = data.path;
+          fs.writeFileSync(outputFile, amdclean.clean({
+            filePath: outputFile, 
+            transformAMDChecks : false,
+            aggressiveOptimizations : true,
+            createAnonymousAMDModule : true,
+            wrap : {
+              start : START_SNIPPET,
+              end : END_SNIPPET
+            }
+
+          }));
+        },
+      }}
     }
   });
 
@@ -86,43 +145,11 @@ module.exports = function(grunt) {
   grunt.loadNpmTasks('grunt-contrib-jshint');
   grunt.loadNpmTasks('grunt-contrib-concat');
   grunt.loadNpmTasks('grunt-remove-logging');
+  grunt.loadNpmTasks('grunt-contrib-requirejs');
 
   // Default task(s).
   grunt.registerTask('default', [
-    'concat', 'jshint', 'removelogging', 'uglify', 
+    'jshint', 'requirejs:js', 'removelogging', 'uglify'
   ]);
 
-
-  grunt.registerTask('browserify', 'Browserifies the source', function(){
-    // task is async
-    var done = this.async();
-
-    // create tmp dir
-    mkdirp("build");
-
-    var ws = fs.createWriteStream('build/pv.js');
-    ws.on('finish', function () {
-      done();
-    });
-
-    // expose the pv viewer
-    var b = browserify({debug: true,hasExports: true});
-    exposeBundles(b);
-    b.bundle().pipe(ws);
-  });
-
-  // exposes the main package
-  // + checks the config whether it should expose other packages
-  function exposeBundles(b){
-    var packageConfig = require("./package.json");
-
-    b.add('./index.js', {expose: packageConfig.name });
-
-    // check for addition exposed packages (not needed here)
-    if(packageConfig.sniper !== undefined && packageConfig.sniper.exposed !== undefined){
-      for(var i=0; i<packageConfig.sniper.exposed.length; i++){
-        b.require(packageConfig.sniper.exposed[i]);
-      }
-    }
-  }
 };

README.md

@@ -75,6 +75,8 @@ Changelog
 - ability to add geometric shapes to the 3D scene through customMesh
 - ability to specify custom color palettes (@andreasprlic)
 - viewerReady event (@andreasprlic)
+- PV can optionally be used as an AMD module without polluting the global namespace
+- added more unit and functional tests. The tests reach a coverage of 80% of the total number of exectuable lines of code.
 
 ### New in Version 1.3.1
 

all-tests.html

@@ -0,0 +1,42 @@
+
+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <title>All PV Functional and Unit Tests</title>
+  <link rel="stylesheet" href="css/qunit.css">
+  <style>
+    #viewer {
+      width: 300px;
+      height: 300px;
+      display:none;
+    }
+    #root {
+      width:100%;
+      padding:0px;
+      margin:0px;
+    }
+  </style>
+</head>
+<body>
+<table id=root><tr>
+<td>
+  <div id="qunit"></div>
+  <div id="qunit-fixture"></div>
+</td><td>
+  <div id="viewer"></div>
+</td>
+</tr></table>
+</body>
+  <script src='js/require.js'></script>
+  <script src='js/qunit.js'></script>
+  <script>
+    QUnit.config.autostart = false;
+    QUnit.config.autoload = false;
+  </script>
+  <script  data-cover-only='//src\/.*/'
+           data-cover-never='//(tests\/.*|src\/gl-matrix\.js)/' 
+           src='js/blanket.min.js'></script>
+
+  <script src='src/tests/all.js'></script>
+</html

demo.js

@@ -1,5 +1,27 @@
-var structure;
 
+requirejs.config({
+  'baseUrl' : 'src' ,
+  // uncomment the following commented-out block to test the contatenated, 
+  // minified PV version. Grunt needs to be run before for this to work.
+  /*
+  paths : {
+    pv : '/js/pv.min'
+  }
+  */
+});
+
+
+// on purpose outside of the require block, so we can inspect the viewer object 
+// from the JavaScript console.
+var viewer;
+
+require(['pv'], function(pv) {
+
+var io = pv.io;
+var viewpoint = pv.viewpoint;
+var color = pv.color;
+
+var structure;
 
 function lines() {
   viewer.clear();
@@ -13,7 +35,7 @@ function cartoon() {
   var go = viewer.cartoon('structure', structure, {
       color : color.ssSuccession(), showRelated : '1',
   });
-  var rotation = principalAxes(go);
+  var rotation = viewpoint.principalAxes(go);
   viewer.setRotation(rotation)
 }
 
@@ -138,3 +160,48 @@ function byChain() {
 function polymerase() {
   load('4UBB');
 };
+
+$(document).foundation();
+$('#1r6a').click(transferase);
+$('#1crn').click(crambin);
+$('#1ake').click(kinase);
+$('#4ubb').click(polymerase);
+$('#4c46').click(longHelices);
+$('#2f8v').click(telethonin);
+$('#style-cartoon').click(cartoon);
+$('#style-tube').click(tube);
+$('#style-line-trace').click(lineTrace);
+$('#style-sline').click(sline);
+$('#style-trace').click(trace);
+$('#style-lines').click(lines);
+$('#style-balls-and-sticks').click(ballsAndSticks);
+$('#style-spheres').click(spheres);
+$('#color-uniform').click(uniform);
+$('#color-element').click(byElement);
+$('#color-chain').click(byChain);
+$('#color-ss-succ').click(ssSuccession);
+$('#color-ss').click(ss);
+$('#color-rainbow').click(rainbow);
+$('#load-from-pdb').change(function() {
+  var pdbId = this.value;
+  this.value = '';
+  this.blur();
+  $.ajax('http://pdb.org/pdb/files/'+pdbId+'.pdb')
+    .done(function(data) {
+      structure = io.pdb(data);
+      cartoon();
+      viewer.autoZoom();
+    })
+});
+viewer = pv.Viewer(document.getElementById('viewer'), { 
+    width : 'auto', height: 'auto', antialias : true, 
+    outline : true, quality : 'medium',
+    background : '#333', animateTime: 500,
+});
+viewer.addListener('viewerReady', longHelices);
+
+window.addEventListener('resize', function() {
+      viewer.fitParent();
+});
+
+});