Biojs snippets

Gruntfile.js

@@ -170,4 +170,53 @@ module.exports = function(grunt) {
 
     grunt.registerTask('build', ['build_x', 'copy:dist', 'copy:dist-examples', 'jsdoc']);
 
+
+    var browserify = require("browserify");
+    var mkdirp = require("mkdirp");
+    var fs = require("fs");
+
+    grunt.registerTask('patch-pviz', 'Makes pviz work for node', function(){
+      var done = this.async();
+      console.log("patching amd");
+
+      var outFile = 'dist/pviz-bundle.js';
+      var modFile = 'dist/pviz.mod.js';
+        fs.readFile(outFile, "utf8", function(err,data){
+          // patch the AMD output - this is VERY ugly (but works)
+          // first patch: backbone-amd needs to be instantiated in via AMD 
+          //data = data.replace(/if \(typeof exports !== 'undefined'\) {\s+?\n\s+\/\/ Node\/CommonJS, no need for jQuery in that case\./, "if (typeof exportsNotDefined !== 'undefined') {");
+          data = data.replace(/if \(typeof exports !== 'undefined'\) {\s+?\/\/ Node\/CommonJS, no need for jQuery in that case\./, "if (typeof exportsNotDefined !== 'undefined') {");
+
+          // second patch: somehow there is sth. wrong with the backbone version and its
+          // router
+          data = data.replace("_.bindAll(this, 'checkUrl');", "//_.bindAll(this, 'checkUrl');");
+
+          console.log("patching finished");
+          fs.writeFile(modFile,data, function(){
+            done();
+          });
+        });
+    });
+
+    grunt.registerTask('build-browser', function(){
+      // task is async
+      var done = this.async();
+
+      // create tmp dir
+      mkdirp("build");
+
+      var packageConfig = require("./package.json");
+
+      // local test build
+      var outFile = 'build/pviz.local.js';
+      var wsExport = fs.createWriteStream(outFile);
+      wsExport.on('finish', function () {
+        done();
+      });
+
+      var b = browserify({debug: false,hasExports: true, insertGlobalVars: []});
+      b.add('./index.js', {expose: packageConfig.name });
+      b.bundle().pipe(wsExport);
+    });
+    grunt.registerTask('browserify', ['build_x','copy:dist', 'patch-pviz','build-browser']);
 };

build-tools/end.frag.txt

@@ -2,5 +2,5 @@
     //this snippet. Ask almond to synchronously require the
     //module value for 'main' here and return it as the
     //value to use for the public API for the built file.
-    return require('PVizExport');
-}));
+    return requirejs('PVizExport');
+}));

build-tools/start.frag.txt

@@ -36,11 +36,13 @@ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
         //see this AMD call, not the internal modules in
         //the closure below.
         define(factory);
-    } else {
+    } else if(typeof exports !== "undefined"){
+   		module.exports = factory();
+    }else {
         //Browser globals case. Just assign the
         //result to a property on the global.
         root.pviz = factory();
     }
 }(this, function () {
     //almond, and your modules will be inlined here
-
+

index.js

@@ -0,0 +1,2 @@
+_ = require("underscore");
+module.exports = require("./dist/pviz.mod.js");

package.json

@@ -1,20 +1,49 @@
 {
   "name": "pviz",
-  "version": "0.1.10",
-  "dependencies": {},
+  "version": "0.1.12-2",
+  "description": "pViz.js is a protein sequence features viewer for modern browsers",
+  "repository": {
+    "type": "git",
+    "url": "github.com/genentech/pviz"
+  },
+  "dependencies": {
+    "underscore": "^1.4.4"
+  },
   "devDependencies": {
+    "biojs-sniper": "^0.1.0",
+    "bower": "~1.2.8",
+    "browserify": "^6.3.2",
     "grunt": "~0.4.2",
+    "grunt-bower-requirejs": "~0.8.0",
+    "grunt-cli": "~0.1.11",
+    "grunt-contrib-clean": "~0.5.0",
+    "grunt-contrib-concat": "~0.3.0",
+    "grunt-contrib-copy": "~0.4.1",
     "grunt-contrib-jshint": "~0.7.2",
     "grunt-contrib-uglify": "~0.2.7",
     "grunt-contrib-watch": "~0.5.3",
-    "bower": "~1.2.8",
-    "grunt-bower-requirejs": "~0.8.0",
     "grunt-devserver": "~0.5.0",
+    "grunt-jsdoc": "^0.5.6",
     "grunt-requirejs": "~0.4.0",
-    "grunt-contrib-concat": "~0.3.0",
-    "grunt-cli": "~0.1.11",
-    "grunt-contrib-copy": "~0.4.1",
-    "grunt-contrib-clean": "~0.5.0",
-    "grunt-jsdoc": "^0.5.6"
-  }
+    "mkdirp": "^0.5.0"
+  },
+  "scripts": {
+    "prepublish": "bower install && grunt build browserify",
+    "sniper": "biojs-sniper ."
+  },
+  "main": "./index.js",
+  "sniper": {
+    "js": [
+      "/build/pviz.local.js"
+    ],
+    "css": [
+      "/src/css/pviz-core.css"
+    ],
+    "first": "example-0"
+  },
+  "keywords": [
+    "feature",
+    "annotation",
+    "biojs"
+  ]
 }

snippets/example-0.js

@@ -0,0 +1,134 @@
+var pviz = require("pviz");
+
+//define the model, a sequence entry with an explicit sequence
+var seq = 'MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLA';
+var seqEntry = new pviz.SeqEntry({
+  sequence : seq
+});
+
+/*
+ * thefined the view, in a backbone.js fashion
+ * model: that's the model, who would have guessed
+ * el: a selector to the target where to insert the view (size and so will be inherited)
+ *
+ * .render(): call the rendering
+ *
+ * NB: even though the features are not yet added to the model, the view will be recomputed at the end of any feature addition.
+ * This is to take into account asynchroncity, when data comes from several remote sources
+ */
+new pviz.SeqEntryAnnotInteractiveView({
+  model : seqEntry,
+  el : yourDiv
+}).render();
+
+/* we can add featureswith properties
+ * group: features will be grouped together on this property. they might no be displayed on the same line, but feature with different grous cannot be on the same line
+ * type: within group, property can have different types
+ * text: to be displayed or use wherever you want
+ * start: initial position, starting at 0
+ * end: last position of the feature (including), starting at 0
+ *
+ * NB: the explicit loading of features could be replaced by a JSON call. But for the sake of a standalone example, ajax does not work with file queries
+ d3.tsv('example-features.tsv', function(err, data) {
+   seqEntry.addFeatures(data);
+ });
+ */
+seqEntry.addFeatures([{
+  category : 'ptms',
+  type : 'mickey',
+  start : 20,
+  end : 20,
+  count : 10
+}, {
+  category : 'ptms',
+  type : 'mickey',
+  start : 22,
+  end : 22,
+  count : 3
+}, {
+  category : 'ptms',
+  type : 'mickey',
+  start : 40,
+  end : 40,
+  count : 10,
+  improbable : true //!! an option attribute
+}, {
+  category : 'ptms',
+  type : 'mickey',
+  start : 50,
+  end : 50,
+  count : 2
+}, {
+  category : 'regions',
+  type : 'topological domain',
+  text : 'extra cellular',
+  start : 22,
+  end : 650
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 24,
+  end : 26
+}, {
+  category : 'secondary structure',
+  type : 'helix',
+  start : 38,
+  end : 49
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 53,
+  end : 57
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 59,
+  end : 63
+}, {
+  category : 'secondary structure',
+  type : 'helix',
+  start : 71,
+  end : 73
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 78,
+  end : 81
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 83,
+  end : 87
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 91,
+  end : 94
+}, {
+  category : 'secondary structure',
+  type : 'turn',
+  start : 108,
+  end : 110
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 111,
+  end : 116
+}, {
+  category : 'secondary structure',
+  type : 'turn',
+  start : 129,
+  end : 131
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 138,
+  end : 140
+}, {
+  category : 'secondary structure',
+  type : 'beta_strand',
+  start : 150,
+  end : 155
+}]);
+
+