Merge pull request #176 from wilzbach/fix_coloring

fix coloring and ES6 exports

src/index.js

@@ -16,7 +16,7 @@ export * as model from "./model";
 
 // extra plugins, extensions
 export * as menu from "./menu";
-export {default as utils} from "./utils";
+export * as utils from "./utils";
 
 // probably needed more often
 export {default as selection} from  "./g/selection/Selection";

src/menu/views/ExportMenu.js

@@ -1,5 +1,5 @@
 import MenuBuilder from "../menubuilder";
-import Exporter from "../../utils/export";
+import Exporter from "../../utils/exporter";
 
 const FastaExporter = require("biojs-io-fasta").writer;
 

src/utils/index.js

@@ -1,5 +1,5 @@
-module.exports.bmath = require("./bmath");
-module.exports.proxy = require("./proxy");
-module.exports.seqgen = require("./seqgen");
-module.exports.file = require("./file");
-module.exports.export = require("./export");
+export bmath from "./bmath";
+export proxy from "./proxy";
+export seqgen from "./seqgen";
+export file from "./file";
+export exporter from "./exporter";

src/utils/seqgen.js

@@ -2,12 +2,12 @@ const Sequence = require("biojs-model").seq;
 import BMath from "./bmath";
 const Stat = require("stat.seqs");
 
-const SeqGen =
-  {_generateSequence: function(len) {
-    var text = "";
-    var end = len - 1;
-    for (var i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
-      text += seqgen.getRandomChar();
+const SeqGen = {
+  _generateSequence: (len) => {
+    let text = "";
+    const end = len - 1;
+    for (let i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
+      text += SeqGen.getRandomChar();
     }
     return text;
   },
@@ -16,50 +16,51 @@ const SeqGen =
   // @param len [int] number of generated sequences
   // @param seqLen [int] length of the generated sequences
   getDummySequences: function(len, seqLen) {
-    var seqs = [];
+    const seqs = [];
     if (!(typeof len !== "undefined" && len !== null)) { len = BMath.getRandomInt(3,5); }
     if (!(typeof seqLen !== "undefined" && seqLen !== null)) { seqLen = BMath.getRandomInt(50,200); }
 
     for (var i = 1; 1 < len ? i <= len : i >= len; 1 < len ? i++ : i--) {
-      seqs.push(new Sequence(seqgen._generateSequence(seqLen), "seq" + i,"r" + i));
+      seqs.push(new Sequence(SeqGen._generateSequence(seqLen), "seq" + i,"r" + i));
     }
     return seqs;
   },
 
-  getRandomChar: function(dict) {
-    var possible = dict || "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
+  getRandomChar: (dict) => {
+    const possible = dict || "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
     return possible.charAt(Math.floor(Math.random() * possible.length));
   },
 
   // generates a dummy sequences
   // @param len [int] number of generated sequences
   // @param seqLen [int] length of the generated sequences
-  genConservedSequences: function(len, seqLen, dict) {
-    var seqs = [];
+  genConservedSequences: (len, seqLen, dict) => {
+    const seqs = [];
     if (!(typeof len !== "undefined" && len !== null)) { len = BMath.getRandomInt(3,5); }
     if (!(typeof seqLen !== "undefined" && seqLen !== null)) { seqLen = BMath.getRandomInt(50,200); }
 
     dict = dict || "ACDEFGHIKLMNPQRSTVWY---";
 
-    for (var i = 1; 1 < len ? i <= len : i >= len; 1 < len ? i++ : i--) {
+    for (let i = 1; 1 < len ? i <= len : i >= len; 1 < len ? i++ : i--) {
       seqs[i-1] = "";
     }
 
-    var tolerance = 0.2;
+    const tolerance = 0.2;
 
-    var conservAim = 1;
-    var end = seqLen - 1;
-    for (var i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
+    let conservAim = 1;
+    const end = seqLen - 1;
+    for (let i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
       if (i % 3 === 0) {
         conservAim = (BMath.getRandomInt(50,100)) / 100;
       }
-      var observed = [];
-      var end1 = len - 1;
-      for (var j = 0; 0 < end1 ? j <= end1 : j >= end1; 0 < end1 ? j++ : j--) {
-        var counter = 0;
+      const observed = [];
+      const end1 = len - 1;
+      for (let j = 0; 0 < end1 ? j <= end1 : j >= end1; 0 < end1 ? j++ : j--) {
+        let counter = 0;
+        let c;
         while (counter < 100) {
-          var c = seqgen.getRandomChar(dict);
-          var cConserv = Stat(observed);
+          c = SeqGen.getRandomChar(dict);
+          const cConserv = Stat(observed);
           cConserv.addSeq(c);
           counter++;
           if (Math.abs(conservAim - cConserv.scale(cConserv.conservation())[0]) < tolerance) {
@@ -71,12 +72,12 @@ const SeqGen =
       }
     }
 
-    var pseqs = [];
+    const pseqs = [];
     for (var i = 1; 1 < len ? i <= len : i >= len; 1 < len ? i++ : i--) {
       pseqs.push(new Sequence(seqs[i-1], "seq" + i, "r" + i));
     }
 
     return pseqs;
   }
-  };
+};
 export default SeqGen;