Merge pull request #13 from 3dbionotes-community/develop

Release 3.3.0

Author: adrianq

README.md

@@ -10,7 +10,7 @@ Original project: https://github.com/ebi-uniprot/ProtVista
 
 ```
 $ npm install
-$ node_modules/.bin/gulp build
+$ npm run build
 ```
 
 ## License

package-lock.json

@@ -1,7 +1,7 @@
 {
   "name": "ProtVista",
   "description": "Protein feature viewer (uniprot annotation, variants, proteomics, ...)",
-  "version": "3.2.0",
+  "version": "3.3.0",
   "homepage": "https://github.com/3dbionotes-community/myProtVista",
   "repository": {
     "type": "git",

package.json

@@ -34,14 +34,13 @@ var uniprotSources = [
     }
 ];
 var otherSources = [
-/*
     {
         // To change later with /lrs/variants/
-        url: 'https://my-json-server.typicode.com/pconesa/demo/',
+        url: '/ws/lrs/features/variants/Genomic_Variants_CNCB/{ID}/',
         source:'cnbc',
-        category: 'VARIATION"'
+        category: 'VARIATION',
+        replace: true
     }
-*/
 ];
 var allSources = [].concat(uniprotSources, otherSources);
 var externalSource;

src/Constants.js

@@ -421,7 +421,9 @@ var loadSources = function(opts, dataSources, loaders, delegates, fv) {
     fv.initLayout(opts);
     _.each(dataSources, function(source, index) {
         if (!_.contains(opts.exclusions, source.category)) {
-            var url = source.url + opts.uniprotacc;
+
+            var url = source.url
+            url = source.replace === true ? url.replace("{ID}", opts.uniprotacc) : url + opts.uniprotacc;
             url = source.useExtension === true ? url + '.json' : url;
             var dataLoader = DataLoader.get(url);
             loaders.push(dataLoader);

src/FeaturesViewer.js

@@ -273,9 +273,19 @@ Tooltip.prototype.addLegend = function(legend) {
     legend.forEach( function(legendItem) {
         const color = legendItem[0];
         const label = legendItem[1];
-        var span = legendTd.append('span');
-        span.text(label);
+        // add the color
+        var span = legendTd.append('div');
         span.style("background-color", color);
+        span.style("border-color", "black");
+        span.style("display", "inline-flex");
+        span.style("width", "10px");
+        span.style("border-width", "1px");
+        span.style("height", "10px");
+
+        // Add teh text
+        var text = legendTd.append('span');
+        text.text(" : " + label);
+        legendTd.append("br");
 
     });
 };

src/TooltipFactory.js

@@ -28,7 +28,7 @@ var defaultFilterCasePrediction = {
     on: true,
     properties: {
         'alternativeSequence': /[^*]/,
-        'sourceType': [Evidence.variantSourceType.lss, null],
+        'sourceType': [Evidence.variantSourceType.uniprot, null],
         'externalData': function(variant) {
             if (!variant.sourceType) {
                 return _.some(variant.externalData, function(data) {

src/VariantFilterDialog.js

@@ -13,7 +13,7 @@ var Constants = require("./Constants");
 
 //'G', 'A', 'V', 'L', 'I' aliphatic. 'S', 'T' hydroxyl. 'C', 'M' sulfur-containing. 'D', 'N', 'E', 'Q' acidic.
 // 'R', 'K', 'H' basic. 'F', 'Y', 'W' aromatic. 'P' imino. '*' stop gained or lost.
-var aaList = ['G', 'A', 'V', 'L', 'I', 'S', 'T', 'C', 'M', 'D', 'N', 'E', 'Q', 'R', 'K', 'H', 'F', 'Y', 'W', 'P', 'd', '*'];
+var aaList = ['G', 'A', 'V', 'L', 'I', 'S', 'T', 'C', 'M', 'D', 'N', 'E', 'Q', 'R', 'K', 'H', 'F', 'Y', 'W', 'P', 'd', '*', '?'];
 
 var plotAreaClip_N = 1;