pre-parsed features and other things I like

css/dalliance-scoped.css

@@ -29,7 +29,7 @@
   display: -webkit-inline-flex;
   flex-direction: column;
   -webkit-flex-direction: column;
-  max-height: 500px;
+  max-height: 1000px;
   width: 100%;
   outline: none;
 }

index.js

@@ -0,0 +1,6 @@
+module.exports = {
+    browser: require('./js/cbrowser').Browser,
+    chainset: require('./js/chainset').Chainset,
+    sourcesAreEqual: require('./js/sourcecompare').sourcesAreEqual,
+    makeElement: require('./js/utils').makeElement
+};

js/bedwig.js

@@ -26,6 +26,8 @@ if (typeof(require) !== 'undefined') {
 
     var utils = require('./utils');
     var shallowCopy = utils.shallowCopy;
+
+    var revalidator = require('revalidator');
 }
 
 
@@ -162,6 +164,87 @@ BedParseSession.prototype.parse = function(line) {
 
 BedParseSession.prototype.flush = function() {};
 
+BedParseSession.prototype.schema = {
+  properties: {
+    segment: {
+      description: 'the name of the region containing the feature',
+      type: 'string',
+      required: true
+    },
+    min: {
+      description: 'the start position of the feature (0-based)',
+      type: 'integer',
+      minimum: 1,
+      required: true
+    },
+    max: {
+      description: 'the end position of the feature (1-based)',
+      type: 'integer',
+      required: true
+    },
+    label: {
+      description: 'the label for a feature',
+      type: 'string'
+    },
+    score: {
+      description: 'score of a feature',
+      type: 'float'
+    },
+    orientation: {
+      description: 'strand of feature',
+      type: 'string',
+      enum: ['+','-','.']
+    },
+    itemRGB: {
+      description: 'rgb color to draw feature',
+      type: 'string',
+      pattern: '^rgb\([0-9]+,[0-9]+,[0-9]+)$'
+    },
+    type: {
+      description: 'type of feature',
+      type: 'string',
+      enum: ['transcript','translation']
+    },
+    readingFrame: {
+      description: 'open reading frame at the start of the interval',
+      type: 'integer',
+      minimum: 0,
+      maximum: 2
+    },
+    groups: {
+      description: 'list of groups that a feature belongs to',
+      type: 'array',
+      items: {
+        type: 'object',
+        properties: {
+          id: {
+            type: 'string',
+            required: true
+          },
+          label: {
+            type: 'string',
+            required: true
+          },
+          type: {
+            type: 'string',
+            required: true
+          }
+        }
+      }
+    }
+  }
+};
+
+BedParseSession.prototype.validate = function(f) {
+  // use revalidator.validate to check if feature f is valid
+  var check = revalidator.validate(f, this.schema);
+  if (check.valid) {
+    this.sink(f);
+  } else {
+    console.log(check.errors);
+  }
+}
+
 function WigParseSession(parser, sink) {
     this.parser = parser;
     this.sink = sink;
@@ -234,6 +317,42 @@ WigParseSession.prototype.parse = function(line) {
 
 WigParseSession.prototype.flush = function() {};
 
+WigParseSession.prototype.schema = {
+  properties: {
+    segment: {
+      description: 'the name of the region containing the feature',
+      type: 'string',
+      required: true
+    },
+    min: {
+      description: 'the start position of the feature',
+      type: 'integer',
+      minimum: 1,
+      required: true
+    },
+    max: {
+      description: 'the end position of the feature',
+      type: 'integer',
+      required: true
+    },
+    score: {
+      description: 'score of a feature',
+      type: 'float',
+      required: true
+    }
+  }
+};
+
+WigParseSession.prototype.validate = function(f) {
+  // use revalidator.validate to check if feature f is valid
+  var check = revalidator.validate(f, this.schema);
+  if (check.valid) {
+    this.sink(f);
+  } else {
+    console.log(check.errors);
+  }
+}
+
 BedWigParser.prototype.getStyleSheet = function(callback) {
     var thisB = this;
     var stylesheet = new DASStylesheet();

js/cbrowser.js

@@ -177,14 +177,39 @@ function Browser(opts) {
     if (opts.baseColors) {
         this.baseColors = opts.baseColors
     } else {
-        this.baseColors = {
-            A: 'green',
-            C: 'blue',
-            G: 'orange',
-            T: 'red',
-            '-' : 'hotpink', // deletion
-            'I' : 'red' // insertion
-        };
+        if (opts.aminoAcids) {
+            this.baseColors = {
+                F: 'rgb(182, 201, 237)',
+                L: 'rgb(213, 236, 213)',
+                I: 'rgb(239, 213, 211)',
+                M: 'rgb(255, 23, 0)',
+                V: 'rgb(255, 172, 0)',
+                S: 'rgb(255, 244, 19)',
+                P: 'rgb(138, 189, 67)',
+                T: 'rgb(36, 153, 57)',
+                A: 'rgb(0, 166, 236)',
+                Y: 'rgb(0, 101, 178)',
+                H: 'rgb(215, 206, 182)',
+                Q: 'rgb(252, 176, 124)',
+                N: 'rgb(159, 148, 186)',
+                K: 'rgb(133, 117, 67)',
+                D: 'rgb(108, 242, 51)',
+                E: 'rgb(0, 253, 255)',
+                C: 'rgb(248, 129, 51)',
+                W: 'rgb(243, 68, 252)',
+                R: 'rgb(207, 207, 207)',
+                G: 'rgb(166, 213, 227)'
+            };
+        } else {
+            this.baseColors = {
+                A: 'green',
+                C: 'blue',
+                G: 'orange',
+                T: 'red',
+                '-' : 'hotpink', // deletion
+                'I' : 'red' // insertion
+            };
+        }
     }
 
     if (opts.viewStart !== undefined && typeof(opts.viewStart) !== 'number') {
@@ -2653,6 +2678,7 @@ if (typeof(module) !== 'undefined') {
     var sa = require('./sourceadapters');
     var TwoBitSequenceSource = sa.TwoBitSequenceSource;
     var EnsemblSequenceSource = sa.EnsemblSequenceSource;
+    var EnsemblProteinSequenceSource = sa.EnsemblProteinSequenceSource;
     var DASSequenceSource = sa.DASSequenceSource;
 
     var KnownSpace = require('./kspace').KnownSpace;

js/memstore.js

@@ -151,6 +151,7 @@ function MemStoreFeatureSource(source) {
     this.source = source;
     FeatureSourceBase.call(this);
     this.storeHolder = new Awaited();
+
     this.parser = dalliance_makeParser(source.payload);
     if (!this.parser) {
         throw "Unsupported memstore payload: " + source.payload;
@@ -164,17 +165,24 @@ function MemStoreFeatureSource(source) {
         } else {
             var store = new MemStore();
             var features = [];
-            var lines = resp.split('\n');
-
             var session = thisB.parser.createSession(function(f) {features.push(f)});
-            for (var li = 0; li < lines.length; ++li) {
-                var line = lines[li];
-                if (line.length > 0) {
-                    session.parse(line);
-                }
+
+            if (err === 'already parsed') {
+                resp.forEach(function(feat) {
+                  session.validate(feat);
+                });
             }
-            session.flush();
+            else {
+                var lines = resp.split('\n');
 
+                for (var li = 0; li < lines.length; ++li) {
+                    var line = lines[li];
+                    if (line.length > 0) {
+                        session.parse(line);
+                    }
+                }
+                session.flush();
+            }
             store.addFeatures(features);
 
             thisB.storeHolder.provide(store);
@@ -191,6 +199,8 @@ MemStoreFeatureSource.prototype._load = function(callback) {
             return callback(r.result, r.error);
         }
         r.readAsText(this.source.blob);
+    } else if (this.source.features) {
+      return callback(this.source.features, 'already parsed');
     } else {
         if (this.source.credentials)
             var opts = {credentials : this.source.credentials};

js/sourceadapters.js

@@ -1,4 +1,4 @@
-/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+//* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
 
 // 
 // Dalliance Genome Explorer
@@ -108,7 +108,11 @@ Browser.prototype.createSources = function(config) {
         if (config.twoBitURI || config.twoBitBlob) {
             ss = new TwoBitSequenceSource(config);
         } else if (config.ensemblURI) {
-            ss = new EnsemblSequenceSource(config);
+            if (config.aminoAcids) {
+                ss = new EnsemblProteinSequenceSource(config);
+            } else {
+                ss = new EnsemblSequenceSource(config);
+            }
         } else {
             ss = new DASSequenceSource(config);
         }
@@ -590,9 +594,7 @@ TwoBitSequenceSource.prototype.getSeqInfo = function(chr, cnt) {
 };
 
 function EnsemblSequenceSource(source) {
-    this.source = source;
-    // http://data.gramene.org/ensembl/info/assembly/triticum_aestivum/2B?content-type=application/json
-    // http://data.gramene.org/ensembl/sequence/region/triticum_aestivum/2B:8001..18000:1?content-type=application/json
+  this.source = source;
 }
 
 EnsemblSequenceSource.prototype.fetch = function(chr, min, max, pool, callback) {
@@ -642,6 +644,55 @@ EnsemblSequenceSource.prototype.getSeqInfo = function(chr, cnt) {
   req.send();
 };
 
+function EnsemblProteinSequenceSource(source) {
+  this.source = source;
+}
+
+EnsemblProteinSequenceSource.prototype.fetch = function(chr, min, max, pool, callback) {
+  var url = this.source.ensemblURI + '/sequence/id/' + chr + '?type=protein&content-type=application/json';
+  var req = new XMLHttpRequest();
+  req.onreadystatechange = function() {
+  	if (req.readyState == 4) {
+	    if (req.status >= 300) {
+        var err = 'Error code ' + req.status;
+        try {
+          var jr = JSON.parse(req.response);
+          if (jr.error) {
+            err = jr.error;
+          }
+        } catch (ex) {};
+
+		    callback(err, null);
+	    } else {
+    		var jr = JSON.parse(req.response);
+        var sequence = new DASSequence(chr, 1, jr.seq.length + 1, 'PEP', jr.seq);
+        return callback(null, sequence);
+      }
+    }
+  }
+  req.open('GET', url, true);
+  req.responseType = 'text';
+  req.send('');
+}
+
+EnsemblProteinSequenceSource.prototype.getSeqInfo = function(chr, cnt) {
+  var url = this.source.ensemblURI + '/sequence/id/' + chr + '?type=protein&content-type=application/json';
+  var req = new XMLHttpRequest();
+  req.onreadystatechange = function() {
+	  if (req.readyState == 4) {
+      if (req.status >= 300) {
+	      cnt();
+      } else {
+  		  var jr = JSON.parse(req.response);
+        cnt({length:jr.seq.length});
+      }
+    }
+  }
+  req.open('GET', url, true);
+  req.responseType = 'text';
+  req.send('');
+}
+
 DASFeatureSource.prototype.getScales = function() {
     return [];
 };
@@ -1753,6 +1804,7 @@ if (typeof(module) !== 'undefined') {
 
         TwoBitSequenceSource: TwoBitSequenceSource,
         EnsemblSequenceSource: EnsemblSequenceSource,
+        EnsemblProteinSequenceSource: EnsemblProteinSequenceSource,
         DASSequenceSource: DASSequenceSource,
         MappedFeatureSource: MappedFeatureSource,
         CachingFeatureSource: CachingFeatureSource,