Merge 50bf169 into f118690

package.json

@@ -14,6 +14,7 @@
   },
   "homepage": "https://github.com/danvk/pileup.js",
   "dependencies": {
+    "backbone": "^1.1.2",
     "d3": "^3.5.5",
     "q": "^1.1.2",
     "react": "^0.12.2",

src/Root.js

@@ -6,9 +6,8 @@
 var React = require('react'),
     Controls = require('./Controls'),
     GenomeTrack = require('./GenomeTrack'),
-    types = require('./types'),
+    types = require('./types');
     // TODO: make this an "import type" when react-tools 0.13.0 is out.
-    TwoBit = require('./TwoBit');
 
 var Root = React.createClass({
   propTypes: {
@@ -23,24 +22,35 @@ var Root = React.createClass({
   },
   componentDidMount: function() {
     // Note: flow is unable to infer this type through `this.propTypes`.
-    var ref: TwoBit = this.props.referenceSource;
-    ref.getContigList().then(contigList => {
-      this.setState({contigList});
+    var source: TwoBitDataSource = this.props.referenceSource;
+    source.needContigs();
+
+    source.on('contigs', () => this.update)
+          .on('newdata', () => this.update);
+
+    source.on('contigs', () => {
       // this is here to facilitate faster iteration
       this.handleRangeChange({
         contig: 'chr1',
         start: 123456,
         stop: 123500
       });
-    }).done();
+    });
+
+    this.update();
+  },
+  update: function() {
+    this.setState({
+      contigList: this.props.referenceSource.contigList(),
+      basePairs: this.props.referenceSource.getRange(this.state.range)
+    });
   },
   handleRangeChange: function(newRange: GenomeRange) {
-    this.setState({range: newRange, basePairs: null});
+    this.setState({range: newRange});
+    this.update();
+
     var ref = this.props.referenceSource;
-    ref.getFeaturesInRange(newRange.contig, newRange.start, newRange.stop)
-       .then(basePairs => {
-         this.setState({basePairs});
-       }).done();
+    ref.rangeChanged(newRange);
   },
   render: function(): any {
     return (

src/TwoBitDataSource.js

@@ -0,0 +1,79 @@
+/**
+ * The "glue" between TwoBit.js and GenomeTrack.js.
+ *
+ * GenomeTrack is pure view code -- it renders data which is already in-memory
+ * in the browser.
+ *
+ * TwoBit is purely for data parsing and fetching. It only knows how to return
+ * promises for various genome features.
+ *
+ * This code acts as a bridge between the two. It maintains a local version of
+ * the data, fetching remote data and informing the view when it becomes
+ * available.
+ *
+ * @flow
+ */
+'use strict';
+
+// import type * as TwoBit from './TwoBit';
+
+var Events = require('backbone').Events,
+    _ = require('underscore');
+
+// Factor by which to over-request data from the network.
+// If a range of 100bp is shown and this is 2.0, then 300 base pairs will be
+// requested over the network (100 * 2.0 too much)
+var EXPANSION_FACTOR = 2.0;
+
+
+var createTwoBitDataSource = function(remoteSource: TwoBit) {
+  // Local cache of genomic data.
+  var contigList = [];
+  var basePairs = {};  // contig -> locus -> letter
+  function getBasePair(contig: string, position: number) {
+    return basePairs[contig] && basePairs[contig][position];
+  }
+  function setBasePair(contig: string, position: number, letter: string) {
+    if (!basePairs[contig]) basePairs[contig] = {};
+    basePairs[contig][position] = letter;
+  }
+
+  function fetch(range: GenomeRange) {
+    return remoteSource.getFeaturesInRange(range.contig, range.start, range.stop)
+        .then(letters => {
+          for (var i = 0; i < letters.length; i++) {
+            setBasePair(range.contig, range.start + i, letters[i]);
+          }
+        });
+  }
+
+  function getRange(range: GenomeRange) {
+    if (!range) return null;
+    return _.range(range.start, range.stop)
+        .map(x => getBasePair(range.contig, x))
+        .join('');
+  }
+
+  var o = {
+    rangeChanged: function(newRange: GenomeRange) {
+      // Range has changed! Fetch new data.
+      // TODO: only fetch it if it isn't cached already.
+      fetch(newRange)
+          .then(() => o.trigger('newdata', newRange))
+          .done();
+    },
+    needContigs: () => {
+      remoteSource.getContigList().then(c => {
+        contigList = c;
+        o.trigger('contigs', contigList);
+      }).done();
+    },
+    getRange: getRange,
+    contigList: () => contigList
+  };
+  _.extend(o, Events);  // Make this an event emitter
+
+  return o;
+};
+
+module.exports = createTwoBitDataSource;

src/main.js

@@ -1,11 +1,13 @@
 /* @flow */
 var React = require('react'),
     TwoBit = require('./TwoBit'),
-    Root = require('./Root');
+    Root = require('./Root'),
+    createTwoBitDataSource = require('./TwoBitDataSource');
 
 var startMs = Date.now();
 // var genome = new TwoBit('http://www.biodalliance.org/datasets/hg19.2bit');
 var genome = new TwoBit('/hg19.2bit');
+var dataSource = createTwoBitDataSource(genome);
 
 genome.getFeaturesInRange('chr22', 19178140, 19178170).then(basePairs => {
   var endMs = Date.now();
@@ -19,5 +21,5 @@ genome.getFeaturesInRange('chr22', 19178140, 19178170).then(basePairs => {
 // pre-load some data to allow network-free panning
 genome.getFeaturesInRange('chr1', 123000, 124000).done();
 
-var root = React.render(<Root referenceSource={genome} />,
+var root = React.render(<Root referenceSource={dataSource} />,
                         document.getElementById('root'));

types/types.js

@@ -1,5 +1,5 @@
 declare class GenomeRange {
   contig: string;
   start: number;
-  stop: number;
+  stop: number;  // XXX inclusive or exclusive?
 }