Merge cabe15c into 7cc3016

lib/underscore.js

@@ -2,6 +2,7 @@
 
 declare module "underscore" {
   declare function find<T>(list: T[], predicate: (val: T)=>boolean): ?T;
+  declare function findIndex<T>(list: T[], predicate: (val: T)=>boolean): number;
   declare function findWhere<T>(list: Array<T>, properties: {[key:string]: any}): ?T;
   declare function clone<T>(obj: T): T;
 

src/main/Controls.js

@@ -5,6 +5,7 @@
 'use strict';
 
 import type {GenomeRange, PartialGenomeRange} from './types';
+import type ContigInterval from './ContigInterval';
 
 import React from 'react';
 import _ from 'underscore';
@@ -14,7 +15,7 @@ import Interval from './Interval';
 
 type Props = {
   range: ?GenomeRange;
-  contigList: string[];
+  contigList: ContigInterval<string>[];
   onChange: (newRange: GenomeRange)=>void;
 };
 
@@ -54,8 +55,8 @@ class Controls extends React.Component<Props, State> {
       // There are major performance issues with having a 'chr' mismatch in the
       // global location object.
       const contig = range.contig;
-      var altContig = _.find(this.props.contigList, ref => utils.isChrMatch(contig, ref));
-      if (altContig) range.contig = altContig;
+      var altContig = _.find(this.props.contigList, ref => utils.isChrMatch(contig, ref.contig));
+      if (altContig) range.contig = altContig.contig;
     }
 
     return (_.extend(_.clone(this.props.range), range) : any);
@@ -86,7 +87,8 @@ class Controls extends React.Component<Props, State> {
     this.refs.position.value = utils.formatInterval(new Interval(r.start, r.stop));
 
     if (this.props.contigList) {
-      var contigIdx = this.props.contigList.indexOf(r.contig);
+      var contigIdx = _.findIndex(this.props.contigList, ref => utils.isChrMatch(r.contig, ref.contig));
+
       this.refs.contig.selectedIndex = contigIdx;
     }
   }
@@ -137,7 +139,7 @@ class Controls extends React.Component<Props, State> {
 
   render(): any {
     var contigOptions = this.props.contigList
-        ? this.props.contigList.map((contig, i) => <option key={i}>{contig}</option>)
+        ? this.props.contigList.map((contig, i) => <option key={i}>{contig.contig}</option>)
         : null;
 
     // Note: input values are set in componentDidUpdate.
@@ -161,6 +163,20 @@ class Controls extends React.Component<Props, State> {
     if (!_.isEqual(prevProps.range, this.props.range)) {
       this.updateRangeUI();
     }
+    // Update slider if we have collected new information about a contig.
+    if (!_.isEqual(prevProps.contigList, this.props.contigList)) {
+      if (this.props.range != undefined) {
+        var range = this.props.range; // flow
+        if (range.contig != undefined) {
+          var newInterval = _.find(this.props.contigList, ref => utils.isChrMatch(range.contig, ref.contig));
+
+          if (newInterval != undefined) {
+            this.refs.slider.min = Math.ceil(-Math.log2(newInterval.stop()) + 1);
+            this.updateSlider(new Interval(range.start, range.stop));
+          }
+        }
+      }
+    }
   }
 
   componentDidMount() {

src/main/Root.js

@@ -7,7 +7,8 @@
 import type {GenomeRange} from './types';
 import type {TwoBitSource} from './sources/TwoBitDataSource';
 import type {VisualizedTrack, VizWithOptions} from './types';
-
+import type ContigInterval from './ContigInterval';
+import utils from './utils';
 import _ from 'underscore';
 
 import React from 'react';
@@ -22,7 +23,7 @@ type Props = {
 };
 
 type State = {
-  contigList: string[];
+  contigList: ContigInterval<string>[];
   range: ?GenomeRange;
   settingsMenuKey: ?string;
   updateSize: boolean;
@@ -50,9 +51,7 @@ class Root extends React.Component<Props, State> {
 
   componentDidMount() {
     this.props.referenceSource.on('contigs', () => {
-      this.setState({
-        contigList: this.props.referenceSource.contigList(),
-      });
+      this.updateOutOfBoundsChromosome();
     });
 
     if (!this.state.range) {
@@ -63,13 +62,33 @@ class Root extends React.Component<Props, State> {
   }
 
   handleRangeChange(newRange: GenomeRange) {
+
+    // copy over range so you don't modify
+    // this.state.range, which is bound to handleRangeChange
+    var modifiedRange =  {
+      contig: newRange.contig,
+      start: newRange.start,
+      stop: newRange.stop,
+    };
+
     // Do not propagate negative ranges
-    if (newRange.start < 0) {
-      newRange.start = 0;
+    if (modifiedRange.start < 0) {
+      modifiedRange.start = 0;
+    }
+    // Do not propogate ranges exceeding contig limit
+    var contigInfo = _.find(this.state.contigList, ref => utils.isChrMatch(modifiedRange.contig, ref.contig));
+
+    if (contigInfo != undefined) {
+      if (modifiedRange.stop > contigInfo.stop()) {
+        modifiedRange.stop = contigInfo.stop();
+        if (modifiedRange.start > modifiedRange.stop) {
+          modifiedRange.start = 0;
+        }
+      }
     }
-    this.props.referenceSource.normalizeRange(newRange).then(range => {
-      this.setState({range: range});
 
+    this.props.referenceSource.normalizeRange(modifiedRange).then(range => {
+      this.setState({range: range});
       // Inform all the sources of the range change (including referenceSource).
       this.props.tracks.forEach(track => {
         track.source.rangeChanged(range);
@@ -160,7 +179,7 @@ class Root extends React.Component<Props, State> {
         </div>
       );
     }
-    
+
     var className = ['track', track.visualization.component.displayName || '', track.track.cssClass || ''].join(' ');
 
     return (
@@ -198,13 +217,60 @@ class Root extends React.Component<Props, State> {
     );
   }
 
+  updateOutOfBoundsChromosome(): any {
+    // We don't want to allow users to go to regions that extend past the end of
+    // a contig. This function truncates queries past the ends of a contig
+    // and updates the required states.
+
+    var current_contig = this.props.initialRange.contig;
+    if (this.state.range) {
+      current_contig = this.state.range.contig;
+    }
+
+    var oldContig = _.find(this.state.contigList, ref =>
+        utils.isChrMatch(current_contig,
+        ref.contig));
+
+    var contigList = this.props.referenceSource.contigList();
+
+    var newContig = _.find(contigList, ref => utils.isChrMatch(current_contig, ref.contig));
+
+    // only update if the current contig has new information regarding
+    // the end of the chromosome AND the current range is out of bounds
+    // with respect to chromosome length
+    if (this.state.contigList.length == 0) {
+      this.setState({
+        contigList: contigList
+      });
+    }
+
+    if (newContig && oldContig) {
+      if (!_.isEqual(oldContig, newContig)) {
+        // only trigger state if current contig changed
+        this.setState({
+          contigList: contigList
+        });
+        if (this.state.range !== null && this.state.range !== undefined) {
+          if (this.state.range.stop > newContig.stop()) {
+            // $FlowIgnore: TODO remove flow suppression
+            this.handleRangeChange(this.state.range);
+          }
+        }
+      }
+    }
+  }
+
   componentDidUpdate(prevProps: Props, prevState: Object) {
     if (this.state.updateSize) {
       for (var i=0;i<this.props.tracks.length;i++) {
         this.trackReactElements[i].setState({updateSize:this.state.updateSize});
       }
       this.state.updateSize=false;
     }
+
+    this.props.referenceSource.on('contigs', () => {
+      this.updateOutOfBoundsChromosome();
+    });
   }
 
 }

src/main/data/TwoBit.js

@@ -6,6 +6,7 @@
 'use strict';
 
 import type RemoteFile from '../RemoteFile';
+import ContigInterval from '../ContigInterval';
 
 import Q from 'q';
 import _ from 'underscore';
@@ -206,9 +207,14 @@ function retryRemoteGet(remoteFile: RemoteFile, start: number, size: number, unt
 class TwoBit {
   remoteFile: RemoteFile;
   header: Q.Promise<TwoBitHeader>;
+  // Stores sequence records already seen.
+  // Used to keep track of lengths of each contig.
+  traversedSequenceRecords: {[key:string]: SequenceRecord};
+
 
   constructor(remoteFile: RemoteFile) {
     this.remoteFile = remoteFile;
+    this.traversedSequenceRecords = {};
     var deferredHeader = Q.defer();
     this.header = deferredHeader.promise;
     retryRemoteGet(
@@ -250,8 +256,17 @@ class TwoBit {
   }
 
   // Returns a list of contig names.
-  getContigList(): Q.Promise<string[]> {
-    return this.header.then(header => header.sequences.map(seq => seq.name));
+  getContigList(): Q.Promise<ContigInterval<string>[]> {
+    return this.header.then(header => {
+      return header.sequences.map(seq => {
+        // fill in numBases if collected
+        var numBases = Number.MAX_VALUE;
+        if (this.traversedSequenceRecords[seq.name]) {
+          numBases = this.traversedSequenceRecords[seq.name].numBases;
+        }
+        return new ContigInterval(seq.name, 0, numBases);
+      });
+    });
   }
 
   _getSequenceHeader(contig: string): Q.Promise<SequenceRecord> {
@@ -263,17 +278,26 @@ class TwoBit {
       }
       var seq = maybeSeq;  // for flow, see facebook/flow#266
 
-      return retryRemoteGet(
-        this.remoteFile,
-        seq.offset,
-        FIRST_SEQUENCE_CHUNKSIZE,
-        MAX_CHUNKSIZE,
-        buffer => {
-          return parseWithException(() => {
-            return parseSequenceRecord(buffer, seq.offset);
-          });
-        }
-      );
+      if (contig in this.traversedSequenceRecords) {
+        return Q.when(this.traversedSequenceRecords[contig]);
+      } else {
+        return retryRemoteGet(
+          this.remoteFile,
+          seq.offset,
+          FIRST_SEQUENCE_CHUNKSIZE,
+          MAX_CHUNKSIZE,
+          buffer => {
+            return parseWithException(() => {
+
+              if (!this.traversedSequenceRecords[seq.name]) {
+                this.traversedSequenceRecords[contig] =
+                  parseSequenceRecord(buffer, seq.offset);
+              }
+              return this.traversedSequenceRecords[contig];
+            });
+          }
+        );
+      }
     }).then(p => {
       return p;
     });

src/main/sources/TwoBitDataSource.js

@@ -42,7 +42,7 @@ export type TwoBitSource = {
   rangeChanged: (newRange: GenomeRange) => void;
   getRange: (range: GenomeRange) => {[key:string]: ?string};
   getRangeAsString: (range: GenomeRange) => string;
-  contigList: () => string[];
+  contigList: () => ContigInterval<string>[];
   normalizeRange: (range: GenomeRange) => Q.Promise<GenomeRange>;
   on: (event: string, handler: Function) => void;
   once: (event: string, handler: Function) => void;
@@ -62,9 +62,13 @@ var createFromTwoBitFile = function(remoteSource: TwoBit): TwoBitSource {
   function fetch(range: ContigInterval<string>) {
     var span = range.length();
     if (span > MAX_BASE_PAIRS_TO_FETCH) {
-      //inform that we won't fetch the data
-      o.trigger('newdatarefused', range);
-      return Q.when();  // empty promise
+      // trigger header collection to get information about this chromosome,
+      // but don't fetch the actual data.
+      return remoteSource._getSequenceHeader(range.contig).then(header => remoteSource.getContigList()).then(c => {
+        contigList = c;
+        o.trigger('contigs', contigList);
+        o.trigger('newdatarefused', range);
+      }).done();
     }
     //now we can add region to covered regions
     //doing it earlier would provide inconsistency
@@ -81,18 +85,27 @@ var createFromTwoBitFile = function(remoteSource: TwoBit): TwoBitSource {
                                      range.start() + letters.length - 1);
         }
         store.setRange(range, letters);
-      }).then(() => {
+      }).then(() => remoteSource.getContigList()).then(c => {
+        contigList = c;
+        o.trigger('contigs', contigList);
         o.trigger('newdata', range);
       }).done();
   }
 
   // This either adds or removes a 'chr' as needed.
   function normalizeRangeSync(range: GenomeRange): GenomeRange {
-    if (contigList.indexOf(range.contig) >= 0) {
+
+    // check for direct match
+    var contigIdx = _.findIndex(contigList, ref => range.contig == ref.contig);
+
+    if (contigIdx >= 0) {
       return range;
     }
     var altContig = utils.altContigName(range.contig);
-    if (contigList.indexOf(altContig) >= 0) {
+
+    contigIdx = _.findIndex(contigList, ref => altContig == ref.contig);
+
+    if (contigIdx >= 0) {
       return {
         contig: altContig,
         start: range.start,

src/test/FakeAlignment.js

@@ -76,7 +76,7 @@ var fakeSource = {
   rangeChanged: dieFn,
   getRange: function(): any { return {}; },
   getRangeAsString: function(): string { return ''; },
-  contigList: function(): string[] { return []; },
+  contigList: function(): ContigInterval<string>[] { return []; },
   normalizeRange: function(range: GenomeRange): Q.Promise<GenomeRange> { return Q.when(range); },
   on: dieFn,
   off: dieFn,

src/test/FakeTwoBit.js

@@ -0,0 +1,32 @@
+/**
+ * fake TwoBit file.
+ * Used to query regions that extend the bounds in
+ * the test twobit files.
+ *
+ * @flow
+ */
+import Q from 'q';
+import TwoBit from '../main/data/TwoBit';
+import RemoteFile from '../main/RemoteFile';
+
+
+class FakeTwoBit extends TwoBit {
+  deferred: Object;
+
+  constructor(remoteFile: RemoteFile) {
+    super(remoteFile);
+    this.deferred = Q.defer();
+  }
+
+  getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise<string> {
+    return this.deferred.promise;
+  }
+
+  release(sequence: string) {
+    this.deferred.resolve(sequence);
+  }
+}
+
+module.exports = {
+  FakeTwoBit
+};