Adjusting canvas height based GenotypeTrack height

.gitignore

@@ -18,6 +18,9 @@ coverage
 
 # Compiled binary addons (http://nodejs.org/api/addons.html)
 build/Release
+
+# Examples folder
+examples
 
 # Dependency directory
 # Commenting this out is preferred by some people, see
@@ -41,3 +44,12 @@ dist
 # Generated files
 src/lib
 *.pyc
+.idea/.name
+.idea/compiler.xml
+.idea/misc.xml
+.idea/modules.xml
+.idea/pileup.js.iml
+.idea/vcs.xml
+.idea/workspace.xml
+.idea/copyright/profiles_settings.xml
+.idea/dictionaries/akmorrow.xml

examples/json/reference.json

@@ -0,0 +1,8 @@
+{
+  "region": {
+    "contig": "chrM",
+    "start": "0",
+    "stop": "500"
+  },
+  "sequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATA"
+}

package.json

@@ -31,7 +31,8 @@
     "flow": "flow status",
     "flow-check": "flow check",
     "coverage": "./scripts/generate-coverage.sh",
-    "build": "./scripts/build.sh"
+    "build": "./scripts/build.sh",
+    "quick-build": "./scripts/quick-build.sh"
   },
   "author": "Dan Vanderkam",
   "contributors": [
@@ -45,9 +46,6 @@
     "url": "https://github.com/hammerlab/pileup.js/issues"
   },
   "homepage": "https://github.com/hammerlab/pileup.js",
-  "prepush": [
-    "lint"
-  ],
   "dependencies": {
     "backbone": "1.1.2",
     "d3": "^3.5.5",
@@ -59,8 +57,7 @@
     "react": "^0.14.0",
     "react-dom": "^0.14.0",
     "shallow-equals": "0.0.0",
-    "underscore": "^1.7.0",
-    "memory-cache": "0.1.6"
+    "underscore": "^1.7.0"
   },
   "devDependencies": {
     "arraybuffer-slice": "^0.1.2",
@@ -84,7 +81,6 @@
     "number-to-locale-string": "^1.0.0",
     "parse-data-uri": "^0.2.0",
     "phantomjs": "1.9.17",
-    "prepush-hook": "^0.1.0",
     "react-addons-test-utils": "^0.14.0",
     "sinon": "^1.12.2",
     "smash": "0.0.14",

scripts/test.sh

@@ -18,4 +18,4 @@ trap finish EXIT
 sleep 1
 
 # Start the tests
-mocha-phantomjs http://localhost:8081/src/test/runner.html "$@"
+mocha-phantomjs http://localhost:8081/src/test/runner.html

src/main/GA4GHAlignment.js

@@ -39,11 +39,12 @@ class GA4GHAlignment /* implements Alignment */ {
   // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl
   constructor(alignment: Object) {
     this.alignment = alignment;
-    this.pos = alignment.alignment.position.position;
-    this.ref = alignment.alignment.position.referenceName;
-    this.name = alignment.fragmentName;
+    // console.log(alignment)
+    this.pos =  alignment.alignment.position.position;
+    this.ref =  alignment.alignment.position.referenceName;
+    this.name =  alignment.fragmentName;
 
-    this.cigarOps = alignment.alignment.cigar.map(
+    this.cigarOps =  alignment.alignment.cigar.map(
         ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length }));
     this._interval = new ContigInterval(this.ref,
                                         this.pos,

src/main/RemoteRequest.js

@@ -9,71 +9,82 @@
 import Q from 'q';
 import ContigInterval from './ContigInterval';
 
+var BASE_PAIRS_PER_FETCH = 1000;
+var MONSTER_REQUEST = 5000000;
+
 class RemoteRequest {
   url: string;
-  cache: Object;
+  basePairsPerFetch: number;
   numNetworkRequests: number;  // track this for debugging/testing
 
-  constructor(url: string) {
-    this.cache = require('memory-cache');
+  constructor(url: string, basePairsPerFetch?: number) {
     this.url = url;
+    if (!basePairsPerFetch)
+      this.basePairsPerFetch = BASE_PAIRS_PER_FETCH;
+    else
+      this.basePairsPerFetch = basePairsPerFetch;
     this.numNetworkRequests = 0;
   }
 
-  get(contig: string, start: number, stop: number): Q.Promise<Object> {
-    var length = stop - start;
+  expandRange(range: ContigInterval<string>): ContigInterval<string> {
+    var roundDown = x => x - x % this.basePairsPerFetch;
+    var newStart = Math.max(1, roundDown(range.start())),
+        newStop = roundDown(range.stop() + this.basePairsPerFetch - 1);
+
+    return new ContigInterval(range.contig, newStart, newStop);
+  }
+
+  getFeaturesInRange(range: ContigInterval<string>, modifier: string = ""): Q.Promise<Object> {
+    var expandedRange = this.expandRange(range);
+    return this.get(expandedRange, modifier);
+  }
+
+  get(range: ContigInterval<string>, modifier: string = ""): Q.Promise<Object> {
+
+    var length = range.stop() - range.start();
     if (length <= 0) {
       return Q.reject(`Requested <0 interval (${length}) from ${this.url}`);
+    } else if (length > MONSTER_REQUEST) {
+      throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`;
     }
-
-    // First check the cache.
-    var contigInterval = new ContigInterval(contig, start, stop);
-    var buf = this.cache.get(contigInterval);
-    if (buf) {
-      return Q.when(buf);
-    }
-
-    // Need to fetch from the network.
-    return this.getFromNetwork(contig, start, stop);
+    // get endpoint
+    var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier);
+    // Fetch from the network
+    return this.getFromNetwork(endpoint);
   }
 
   /**
    * Request must be of form "url/contig?start=start&end=stop"
   */
-  getFromNetwork(contig: string, start: number, stop: number): Q.Promise<Object> {
-    var length = stop - start;
-    if (length > 5000000) {
-      throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`;
-    }
+  getFromNetwork(endpoint: string): Q.Promise<Object> {
     var xhr = new XMLHttpRequest();
-    var endpoint = this.getEndpointFromContig(contig, start, stop);
     xhr.open('GET', endpoint);
     xhr.responseType = 'json';
     xhr.setRequestHeader('Content-Type', 'application/json');
 
-    return this.promiseXHR(xhr).then(json => {
-      // extract response from promise
-      var buffer = json[0];
-      var contigInterval = new ContigInterval(contig, start, stop);
-      this.cache.put(contigInterval, buffer);
-      return buffer;
+    return this.promiseXHR(xhr).then(e => {
+      // send back response and status
+      return e[0];
     });
   }
 
-  getEndpointFromContig(contig: string, start: number, stop: number): string {
-    return `${this.url}/${contig}?start=${start}&end=${stop}`;
+  getEndpointFromContig(contig: string, start: number, stop: number, modifier: string = ""): string {
+    if (modifier.length < 1)
+      return `${this.url}/${contig}?start=${start}&end=${stop}`;
+    else
+      return `${this.url}/${contig}?start=${start}&end=${stop}&${modifier}`;
   }
 
   // Wrapper to convert XHRs to Promises.
   // The promised values are the response (e.g. an ArrayBuffer) and the Event.
-  promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any, Event]> {
+  promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any]> {
     var url = this.url;
     var deferred = Q.defer();
     xhr.addEventListener('load', function(e) {
       if (this.status >= 400) {
         deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`);
       } else {
-        deferred.resolve([this.response, e]);
+        deferred.resolve([this]);
       }
     });
     xhr.addEventListener('error', function(e) {
@@ -85,4 +96,9 @@ class RemoteRequest {
   }
 }
 
-module.exports = RemoteRequest;
+module.exports = {
+  RemoteRequest,
+  MONSTER_REQUEST: MONSTER_REQUEST
+};
+
+//module.exports = RemoteRequest;