From e6a0555667da6a865b0428ff0484f696874ad731 Mon Sep 17 00:00:00 2001
From: Jim Robinson <jrobinso@broadinstitute.org>
Date: Thu, 19 Nov 2020 09:10:58 -0800
Subject: [PATCH] Bug fix -- annotation tracks not searchable.   See issue
 #1227

---
 js/bigwig/bwSource.js           | 4 ++--
 js/feature/featureSource.js     | 8 ++++----
 js/feature/featureTrack.js      | 9 ++++-----
 js/feature/textFeatureSource.js | 8 +++++---
 js/tdf/tdfSource.js             | 4 ++--
 5 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/js/bigwig/bwSource.js b/js/bigwig/bwSource.js
index b5f60179a..bc6a19ffb 100755
--- a/js/bigwig/bwSource.js
+++ b/js/bigwig/bwSource.js
@@ -28,9 +28,9 @@ import pack from "../feature/featurePacker.js";
 
 class BWSource {
 
-    constructor(config, genome) {
+    constructor(config, browser) {
         this.reader = new BWReader(config, genome);
-        this.genome = genome;
+        this.genome = browser.genome;
         this.format = config.format || "bigwig";
         this.wgValues = {};
     }
diff --git a/js/feature/featureSource.js b/js/feature/featureSource.js
index 0fe8b7865..8a755594a 100755
--- a/js/feature/featureSource.js
+++ b/js/feature/featureSource.js
@@ -28,15 +28,15 @@ import BWSource from "../bigwig/bwSource.js"
 import TDFSource from "../tdf/tdfSource.js"
 
 
-function FeatureSource(config, genome) {
+function FeatureSource(config, browser) {
 
     const format = config.format ? config.format.toLowerCase() : undefined;
     if ('bigwig' === format || 'bigbed' === format || 'bb' === format) {
-        return new BWSource(config, genome);
+        return new BWSource(config, browser);
     } else if ("tdf" === format) {
-        return new TDFSource(config, genome);
+        return new TDFSource(config, browser);
     } else {
-        return new TextFeatureSource(config, genome);
+        return new TextFeatureSource(config, browser);
     }
 }
 
diff --git a/js/feature/featureTrack.js b/js/feature/featureTrack.js
index 263744ccc..9fcfbe8a1 100755
--- a/js/feature/featureTrack.js
+++ b/js/feature/featureTrack.js
@@ -61,7 +61,7 @@ class FeatureTrack extends TrackBase {
         } else {
             this.featureSource = config.featureSource ?
                 config.featureSource :
-                FeatureSource(config, browser.genome);
+                FeatureSource(config, browser);
         }
 
         // Set default heights
@@ -144,8 +144,7 @@ class FeatureTrack extends TrackBase {
     async getFeatures(chr, start, end, bpPerPixel) {
         const visibilityWindow = this.visibilityWindow;
         return this.featureSource.getFeatures({chr, start, end, bpPerPixel, visibilityWindow});
-    };
-
+    }
 
     /**
      * The required height in pixels required for the track content.   This is not the visible track height, which
@@ -175,7 +174,7 @@ class FeatureTrack extends TrackBase {
 
         }
 
-    };
+    }
 
     draw(options) {
 
@@ -237,7 +236,7 @@ class FeatureTrack extends TrackBase {
             console.log("No feature list");
         }
 
-    };
+    }
 
     clickedFeatures(clickState) {
 
diff --git a/js/feature/textFeatureSource.js b/js/feature/textFeatureSource.js
index 2fafe5933..345630940 100644
--- a/js/feature/textFeatureSource.js
+++ b/js/feature/textFeatureSource.js
@@ -45,9 +45,11 @@ import pack from "../feature/featurePacker.js";
  */
 class TextFeatureSource {
 
-    constructor(config, genome) {
+    constructor(config, browser) {
 
+        const genome = browser.genome;
         this.config = config || {};
+        this.browser = browser;
         this.genome = genome;
         this.sourceType = (config.sourceType === undefined ? "file" : config.sourceType);
         this.visibilityWindow = config.visibilityWindow;
@@ -232,10 +234,10 @@ class TextFeatureSource {
         for (let feature of featureList) {
             if (feature.name) {
                 //TODO igv.browser => igv.Globals or igv.FeatureDB
-                this.config.browser.featureDB[feature.name.toUpperCase()] = feature;
+                this.browser.featureDB[feature.name.toUpperCase()] = feature;
             }
             if (feature.gene && feature.gene.name) {
-                this.config.browser.featureDB[feature.gene.name.toUpperCase()] = feature;
+                this.browser.featureDB[feature.gene.name.toUpperCase()] = feature;
             }
         }
     }
diff --git a/js/tdf/tdfSource.js b/js/tdf/tdfSource.js
index 5fa71b159..46d6193de 100644
--- a/js/tdf/tdfSource.js
+++ b/js/tdf/tdfSource.js
@@ -29,9 +29,9 @@ import GenomicInterval from "../genome/genomicInterval.js";
 
 class TDFSource {
 
-    constructor(config, genome) {
+    constructor(config, browser) {
 
-        this.genome = genome;
+        this.genome = browser.genome;
         this.windowFunction = config.windowFunction || "mean";
         this.reader = new TDFReader(config, genome);
     }