From ff96a557835f162306338f1e5dd2769a9fa05db5 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Sun, 18 Nov 2018 09:18:27 -0500
Subject: [PATCH] Don't render click maps when doing arc views

---
 src/JBrowse/View/FeatureGlyph/PairedArc.js |  8 +-------
 src/JBrowse/View/Track/Alignments2.js      | 13 ++++++++++++-
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/JBrowse/View/FeatureGlyph/PairedArc.js b/src/JBrowse/View/FeatureGlyph/PairedArc.js
index be1f2cf496..17507339f3 100644
--- a/src/JBrowse/View/FeatureGlyph/PairedArc.js
+++ b/src/JBrowse/View/FeatureGlyph/PairedArc.js
@@ -2,7 +2,7 @@ define([
     'dojo/_base/declare',
     'dojo/_base/array',
     'dojo/_base/lang',
-    'JBrowse/View/FeatureGlyph/Box',
+    'JBrowse/View/FeatureGlyph/Alignment',
     'JBrowse/View/FeatureGlyph/AlignmentColoring'
 ],
 function(
@@ -18,11 +18,6 @@ function(
             return this._mergeConfigs(lang.clone(this.inherited(arguments)), {
                 style: {
                     color: AlignmentColoring.colorArcs,
-                    color_pair_lr: 'grey',
-                    color_pair_rr: 'navy',
-                    color_pair_rl: 'teal',
-                    color_pair_ll: 'green',
-                    color_nostrand: '#999999',
                     mouseovercolor: 'rgba(0,0,0,0)',
                     strandArrow: false,
                     orientationType: 'fr' // default illumina adapter sequence --> <--
@@ -50,7 +45,6 @@ function(
                     context.lineTo(r.drawTo, 1000)
                 } else {
                     context.arc(r.drawTo + r.r, 0, Math.abs(r.r), 0, Math.PI)
-
                 }
             }
             context.stroke();
diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
index 470158f607..71a00877b6 100644
--- a/src/JBrowse/View/Track/Alignments2.js
+++ b/src/JBrowse/View/Track/Alignments2.js
@@ -4,6 +4,7 @@ define( [
             'dijit/MenuItem',
             'JBrowse/Util',
             'JBrowse/View/Track/CanvasFeatures',
+            'JBrowse/View/Track/BlockBased',
             'JBrowse/View/Track/_AlignmentsMixin'
         ],
         function(
@@ -12,6 +13,7 @@ define( [
             MenuItem,
             Util,
             CanvasFeatureTrack,
+			BlockBased,
             AlignmentsMixin
         ) {
 
@@ -42,7 +44,7 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 viewAsPairs: false,
                 viewAsSpans: false,
                 showInterchromosomalArcs: true,
-                maxInsertSize: 200000,
+                maxInsertSize: 2000000,
 
                 histograms: {
                     description: 'coverage depth',
@@ -264,6 +266,15 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
         this.addFeatureFilter(feat => {
             return (this.config.viewAsPairs && feat.get('end') - feat.get('start') < this.config.maxInsertSize) || !this.config.viewAsPairs
         })
+    },
+
+    renderClickMap() {
+        if(this.config.glyph == 'JBrowse/View/FeatureGlyph/PairedArc'
+        || this.config.glyph == 'JBrowse/View/FeatureGlyph/PairedReadCloud') {
+            return
+        } else {
+            this.inherited(arguments)
+        }
     }
 });
 });