From d9e4474edddcda243120cc252f3bbd4b94e93094 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Thu, 23 Nov 2017 16:40:57 +0100
Subject: [PATCH 1/3] js/clone.js: remove dead code on .shortName

This was never used, due to a always false condition in .getCode().
See #2892.
---
 browser/js/clone.js | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/browser/js/clone.js b/browser/js/clone.js
index 822b6241f..23ea1bc4b 100644
--- a/browser/js/clone.js
+++ b/browser/js/clone.js
@@ -48,15 +48,7 @@ function Clone(data, model, index, virtual) {
     }
 
     this.seg = this.m.convertSeg(this.seg)
-    
-    if (typeof (this.getSequence()) != 'undefined' && typeof (this.name) != 'undefined') {
-        this.shortName = this.name.replace(new RegExp('IGHV', 'g'), "VH");
-        this.shortName = this.shortName.replace(new RegExp('IGHD', 'g'), "DH");
-        this.shortName = this.shortName.replace(new RegExp('IGHJ', 'g'), "JH");
-        this.shortName = this.shortName.replace(new RegExp('TRG', 'g'), "");
-        this.shortName = this.shortName.replace(new RegExp('\\*..', 'g'), "");
-    }
-    
+        
     this.m.clusters[index]=[index]
     this.m.clones[index]=this
     this.tag = this.getTag();
-- 
GitLab


From f0f8092dad9201ac4011c19d28626ddc526c66e3 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Thu, 23 Nov 2017 16:48:00 +0100
Subject: [PATCH 2/3] js/clone.js: extract 'computeShortName' from
 'getShortName'

We do not want to re-compute the clone name at each update.
Not directly related to #2892.
---
 browser/js/clone.js | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/browser/js/clone.js b/browser/js/clone.js
index 23ea1bc4b..eb8decfdd 100644
--- a/browser/js/clone.js
+++ b/browser/js/clone.js
@@ -55,6 +55,8 @@ function Clone(data, model, index, virtual) {
     this.computeGCContent()
     this.computeCoverage()
     this.computeEValue()
+
+    this.computeShortName()
 }
 
 function nullIfZero(x) { return (x === 0 || x === '0') ? '' : x }
@@ -102,7 +104,12 @@ Clone.prototype = {
         return size;
     },
 
-    getShortName: function () {
+
+    /**
+     * Compute a .shortName from .getName()
+     */
+
+    computeShortName: function () {
 
         name_items = this.getName().split(' ')
         short_name_items = []
@@ -164,7 +171,11 @@ Clone.prototype = {
             short_name_items.push(s)
         }
 
-        return short_name_items.join(' ')
+        this.shortName = short_name_items.join(' ')
+    },
+
+    getShortName: function () {
+        return this.shortName
     },
 
     /**
-- 
GitLab


From 80d43b36acb843e1f3ecf2d01513d852f61cc081 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Fri, 24 Nov 2017 11:10:00 +0100
Subject: [PATCH 3/3] js/model.js: calls clone.computeShortName() when needed

Not directly related to #2892.
---
 browser/js/model.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/browser/js/model.js b/browser/js/model.js
index 3a489a768..b333bcccf 100644
--- a/browser/js/model.js
+++ b/browser/js/model.js
@@ -297,12 +297,18 @@ Model.prototype = {
 
 changeCloneNotation: function(cloneNotationType) {
     this.cloneNotationType = cloneNotationType;
+
+    for (var i = 0; i < this.clones.length; i++)
+        this.clone(i).computeShortName()
     this.update();
 },
 
 
 changeAlleleNotation: function(alleleNotation) {
     this.alleleNotation = alleleNotation;
+
+    for (var i = 0; i < this.clones.length; i++)
+        this.clone(i).computeShortName()
     this.update();
 },
     
-- 
GitLab