From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Feb 2018 09:32:12 +0000 (+0000)
Subject: JAL-2897 more informative description on synonymous variants
X-Git-Tag: Release_2_11_0~60
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3d3719543b0cb6a65064b169fd9884833e434063;p=jalview.git

JAL-2897 more informative description on synonymous variants

Conflicts:
	test/jalview/analysis/AlignmentUtilsTests.java
---

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 0559e6b..37b93fd 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2218,21 +2218,6 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
 
-    // AAA -> AAG synonymous
-    sf = sfs.get(4);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
-    assertEquals("synonymous_variant", sf.getType());
-    assertEquals("AAG", sf.getDescription());
-    assertEquals("var4", sf.getValue("ID"));
-    assertEquals("None", sf.getValue("clinical_significance"));
-    assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
-    assertEquals(1, sf.links.size());
-    assertEquals(
-            "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
-            sf.links.get(0));
-    assertEquals(cosmic, sf.getFeatureGroup());
-
     // TTT -> TTC synonymous
     sf = sfs.get(5);
     assertEquals(2, sf.getBegin());