Merge branch 'spikes/mungo' into trialMerge

Conflicts:
	src/jalview/analysis/AlignmentUtils.java
	test/jalview/analysis/AlignmentUtilsTests.java

diff --cc src/jalview/analysis/AlignmentUtils.java
Simple merge

diff --cc test/jalview/analysis/AlignmentUtilsTests.java
index be6ba60,37b93fd..2b45eee
--- 1/test/jalview/analysis/AlignmentUtilsTests.java
--- 2/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@@ -2208,13 -2208,13 +2208,28 @@@ public class AlignmentUtilsTest
      assertEquals(1, sf.getBegin());
      assertEquals(1, sf.getEnd());
      assertEquals("synonymous_variant", sf.getType());
 -    assertEquals("aaA/aaG", sf.getDescription());
 +    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(
 -            "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
++            "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
++            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());