Merge branch 'develop' into feature/JAL-3121gffAttributeMap

[jalview.git] / test / jalview / datamodel / MappedFeaturesTest.java

diff --git a/test/jalview/datamodel/MappedFeaturesTest.java b/test/jalview/datamodel/MappedFeaturesTest.java
index e4caac3..de4ce6c 100644 (file)
--- a/test/jalview/datamodel/MappedFeaturesTest.java
+++ b/test/jalview/datamodel/MappedFeaturesTest.java
@@ -13,7 +13,7 @@ import org.testng.annotations.Test;
 
 public class MappedFeaturesTest
 {
-  @Test
+  @Test(groups = "Functional")
   public void testFindProteinVariants()
   {
     /*
@@ -21,7 +21,7 @@ public class MappedFeaturesTest
      * dna/10-20 aCGTaGctGAa (codons CGT=R, GGA = G)
      * mapping: 3:1 from [11-13,15,18-19] to peptide/1-2 RG 
      */
-    SequenceI from = new Sequence("dna/10-20", "ACGTAGCTGAA");
+    SequenceI from = new Sequence("dna/10-20", "acgTAGCTGAA");
     SequenceI to = new Sequence("peptide", "RG");
     MapList map = new MapList(new int[] { 11, 13, 15, 15, 18, 19 },
             new int[]
@@ -68,13 +68,20 @@ public class MappedFeaturesTest
     assertEquals(variant, "c.13T>C(p.=)");
 
     /*
-     * CSQ:HGVSp value is used if present
+     * CSQ:HGVSp value is used if present 
+     * _and_ it contains "p." following a colon
      */
     Map<String, String> csq = new HashMap<>();
     csq.put("HGVSp", "hello:world");
     sf2.setValue("CSQ", csq);
     variant = mf.findProteinVariants(sf2);
-    assertEquals(variant, "world");
+    assertEquals(variant, "c.13T>C(p.=)");
+    csq.put("HGVSp", "p.HelloWorld");
+    variant = mf.findProteinVariants(sf2);
+    assertEquals(variant, "c.13T>C(p.=)");
+    csq.put("HGVSp", "try this:hellop.world");
+    variant = mf.findProteinVariants(sf2);
+    assertEquals(variant, "hellop.world");
 
     /*
      * missense and indel variants in second codon