X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FMappedFeaturesTest.java;h=f549ff4d2d467f259b2a38a8e5e9c296b52e672b;hb=refs%2Fheads%2Fbug%2FJAL-4313-make-visible-annot-fix;hp=e4caac31860a11b8c592861d10f0f9adeb20053b;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git

diff --git a/test/jalview/datamodel/MappedFeaturesTest.java b/test/jalview/datamodel/MappedFeaturesTest.java
index e4caac3..f549ff4 100644
--- a/test/jalview/datamodel/MappedFeaturesTest.java
+++ b/test/jalview/datamodel/MappedFeaturesTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.Assert.assertEquals;
@@ -13,7 +33,7 @@ import org.testng.annotations.Test;
 
 public class MappedFeaturesTest
 {
-  @Test
+  @Test(groups = "Functional")
   public void testFindProteinVariants()
   {
     /*
@@ -21,7 +41,7 @@ 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[]
@@ -34,8 +54,8 @@ public class MappedFeaturesTest
      * T>C at dna13, consequence CGT>CGC synonymous
      */
     List<SequenceFeature> features = new ArrayList<>();
-    SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T",
-            11, 11, null);
+    SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T", 11,
+            11, null);
     sf1.setValue("alleles", "C,T");
     features.add(sf1);
     SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
@@ -46,8 +66,7 @@ public class MappedFeaturesTest
     /*
      * missense variant in first codon
      */
-    MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R',
-            features);
+    MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R', features);
     String variant = mf.findProteinVariants(sf1);
     assertEquals(variant, "p.Arg1Cys");
 
@@ -68,13 +87,20 @@ 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