From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 22 Aug 2019 15:06:05 +0000 (+0100)
Subject: JAL-3187 case-insensitive codon variant calculation
X-Git-Tag: Release_2_11_1_0~22^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=be38fa8acaa8061b501a4e94fb7dea4b7ed8ed41;p=jalview.git

JAL-3187 case-insensitive codon variant calculation
---

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 4b558a5..0fa03cf 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -91,9 +91,12 @@ public class MappedFeatures
       codonPos = codonPositions;
       baseCodon = new char[3];
       int cdsStart = fromSeq.getStart();
-      baseCodon[0] = fromSeq.getCharAt(codonPos[0] - cdsStart);
-      baseCodon[1] = fromSeq.getCharAt(codonPos[1] - cdsStart);
-      baseCodon[2] = fromSeq.getCharAt(codonPos[2] - cdsStart);
+      baseCodon[0] = Character
+              .toUpperCase(fromSeq.getCharAt(codonPos[0] - cdsStart));
+      baseCodon[1] = Character
+              .toUpperCase(fromSeq.getCharAt(codonPos[1] - cdsStart));
+      baseCodon[2] = Character
+              .toUpperCase(fromSeq.getCharAt(codonPos[2] - cdsStart));
     }
     else
     {
diff --git a/test/jalview/datamodel/MappedFeaturesTest.java b/test/jalview/datamodel/MappedFeaturesTest.java
index e4caac3..de4ce6c 100644
--- 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