JAL-3187 case-insensitive codon variant calculation

[jalview.git] / src / jalview / datamodel / MappedFeatures.java

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 4b558a5..0fa03cf 100644 (file)
--- 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
     {