JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places...

[jalview.git] / src / jalview / io / gff / ExonerateHelper.java

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index 91add1a..9ce4cc6 100644 (file)
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.gff;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappingType;
@@ -341,7 +343,7 @@ public class ExonerateHelper extends Gff2Helper
     // e.g. exonerate:protein2genome:local
     if (model != null)
     {
-      String mdl = model.toLowerCase();
+      String mdl = model.toLowerCase(Locale.ROOT);
       if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
               || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
               || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
@@ -353,12 +355,16 @@ public class ExonerateHelper extends Gff2Helper
     return false;
   }
 
+  /**
+   * An override to set feature group to "exonerate" instead of the default GFF
+   * source value (column 2)
+   */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> set)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, set);
-    sf.setFeatureGroup("exonerate");
+    SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+            "exonerate", set);
 
     return sf;
   }