JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index df268f8..bbf1b45 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -608,19 +608,19 @@ public class SequenceFeature implements FeatureLocationI
     sb.append(String.format(ROW_DATA, "Location", name,
             begin == end ? begin
                     : begin + (isContactFeature() ? ":" : "-") + end));
+
+    String consequence = "";
     if (mf != null)
     {
-      int[] beginRange = mf.getMappedPositions(begin, begin);
-      int[] endRange = mf.getMappedPositions(end, end);
-      int from = beginRange[0];
-      int to = endRange[endRange.length - 1];
+      int[] localRange = mf.getMappedPositions(begin, end);
+      int from = localRange[0];
+      int to = localRange[localRange.length - 1];
       String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
       sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
               : from + (isContactFeature() ? ":" : "-") + to));
       if (mf.isFromCds())
       {
-        sb.append(String.format(ROW_DATA, "Consequence",
-                mf.findProteinVariants(this), ""));
+        consequence = mf.findProteinVariants(this);
       }
     }
     sb.append(String.format(ROW_DATA, "Type", type, ""));
@@ -635,6 +635,12 @@ public class SequenceFeature implements FeatureLocationI
       sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
     }
 
+    if (!consequence.isEmpty())
+    {
+      sb.append(String.format(ROW_DATA, "Consequence",
+              "<i>Translated by Jalview</i>", consequence));
+    }
+
     if (otherDetails != null)
     {
       TreeMap<String, Object> ordered = new TreeMap<>(