X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=ce71f02390e435b1b216349084e174b0c94af254;hb=refs%2Fheads%2Fbug%2FJAL-3725overlappingVirtualFeatures;hp=8e4e78305e2c41e01d172b21eee8babf757cf1c5;hpb=3080e71dc351c70df9b01ecc58fb063de898c724;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8e4e783..ce71f02 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -207,12 +207,27 @@ public class SequenceAnnotationReport
      * if this is a virtual features, convert begin/end to the
      * coordinates of the sequence it is mapped to
      */
-    int[] beginRange = null;
-    int[] endRange = null;
+    int[] beginRange = null; // feature start in local coordinates
+    int[] endRange = null; // feature end in local coordinates
     if (mf != null)
     {
-      beginRange = mf.getMappedPositions(begin, begin);
-      endRange = mf.getMappedPositions(end, end);
+      if (feature.isContactFeature())
+      {
+        /*
+         * map start and end points individually
+         */
+        beginRange = mf.getMappedPositions(begin, begin);
+        endRange = begin == end ? beginRange
+                : mf.getMappedPositions(end, end);
+      }
+      else
+      {
+        /*
+         * map the feature extent
+         */
+        beginRange = mf.getMappedPositions(begin, end);
+        endRange = beginRange;
+      }
       if (beginRange == null || endRange == null)
       {
         // something went wrong