X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=a4c489572e885a216e8e9308af3c53392fffaee1;hp=27c1652943c77b81c4bee965bed0d052b04f2cff;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hpb=c17981672620e0b780a2338bd0c74e55cf9ddec2

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 27c1652..a4c4895 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -210,12 +210,27 @@ 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