JAL-3725 restrict mapped virtual feature location to mapped region

[jalview.git] / src / jalview / io / SequenceAnnotationReport.java

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 27c1652..a4c4895 100644 (file)
--- 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
      */
      * 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)
     {
     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
       if (beginRange == null || endRange == null)
       {
         // something went wrong