JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 87609c6..57c8c37 100644 (file)
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.util.HashSet;
@@ -274,8 +294,8 @@ public class MappedFeatures
   public int[] getMappedPositions(int begin, int end)
   {
     MapList map = mapping.getMap();
-    return mapping.to == featureSequence ? map.locateInFrom(begin, end)
-            : map.locateInTo(begin, end);
+    return mapping.to == featureSequence ? map.getOverlapsInFrom(begin, end)
+            : map.getOverlapsInTo(begin, end);
   }
 
   /**