JAL-3706 handle e.g. mapped exon feature extending beyond mapped range

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

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 87609c6..2bc82bc 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;
@@ -256,7 +276,8 @@ public class MappedFeatures
 
   /**
    * Answers the mapped ranges (as one or more [start, end] positions) which
-   * correspond to the given [begin, end] range of the linked sequence.
+   * correspond to the given [begin, end] range of (some feature on) the linked
+   * sequence.
    * 
    * <pre>
    * Example: MappedFeatures with CDS features mapped to peptide 
@@ -273,9 +294,36 @@ public class MappedFeatures
    */
   public int[] getMappedPositions(int begin, int end)
   {
+    int[] result = null;
     MapList map = mapping.getMap();
-    return mapping.to == featureSequence ? map.locateInFrom(begin, end)
-            : map.locateInTo(begin, end);
+    
+    /*
+     * mapping may be in either direction, so handle either case;
+     * limit feature extent to the range of the mapping if it is greater
+     * (e.g. an overlapping exon); if that still fails, try reducing by
+     * 3 positions (to omit a mapped stop codon)
+     */
+    if (mapping.to == featureSequence)
+    {
+      begin = Math.max(begin, map.getToLowest());
+      end = Math.min(end,  map.getToHighest());
+      result = map.locateInFrom(begin, end);
+      if (result == null)
+      {
+        result = map.locateInFrom(begin, end-3);
+      }
+    }
+    else
+    {
+      begin = Math.max(begin, map.getFromLowest());
+      end = Math.min(end,  map.getFromHighest());
+      result = map.locateInTo(begin, end);
+      if (result == null)
+      {
+        result = map.locateInTo(begin, end-3);
+      }
+    }
+    return result;
   }
 
   /**