Merge branch 'develop' into features/JAL-2110_crossRefDuplications

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index eb49711..b750973 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -21,6 +21,7 @@
 package jalview.datamodel.xdb.embl;
 
 import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
@@ -34,6 +35,7 @@ import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
+import java.text.ParseException;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
@@ -567,7 +569,7 @@ public class EmblEntry
   }
 
   /**
-   * Returns the CDS positions as a list of [start, end, start, end...]
+   * Returns the CDS positions as a single array of [start, end, start, end...]
    * positions. If on the reverse strand, these will be in descending order.
    * 
    * @param feature
@@ -579,8 +581,18 @@ public class EmblEntry
     {
       return new int[] {};
     }
-    List<int[]> ranges = DnaUtils.parseLocation(feature.location);
-    return ranges == null ? new int[] {} : listToArray(ranges);
+
+    try
+    {
+      List<int[]> ranges = DnaUtils.parseLocation(feature.location);
+      return listToArray(ranges);
+    } catch (ParseException e)
+    {
+      Cache.log.warn(String.format(
+              "Not parsing inexact CDS location %s in ENA %s",
+              feature.location, this.accession));
+      return new int[] {};
+    }
   }
 
   /**