X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=727d3ef8b243d5c45048845f7e81283f2649bb33;hb=1cb8662ae0ce8b7c29fa510809a6e883c769dcdc;hp=52da8c793b81ccc531a15f35fd9d8ca5c901a775;hpb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 52da8c7..727d3ef 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.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.features;
 
 import jalview.datamodel.ContiguousI;
@@ -67,7 +87,7 @@ public class SequenceFeatures implements SequenceFeaturesI
      */
     // featureStore = Collections
     // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
-    featureStore = new TreeMap<String, FeatureStore>();
+    featureStore = new TreeMap<>();
   }
 
   /**
@@ -149,6 +169,14 @@ public class SequenceFeatures implements SequenceFeaturesI
     }
 
     Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+    if (featureTypes.isEmpty())
+    {
+      /*
+       * no features of the specified type or any sub-type
+       */
+      return new ArrayList<>();
+    }
+
     return getAllFeatures(featureTypes.toArray(new String[featureTypes
             .size()]));
   }
@@ -354,9 +382,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   }
 
   /**
-   * Answers true if the given type is one of the specified sequence ontology
-   * terms (or a sub-type of one), or if no terms are supplied. Answers false if
-   * filter terms are specified and the given term does not match any of them.
+   * Answers true if the given type matches one of the specified terms (or is a
+   * sub-type of one in the Sequence Ontology), or if no terms are supplied.
+   * Answers false if filter terms are specified and the given term does not
+   * match any of them.
    * 
    * @param type
    * @param soTerm
@@ -371,7 +400,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     for (String term : soTerm)
     {
-      if (so.isA(type, term))
+      if (type.equals(term) || so.isA(type, term))
       {
         return true;
       }