JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / datamodel / features / SequenceFeatures.java

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 93ee71b..ba8396a 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -109,10 +109,12 @@ public class SequenceFeatures implements SequenceFeaturesI
           String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
+
     for (FeatureStore featureSet : varargToTypes(type))
     {
       result.addAll(featureSet.findOverlappingFeatures(from, to));
     }
+
     return result;
   }
 
@@ -217,7 +219,6 @@ public class SequenceFeatures implements SequenceFeaturesI
       return featureStore.values();
     }
 
-
     List<FeatureStore> types = new ArrayList<>();
     List<String> args = Arrays.asList(type);
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
@@ -372,7 +373,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     for (String term : soTerm)
     {
       if (type.equals(term) || so.isA(type, term))
@@ -464,21 +465,4 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     featureStore.clear();
   }
-
-  /**
-   * Simplified find for features associated with a given position.
-   * 
-   * @author Bob Hanson 2019.07.30
-   */
-  @Override
-  public void findFeatures(int pos, String type, List<SequenceFeature> list)
-  {
-    FeatureStore fs = featureStore.get(type);
-    if (fs != null)
-    {
-      fs.findOverlappingFeatures(pos, list);
-    }
-  }
-
-
 }