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 0d29184..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))
@@ -464,70 +465,4 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     featureStore.clear();
   }
-
-  /**
-   * Simplified find for features associated with a given position.
-   * 
-   * JavaScript set to not use IntervalI, but easily testable by setting false
-   * to true in javadoc
-   * 
-   * FeatureRenderer has checked already that featureStore does contain type.
-   * 
-   * @author Bob Hanson 2019.07.30
-   */
-  @Override
-  public List<SequenceFeature> findFeatures(int pos, String type,
-          List<SequenceFeature> list)
-  {
-    FeatureStore fs = featureStore.get(type);
-    boolean useIntervalStore = /**
-                                * @j2sNative false &&
-                                */
-            true;
-    return (useIntervalStore ? fs.findOverlappingFeatures(pos, pos)
-            : fs.findOverlappingFeatures(pos, list));
-  }
-
-  // Chrome; developer console closed
-
-  // BH 2019.08.01 useIntervalStore true, redraw false:
-  // Platform: timer mark 13.848 0.367 overviewrender 16000 pixels row:14
-  // Platform: timer mark 15.391 0.39 overviewrender 16000 pixels row:14
-  // Platform: timer mark 16.498 0.39 overviewrender 16000 pixels row:14
-  // Platform: timer mark 17.596 0.401 overviewrender 16000 pixels row:14
-  // Platform: timer mark 18.738 0.363 overviewrender 16000 pixels row:14
-  // Platform: timer mark 19.659 0.358 overviewrender 16000 pixels row:14
-  // Platform: timer mark 20.737 0.359 overviewrender 16000 pixels row:14
-  // Platform: timer mark 21.797 0.391 overviewrender 16000 pixels row:14
-  // Platform: timer mark 22.851 0.361 overviewrender 16000 pixels row:14
-  // Platform: timer mark 24.019 0.395 overviewrender 16000 pixels row:14
-
-  // BH 2019.08.01 useIntervalStore false, redraw false:
-  // Platform: timer mark 19.011 0.181 overviewrender 16000 pixels row:14
-  // Platform: timer mark 20.311 0.183 overviewrender 16000 pixels row:14
-  // Platform: timer mark 21.368 0.175 overviewrender 16000 pixels row:14
-  // Platform: timer mark 22.347 0.178 overviewrender 16000 pixels row:14
-  // Platform: timer mark 23.605 0.216 overviewrender 16000 pixels row:14
-  // Platform: timer mark 24.836 0.191 overviewrender 16000 pixels row:14
-  // Platform: timer mark 26.016 0.181 overviewrender 16000 pixels row:14
-  // Platform: timer mark 27.278 0.178 overviewrender 16000 pixels row:14
-  // Platform: timer mark 28.158 0.181 overviewrender 16000 pixels row:14
-  // Platform: timer mark 29.227 0.196 overviewrender 16000 pixels row:14
-  // Platform: timer mark 30.1 0.171 overviewrender 16000 pixels row:14
-  // Platform: timer mark 31.684 0.196 overviewrender 16000 pixels row:14
-  // Platform: timer mark 32.779 0.18 overviewrender 16000 pixels row:14
-  // Platform: timer mark 52.355 0.185 overviewrender 16000 pixels row:14
-  // Platform: timer mark 53.829 0.186 overviewrender 16000 pixels row:14
-
-
-
-  /**
-   * @author Bob Hanson 2019.08.01
-   */
-  @Override
-  public boolean hasFeatures(String type)
-  {
-    return featureStore.containsKey(type);
-  }
-
 }