JAL-3383 JAL-3253-applet additional efficiencies; FeatureStore

[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 5390975..0d29184 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -109,12 +109,10 @@ 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;
   }
 
@@ -219,6 +217,7 @@ 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())
@@ -373,7 +372,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
       if (type.equals(term) || so.isA(type, term))
@@ -447,13 +446,88 @@ public class SequenceFeatures implements SequenceFeaturesI
    * {@inheritDoc}
    */
   @Override
-  public boolean shiftFeatures(int shift)
+  public boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     boolean modified = false;
     for (FeatureStore fs : featureStore.values())
     {
-      modified |= fs.shiftFeatures(shift);
+      modified |= fs.shiftFeatures(fromPosition, shiftBy);
     }
     return modified;
   }
-}
\ No newline at end of file
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void deleteAll()
+  {
+    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);
+  }
+
+}