JAL-3253-applet JAL-3397 switch back to original (MC) IS+NCList after

[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..cb2b8cc 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -23,6 +23,7 @@ package jalview.datamodel.features;
 import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -50,7 +51,33 @@ public class SequenceFeatures implements SequenceFeaturesI
    * map from feature type to structured store of features for that type
    * null types are permitted (but not a good idea!)
    */
-  private Map<String, FeatureStore> featureStore;
+  private Map<String, FeatureStoreI> featureStore;
+
+  /**
+   * original NCList-based IntervalStore
+   */
+  private final static int INTERVAL_STORE_NCLIST = 0;
+
+  /**
+   * linked-list deferred-sort IntervalStore - experimental only; unused
+   */
+  private final static int INTERVAL_STORE_LINKED_LIST_NO_PRESORT = 1;
+
+  /**
+   * linked-list IntervalStore option for JavaScript
+   */
+  private final static int INTERVAL_STORE_LINKED_LIST = -1;
+
+  /**
+   * mode for Java or JavaScript; can be set differently for testing, but
+   * default is LINKED_LIST for JalviewJS and NCLIST for Java
+   */
+  private final int INTERVAL_STORE_MODE = (
+  // true || //
+  Platform.isJS() ? //
+          INTERVAL_STORE_LINKED_LIST //
+          : INTERVAL_STORE_NCLIST//
+  );
 
   /**
    * Constructor
@@ -62,7 +89,7 @@ public class SequenceFeatures implements SequenceFeaturesI
      * ? wrap as a synchronized map for add and delete operations
      */
     // featureStore = Collections
-    // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
+    // .synchronizedSortedMap(new TreeMap<String, FeatureStoreI>());
     featureStore = new TreeMap<>();
   }
 
@@ -96,11 +123,25 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     if (featureStore.get(type) == null)
     {
-      featureStore.put(type, new FeatureStore());
+      featureStore.put(type, newFeatureStore());
     }
     return featureStore.get(type).addFeature(sf);
   }
 
+  private FeatureStoreI newFeatureStore()
+  {
+    switch (INTERVAL_STORE_MODE)
+    {
+    default:
+    case INTERVAL_STORE_NCLIST:
+      return new FeatureStoreImpl(true);
+    case INTERVAL_STORE_LINKED_LIST_NO_PRESORT:
+      return new FeatureStoreImpl(false);
+    case INTERVAL_STORE_LINKED_LIST:
+      return new FeatureStoreJS();
+    }
+  }
+
   /**
    * {@inheritDoc}
    */
@@ -109,9 +150,13 @@ public class SequenceFeatures implements SequenceFeaturesI
           String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.findOverlappingFeatures(from, to));
+      // System.err.println("SF findFeature " + System.currentTimeMillis()
+      // + " " + from + " " + to + " "
+      // + featureSet.getPositionalFeatures().get(0).type);
+      //
+      result.addAll(featureSet.findOverlappingFeatures(from, to, null));
     }
     return result;
   }
@@ -151,8 +196,8 @@ public class SequenceFeatures implements SequenceFeaturesI
       return new ArrayList<>();
     }
 
-    return getAllFeatures(featureTypes.toArray(new String[featureTypes
-            .size()]));
+    return getAllFeatures(
+            featureTypes.toArray(new String[featureTypes.size()]));
   }
 
   /**
@@ -163,7 +208,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       result += featureSet.getFeatureCount(positional);
     }
@@ -178,7 +223,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       result += featureSet.getTotalFeatureLength();
     }
@@ -193,9 +238,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     List<SequenceFeature> result = new ArrayList<>();
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getPositionalFeatures());
+      featureSet.getPositionalFeatures(result);
     }
     return result;
   }
@@ -207,7 +252,7 @@ public class SequenceFeatures implements SequenceFeaturesI
    * @param type
    * @return
    */
-  protected Iterable<FeatureStore> varargToTypes(String... type)
+  protected Iterable<FeatureStoreI> varargToTypes(String... type)
   {
     if (type == null || type.length == 0)
     {
@@ -217,10 +262,9 @@ public class SequenceFeatures implements SequenceFeaturesI
       return featureStore.values();
     }
 
-
-    List<FeatureStore> types = new ArrayList<>();
+    List<FeatureStoreI> types = new ArrayList<>();
     List<String> args = Arrays.asList(type);
-    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
     {
       if (args.contains(featureType.getKey()))
       {
@@ -238,9 +282,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     List<SequenceFeature> result = new ArrayList<>();
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getContactFeatures());
+      featureSet.getContactFeatures(result);
     }
     return result;
   }
@@ -253,9 +297,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     List<SequenceFeature> result = new ArrayList<>();
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getNonPositionalFeatures());
+      featureSet.getNonPositionalFeatures(result);
     }
     return result;
   }
@@ -266,7 +310,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public boolean delete(SequenceFeature sf)
   {
-    for (FeatureStore featureSet : featureStore.values())
+    for (FeatureStoreI featureSet : featureStore.values())
     {
       if (featureSet.delete(sf))
       {
@@ -282,7 +326,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public boolean hasFeatures()
   {
-    for (FeatureStore featureSet : featureStore.values())
+    for (FeatureStoreI featureSet : featureStore.values())
     {
       if (!featureSet.isEmpty())
       {
@@ -301,7 +345,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     Set<String> groups = new HashSet<>();
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
     }
@@ -318,10 +362,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     Set<String> result = new HashSet<>();
 
-    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
     {
-      Set<String> featureGroups = featureType.getValue().getFeatureGroups(
-              positionalFeatures);
+      Set<String> featureGroups = featureType.getValue()
+              .getFeatureGroups(positionalFeatures);
       for (String group : groups)
       {
         if (featureGroups.contains(group))
@@ -345,7 +389,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureTypes(String... soTerm)
   {
     Set<String> types = new HashSet<>();
-    for (Entry<String, FeatureStore> entry : featureStore.entrySet())
+    for (Entry<String, FeatureStoreI> entry : featureStore.entrySet())
     {
       String type = entry.getKey();
       if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
@@ -389,8 +433,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public float getMinimumScore(String type, boolean positional)
   {
-    return featureStore.containsKey(type) ? featureStore.get(type)
-            .getMinimumScore(positional) : Float.NaN;
+    return featureStore.containsKey(type)
+            ? featureStore.get(type).getMinimumScore(positional)
+            : Float.NaN;
   }
 
   /**
@@ -399,8 +444,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public float getMaximumScore(String type, boolean positional)
   {
-    return featureStore.containsKey(type) ? featureStore.get(type)
-            .getMaximumScore(positional) : Float.NaN;
+    return featureStore.containsKey(type)
+            ? featureStore.get(type).getMaximumScore(positional)
+            : Float.NaN;
   }
 
   /**
@@ -432,7 +478,7 @@ public class SequenceFeatures implements SequenceFeaturesI
           String group, String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       if (featureSet.getFeatureGroups(positional).contains(group))
       {
@@ -449,7 +495,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   public boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     boolean modified = false;
-    for (FeatureStore fs : featureStore.values())
+    for (FeatureStoreI fs : featureStore.values())
     {
       modified |= fs.shiftFeatures(fromPosition, shiftBy);
     }
@@ -479,13 +525,8 @@ public class SequenceFeatures implements SequenceFeaturesI
   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));
+    FeatureStoreI fs = featureStore.get(type);
+    return fs.findOverlappingFeatures(pos, pos, list);
   }
 
   // Chrome; developer console closed
@@ -519,8 +560,6 @@ public class SequenceFeatures implements SequenceFeaturesI
   // 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
    */