JAL-3383 JAL-3253-applet

[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..54102ce 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 +51,9 @@ 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;
+
+  private static boolean useIntervalStore = !Platform.isJS();
 
   /**
    * Constructor
@@ -62,7 +65,7 @@ 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 +99,17 @@ 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()
+  {
+    // TODO Auto-generated method stub
+    return (useIntervalStore ? new FeatureStoreImpl() : new FeatureStoreJS());
+  }
+
   /**
    * {@inheritDoc}
    */
@@ -109,9 +118,9 @@ 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));
+      result.addAll(featureSet.findOverlappingFeatures(from, to, null));
     }
     return result;
   }
@@ -163,7 +172,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       result += featureSet.getFeatureCount(positional);
     }
@@ -178,7 +187,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (FeatureStore featureSet : varargToTypes(type))
+    for (FeatureStoreI featureSet : varargToTypes(type))
     {
       result += featureSet.getTotalFeatureLength();
     }
@@ -193,9 +202,9 @@ 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 +216,7 @@ 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)
     {
@@ -218,9 +227,9 @@ public class SequenceFeatures implements SequenceFeaturesI
     }
 
 
-    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 +247,9 @@ 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 +262,9 @@ 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 +275,7 @@ 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 +291,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public boolean hasFeatures()
   {
-    for (FeatureStore featureSet : featureStore.values())
+    for (FeatureStoreI featureSet : featureStore.values())
     {
       if (!featureSet.isEmpty())
       {
@@ -301,7 +310,7 @@ 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));
     }
@@ -318,7 +327,7 @@ 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);
@@ -345,7 +354,7 @@ 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))
@@ -432,7 +441,7 @@ 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 +458,7 @@ 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 +488,8 @@ 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