temp push

[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 db2f0e1..bc38942 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -23,8 +23,11 @@ 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;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -44,7 +47,6 @@ import intervalstore.api.IntervalI;
  */
 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!)
@@ -108,12 +110,11 @@ public class SequenceFeatures implements SequenceFeaturesI
           String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
-
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.findOverlappingFeatures(from, to));
+       // BH MUCH more efficient to pass the list
+      featureSet.findFeatures(from, to, result);
     }
-
     return result;
   }
 
@@ -196,7 +197,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getPositionalFeatures());
+      featureSet.getPositionalFeatures(result);
     }
     return result;
   }
@@ -241,7 +242,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getContactFeatures());
+      featureSet.getContactFeatures(result);
     }
     return result;
   }
@@ -256,7 +257,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getNonPositionalFeatures());
+      featureSet.getNonPositionalFeatures(result);
     }
     return result;
   }
@@ -300,7 +301,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureGroups(boolean positionalFeatures,
           String... type)
   {
-    Set<String> groups = new HashSet<>();
+    // BH 2020.03.21 This is the set that orders the list of groups
+    // at the top of the FeatureSettings panel.
+       // In order to keep the same order as a Java HashSet, we must
+       // request that specifically. See Platform.
+    Set<String> groups = Platform.getJavaOrderedHashSet();
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
@@ -317,7 +322,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
           String... groups)
   {
-    Set<String> result = new HashSet<>();
+    // BH 2020.03.21 This set is the one that sets the initial ordering for
+    // feature rendering. We set it to new HashSet<>(16,0.75) to force it to
+    // be backed by a Java hash-ordered HashMap instead of a JavaScript Map.
+    Set<String> result = Platform.getJavaOrderedHashSet();
 
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
     {
@@ -345,7 +353,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public Set<String> getFeatureTypes(String... soTerm)
   {
-    Set<String> types = new HashSet<>();
+    Set<String> types = Platform.getJavaOrderedHashSet();
     for (Entry<String, FeatureStore> entry : featureStore.entrySet())
     {
       String type = entry.getKey();
@@ -373,7 +381,7 @@ 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))
@@ -465,4 +473,24 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     featureStore.clear();
   }
+
+  @Override
+  public List<SequenceFeature> findFeatures(int pos, String type,
+          List<SequenceFeature> list)
+  {
+    FeatureStore fs = featureStore.get(type);
+    if (fs == null)
+    {
+      return list == null ? new ArrayList<>() : list;
+    }
+    return fs.findFeatures(pos, pos, list);
+  }
+
+  @Override
+  public boolean hasFeatures(String type)
+  {
+    return featureStore.containsKey(type)
+            && !featureStore.get(type).isEmpty();
+  }
+
 }