Dataset.createTransformers fix for DatasetView/TransformTrainer (#364)

* Fix a bug where transformations would be incorrectly computed if called on a DatasetView.

* Fix copyright year.

* More fixes for things which access Dataset.data when they shouldn't. Also a fix for DatasetView's provenance recording which was picking up the wrong indices field.

* Fixing copyright.

* More fixing copyright.

Core/src/main/java/org/tribuo/Dataset.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015, 2022, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2015, 2024, Oracle and/or its affiliates. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -72,7 +72,7 @@ public abstract class Dataset<T extends Output<T>> implements Iterable<Example<T
     /**
      * Users of this RNG should synchronize on the Dataset to prevent replicability issues.
      */
-    private static final SplittableRandom rng = new SplittableRandom(Trainer.DEFAULT_SEED);
+    protected static final SplittableRandom rng = new SplittableRandom(Trainer.DEFAULT_SEED);
 
     /**
      * The data in this data set.
@@ -395,7 +395,7 @@ public TransformerMap createTransformers(TransformationMap transformations, bool
             }
             // Add the queue to the map for that feature
             featureStats.put(entry.getKey(),l);
-            sparseCount.put(entry.getKey(), new MutableLong(data.size()));
+            sparseCount.put(entry.getKey(), new MutableLong(size()));
         }
         if (!transformations.getGlobalTransformations().isEmpty()) {
             // Append all the global transformations
@@ -411,7 +411,7 @@ public TransformerMap createTransformers(TransformationMap transformations, bool
                 // Add the queue to the map for that feature
                 featureStats.put(v, l);
                 // Generate the sparse count initialised to the number of features.
-                sparseCount.putIfAbsent(v, new MutableLong(data.size()));
+                sparseCount.putIfAbsent(v, new MutableLong(size()));
                 ndone++;
                 if(logger.isLoggable(Level.FINE) && ndone % 10000 == 0) {
                     logger.fine(String.format("Completed %,d of %,d global transformations", ndone, ntransform));
@@ -424,7 +424,7 @@ public TransformerMap createTransformers(TransformationMap transformations, bool
         boolean initialisedSparseCounts = false;
         // Iterate through the dataset max(transformations.length) times.
         while (!featureStats.isEmpty()) {
-            for (Example<T> example : data) {
+            for (Example<T> example : this) {
                 for (Feature f : example) {
                     if (featureStats.containsKey(f.getName())) {
                         if (!initialisedSparseCounts) {

Core/src/main/java/org/tribuo/dataset/DatasetView.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015, 2022, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2015, 2024, Oracle and/or its affiliates. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -373,9 +373,22 @@ public ImmutableOutputInfo<T> getOutputInfo() {
         return outputIDInfo;
     }
 
+    @Override
+    public synchronized void shuffle(boolean shuffle) {
+        if (shuffle) {
+            indices = Util.randperm(size(), rng);
+        } else {
+            indices = null;
+        }
+    }
+
     @Override
     public Iterator<Example<T>> iterator() {
-        return new ViewIterator<>(this);
+        if (indices != null) {
+            return new ShuffledViewIterator<>(this);
+        } else{
+            return new ViewIterator<>(this);
+        }
     }
 
     @Override
@@ -459,6 +472,29 @@ private static boolean validateIndices(int size, int[] indices) {
         return valid;
     }
 
+    private static final class ShuffledViewIterator<T extends Output<T>> implements Iterator<Example<T>> {
+
+        private int counter = 0;
+        private final DatasetView<T> dataset;
+
+        ShuffledViewIterator(DatasetView<T> dataset) {
+            this.dataset = dataset;
+        }
+
+        @Override
+        public boolean hasNext() {
+            return counter < dataset.size();
+        }
+
+        @Override
+        public Example<T> next() {
+            Example<T> example = dataset.getExample(dataset.indices[counter]);
+            counter++;
+            return example;
+        }
+
+    }
+
     private static final class ViewIterator<T extends Output<T>> implements Iterator<Example<T>> {
 
         private int counter = 0;
@@ -509,7 +545,7 @@ <T extends Output<T>> DatasetViewProvenance(DatasetView<T> dataset, boolean stor
             this.weighted = new BooleanProvenance(WEIGHTED,dataset.weighted);
             this.sampled = new BooleanProvenance(SAMPLED,dataset.sampled);
             this.tag = new StringProvenance(TAG,dataset.tag);
-            this.indices = storeIndices ? dataset.indices : new int[0];
+            this.indices = storeIndices ? dataset.exampleIndices : new int[0];
         }
 
         /**
@@ -525,7 +561,7 @@ public DatasetViewProvenance(Map<String,Provenance> map) {
             this.sampled = ObjectProvenance.checkAndExtractProvenance(map,SAMPLED,BooleanProvenance.class, DatasetViewProvenance.class.getSimpleName());
             @SuppressWarnings("unchecked") // List provenance cast
             ListProvenance<IntProvenance> listIndices = ObjectProvenance.checkAndExtractProvenance(map,INDICES,ListProvenance.class, DatasetViewProvenance.class.getSimpleName());
-            if (listIndices.getList().size() > 0) {
+            if (!listIndices.getList().isEmpty()) {
                 try {
                     IntProvenance i = listIndices.getList().get(0);
                 } catch (ClassCastException e) {