samoa-instances/src/main/java/org/apache/samoa/instances/Instances.java - incubator-samoa - Git at Google

 package org.apache.samoa.instances;

 import java.io.InputStream;

 /*
  * #%L
  * SAMOA
  * %%
  * Copyright (C) 2014 - 2015 Apache Software Foundation
  * %%
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
  *
  *      http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * #L%
  */

 import java.io.Reader;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Random;

 /**
  * Class Instances that stores a set of instances and their structure.
  */
 public class Instances implements Serializable {

   /**
    * The keyword used to denote the start of an arff header
    */
   public final static String ARFF_RELATION = "@relation";

   /**
    * The keyword used to denote the start of the arff data section
    */
   public final static String ARFF_DATA = "@data";

   private static final long serialVersionUID = 8110510475535581577L;
   /**
    * The instance information.
    */
   protected InstanceInformation instanceInformation;
   /**
    * The instances.
    */
   protected List<Instance> instances;

   protected static enum AVRO_ENCODING_FORMAT {
     JSON, BINARY
   }

   protected int classAttribute;

   /**
    * A Hash that stores the indices of features.
    */
   protected HashMap<String, Integer> hsAttributesIndices;

   transient protected Loader loader;

 /**
    * Indices of relevant features.
    */
   protected int[] indicesRelevants;

   /**
    * Indices of irrelevant features.
    */
   protected int[] indicesIrrelevants;

   /**
    * Instantiates a new instances.
    *
    * @param chunk the chunk
    */
   public Instances(Instances chunk) {
     this(chunk, chunk.numInstances());
     chunk.copyInstances(0, this, chunk.numInstances());
     this.computeAttributesIndices();
     if(chunk.indicesRelevants != null) {
         this.indicesRelevants = chunk.indicesRelevants.clone();
         this.indicesIrrelevants = chunk.indicesIrrelevants.clone();
     }
   }

   /**
    * Instantiates a new instances.
    */
   public Instances() {
   }

   /**
    * Instantiates a new instances.
    *
    * @param reader the reader
    * @param size the size
    * @param classAttribute the class attribute
    */
   public Instances(Reader reader, int size, int classAttribute) {
     this.loader = new ArffLoader(reader, 0, classAttribute);
     this.instanceInformation = loader.getStructure();
     this.instances = new ArrayList<Instance>();
     this.computeAttributesIndices();
   }

   /**
    * Instantiates a new instances.
    *
    * @param reader the reader
    * @param range
    */
   public Instances(Reader reader, Range range) {
     this.loader = new MultiTargetArffLoader(reader, range); //new ArffLoader(reader, 0, classAttribute);
     this.instanceInformation = loader.getStructure();
     this.instances = new ArrayList<Instance>();
     this.computeAttributesIndices();
   }

   public Instances(InputStream inputStream, int classAttribute, String encodingFormat) {
     this.classAttribute = classAttribute;

     if (encodingFormat.equalsIgnoreCase(AVRO_ENCODING_FORMAT.BINARY.toString()))
       loader = new AvroBinaryLoader(inputStream, classAttribute);
     else
       loader = new AvroJsonLoader(inputStream, classAttribute);

     this.instanceInformation = loader.getStructure();
     this.instances = new ArrayList<>();
   }

   /**
    * Instantiates a new instances.
    *
    * @param chunk the chunk
    * @param capacity the capacity
    */
   public Instances(Instances chunk, int capacity) {
     this.instanceInformation = chunk.instanceInformation();
     if (capacity < 0) {
       capacity = 0;
     }
     this.instances = new ArrayList<Instance>(capacity);
     this.computeAttributesIndices();
     if(chunk.indicesRelevants != null) {
         this.indicesRelevants = chunk.indicesRelevants.clone();
         this.indicesIrrelevants = chunk.indicesIrrelevants.clone();
     }
   }

     /**
      * Instantiates a new instances.
      *
      * @param st the st
      * @param v the v
      * @param capacity the capacity
      */
     public Instances(String st, Attribute[] v, int capacity) {
       this.instanceInformation = new InstanceInformation(st, v);
       this.instances = new ArrayList<Instance>(capacity);
       this.computeAttributesIndices();
   }

   /**
    * Instantiates a new instances.
    *
    * @param st the st
    * @param v the v
    * @param capacity the capacity
    */
   public Instances(String st, List<Attribute> v, int capacity) {
     Attribute[] attributes = new Attribute[v.size()];
     for (int i = 0; i < v.size(); i++) {
         attributes[i]= v.get(i);
     }
     this.instanceInformation = new InstanceInformation(st, attributes);
     this.instances = new ArrayList<Instance>(capacity);
     this.computeAttributesIndices();
   }

   /**
    * Instantiates a new instances.
    *
    * @param chunk the chunk
    * @param first the first instance
    * @param toCopy the j
    */
   public Instances(Instances chunk, int first, int toCopy) {

     this(chunk, toCopy);

     if ((first < 0) || ((first + toCopy) > chunk.numInstances())) {
       throw new IllegalArgumentException("Parameters first and/or toCopy out "
           + "of range");
     }
     chunk.copyInstances(first, this, toCopy);
     this.computeAttributesIndices();
   }

   /**
    * Instantiates a new instances.
    *
    * @param st the st
    * @param capacity the capacity
    */
   public Instances(StringReader st, int capacity) {
     this.instances = new ArrayList<Instance>(capacity);
     this.computeAttributesIndices();
   }

   //Information Instances
   /**
    * Sets the relation name.
    *
    * @param string the new relation name
    */
   public void setRelationName(String string) {
     this.instanceInformation.setRelationName(string);
   }

   /**
    * Gets the relation name.
    *
    * @return the relation name
    */
   public String getRelationName() {
     return this.instanceInformation.getRelationName();
   }

   /**
    * Class index.
    *
    * @return the int
    */
   public int classIndex() {
     return this.instanceInformation.classIndex();
   }

   /**
    * Sets the class index.
    *
    * @param classIndex the new class index
    */
   public void setClassIndex(int classIndex) {
     this.instanceInformation.setClassIndex(classIndex);
   }

   /**
    * Class attribute.
    *
    * @return the attribute
    */
   public Attribute classAttribute() {
     return this.instanceInformation.classAttribute();
   }

   /**
    * Num attributes.
    *
    * @return the int
    */
   public int numAttributes() {
     return this.instanceInformation.numAttributes();
   }

   /**
    * Attribute.
    *
    * @param w the w
    * @return the attribute
    */
   public Attribute attribute(int w) {
     return this.instanceInformation.attribute(w);
   }

   /**
    * Num classes.
    *
    * @return the int
    */
   public int numClasses() {
     return this.instanceInformation.numClasses();
   }

   /**
    * Delete attribute at.
    *
    * @param integer the integer
    */
   public void deleteAttributeAt(Integer integer) {
     this.instanceInformation.deleteAttributeAt(integer);
     for (int i = 0; i < numInstances(); i++) {
       instance(i).setDataset(null);
       instance(i).deleteAttributeAt(integer);
       instance(i).setDataset(this);
   }
   }

   /**
      * Insert attribute at.
      *
      * @param attribute the attribute
      * @param position the position
      */
     public void insertAttributeAt(Attribute attribute, int position) {
       if (this.instanceInformation == null) {
           this.instanceInformation = new InstanceInformation();
       }
       this.instanceInformation.insertAttributeAt(attribute, position);
       for (int i = 0; i < numInstances(); i++) {
           instance(i).setDataset(null);
           instance(i).insertAttributeAt(i);
           instance(i).setDataset(this);
       }
   }


   //List of Instances
   /**
    * Instance.
    *
    * @param num the num
    * @return the instance
    */
   public Instance instance(int num) {
     return this.instances.get(num);
   }

   /**
    * Num instances.
    *
    * @return the int
    */
   public int numInstances() {
     return this.instances.size();
   }

   /**
    * Adds the.
    *
    * @param inst the inst
    */
   public void add(Instance inst) {
     this.instances.add(inst);
   }

   /**
    * Randomize.
    *
    * @param random the random
    */
   public void randomize(Random random) {
     for (int j = numInstances() - 1; j > 0; j--) {
       swap(j, random.nextInt(j + 1));
     }
   }

   /**
    * Stratify.
    *
    * @param numFolds the num folds
    */
   public void stratify(int numFolds) {

     if (classAttribute().isNominal()) {

       // sort by class
       int index = 1;
       while (index < numInstances()) {
         Instance instance1 = instance(index - 1);
         for (int j = index; j < numInstances(); j++) {
           Instance instance2 = instance(j);
           if ((instance1.classValue() == instance2.classValue())
               || (instance1.classIsMissing()
                   && instance2.classIsMissing())) {
             swap(index, j);
             index++;
           }
         }
         index++;
       }
       stratStep(numFolds);
     }
   }

   protected void stratStep(int numFolds) {
     ArrayList<Instance> newVec = new ArrayList<Instance>(this.instances.size());
     int start = 0, j;

     // create stratified batch
     while (newVec.size() < numInstances()) {
       j = start;
       while (j < numInstances()) {
         newVec.add(instance(j));
         j = j + numFolds;
       }
       start++;
     }
     this.instances = newVec;
   }

   /**
    * Train cv.
    *
    * @param numFolds the num folds
    * @param numFold
    * @param random the random
    * @return the instances
    */
   public Instances trainCV(int numFolds, int numFold, Random random) {
     Instances train = trainCV(numFolds, numFold);
     train.randomize(random);
     return train;
   }

   public Instances trainCV(int numFolds, int numFold) {
     int numInstForFold, first, offset;
     Instances train;

     numInstForFold = numInstances() / numFolds;
     if (numFold < numInstances() % numFolds) {
       numInstForFold++;
       offset = numFold;
     } else {
       offset = numInstances() % numFolds;
     }
     train = new Instances(this, numInstances() - numInstForFold);
     first = numFold * (numInstances() / numFolds) + offset;
     copyInstances(0, train, first);
     copyInstances(first + numInstForFold, train,
         numInstances() - first - numInstForFold);
     return train;
   }

   protected void copyInstances(int from, Instances dest, int num) {
     for (int i = 0; i < num; i++) {
       dest.add(instance(from + i));
     }
   }

   /**
    * Test cv.
    *
    * @param numFolds the num folds
    * @param numFold the num fold
    * @return the instances
    */
   public Instances testCV(int numFolds, int numFold) {

     int numInstForFold, first, offset;
     Instances test;

     numInstForFold = numInstances() / numFolds;
     if (numFold < numInstances() % numFolds) {
       numInstForFold++;
       offset = numFold;
     } else {
       offset = numInstances() % numFolds;
     }
     test = new Instances(this, numInstForFold);
     first = numFold * (numInstances() / numFolds) + offset;
     copyInstances(first, test, numInstForFold);
     return test;
   }

   /*  public Instances dataset() {
      throw new UnsupportedOperationException("Not yet implemented");
      }*/
   /**
    * Mean or mode.
    *
    * @param j the j
    * @return the double
    */
   public double meanOrMode(int j) {
     throw new UnsupportedOperationException("Not yet implemented"); //CobWeb
   }

   /**
    * Read instance.
    *
    * @param fileReader the file reader
    * @return true, if successful
    */
   public boolean readInstance(Reader fileReader) {

     //ArffReader arff = new ArffReader(reader, this, m_Lines, 1);
     if (loader == null) {
       loader = new ArffLoader(fileReader, 0, this.classAttribute);
     }
     Instance inst = loader.readInstance();
     if (inst != null) {
       inst.setDataset(this);
       add(inst);
       return true;
     } else {
       return false;
     }
   }

   public boolean readInstance() {

     Instance inst = loader.readInstance();
     if (inst != null) {
       inst.setDataset(this);
       add(inst);
       return true;
     } else {
       return false;
     }
   }

   /**
    * Delete.
    */
   public void delete() {
     this.instances = new ArrayList<Instance>();
   }

   /**
    * Delete.
    */
   public void delete(int index) {
     this.instances.remove(index);
   }

   /**
    * Swap.
    *
    * @param i the i
    * @param j the j
    */
   public void swap(int i, int j) {
     Instance in = instances.get(i);
     instances.set(i, instances.get(j));
     instances.set(j, in);
   }

   /**
    * Instance information.
    *
    * @return the instance information
    */
   private InstanceInformation instanceInformation() {
     return this.instanceInformation;
   }

   public Attribute attribute(String name) {

     for (int i = 0; i < numAttributes(); i++) {
       if (attribute(i).name().equals(name)) {
         return attribute(i);
       }
     }
     return null;
   }

   public int size() {
     return this.numInstances();
   }

   public void set(int i, Instance inst) {
     this.instances.set(i, inst);
   }

   public Instance get(int k) {
     return this.instance(k);
   }

   public void setRangeOutputIndices(Range range) {
     this.instanceInformation.setRangeOutputIndices(range);

   }

  public void setAttributes(Attribute[] v) {
     if (this.instanceInformation == null) {
         this.instanceInformation = new InstanceInformation();
     }
     this.instanceInformation.setAttributes(v);
 }

 public void setAttributes(Attribute[] v, int[] indexValues) {
     if (this.instanceInformation == null) {
       this.instanceInformation = new InstanceInformation();
     }
     this.instanceInformation.setAttributes(v, indexValues);
   }

   public void setAttributes(List<Attribute> v, List<Integer> indexValues) {
     int[] ret = new int[indexValues.size()];
     for(int i = 0;i < ret.length;i++)
         ret[i] = indexValues.get(i);
     Attribute[] attributes = new Attribute[v.size()];
     for (int i = 0; i < v.size(); i++) {
         attributes[i]= v.get(i);
     }
     setAttributes(attributes, ret);
   }

   /**
    * Returns the dataset as a string in ARFF format. Strings are quoted if
    * they contain whitespace characters, or if they are a question mark.
    *
    * @return the dataset in ARFF format as a string
    */
   public String toString() {

     StringBuffer text = new StringBuffer();

     text.append(ARFF_RELATION).append(" ").
     append(Utils.quote(this.instanceInformation.getRelationName())).append("\n\n");
     for (int i = 0; i < numAttributes(); i++) {
       text.append(attribute(i).toString()).append("\n");
     }
     text.append("\n").append(ARFF_DATA).append("\n");

     text.append(stringWithoutHeader());
     return text.toString();
   }

   /**
    * Returns the dataset as a string in ARFF format. Strings are quoted if
    * they contain whitespace characters, or if they are a question mark.
    *
    * @return the dataset in ARFF format as a string
    */
   public String toStringArff() {

     StringBuffer text = new StringBuffer();

     text.append(ARFF_RELATION).append(" ").
     append(Utils.quote(this.instanceInformation.getRelationName())).append("\n\n");
     for (int i = 0; i < numAttributes(); i++) {
       text.append(attribute(i).toString()).append("\n");
     }
     text.append("\n").append(ARFF_DATA).append("\n");

     text.append(stringWithoutHeader());
     return text.toString();
   }

   /**
    * Returns the instances in the dataset as a string in ARFF format. Strings
    * are quoted if they contain whitespace characters, or if they are a
    * question mark.
    *
    * @return the dataset in ARFF format as a string
    */
   protected String stringWithoutHeader() {

     StringBuffer text = new StringBuffer();

     for (int i = 0; i < numInstances(); i++) {
       text.append(instance(i));
       if (i < numInstances() - 1) {
         text.append('\n');
       }
     }
     return text.toString();

   }

   /**
    * Returns the index of an Attribute.
    *
    * @param att, the attribute.
    */
   protected int indexOf(Attribute att) {
     if (this.hsAttributesIndices == null || !this.hsAttributesIndices.containsKey(att.name)) {
       computeAttributesIndices();
     }

     return this.hsAttributesIndices.get(att.name());
   }

   /**
    * Completes the hashset with attributes indices.
    */
   private void computeAttributesIndices() {
     this.hsAttributesIndices = new HashMap<String, Integer>();
     // iterates through all existing attributes
     // and sets an unique identifier for each one of them
     for (int i = 0; i < this.numAttributes(); i++) {
       hsAttributesIndices.put(this.attribute(i).name(), i);
     }
   }

     /**
      * Returns the indices of the relevant features indicesRelevants.
      * @return indicesRelevants
      */
     public int[] getIndicesRelevants() {
       return indicesRelevants;
   }

   /**
    * Returns the indices of the irrelevant features indicesIrrelevants.
    * @return indicesIrrelevants
    */
   public int[] getIndicesIrrelevants() {
       return indicesIrrelevants;
   }

   /**
    * Sets the indices of relevant features.
    * This method also sets the irrelevant ones since
    * it is the set complement.
    *
    * @param indicesRelevants
    */
   public void setIndicesRelevants(int[] indicesRelevants) {
       this.indicesRelevants = indicesRelevants;
       // -1 to skip the class attribute
       int numIrrelevantFeatures = this.numAttributes() - this.indicesRelevants.length - 1;
       this.indicesIrrelevants = new int[numIrrelevantFeatures];

       // Infers and sets the set of irrelevant features
       int index = 0;
       int indexRel = 0;
       for(int i = 0; i < numAttributes(); i++){
           if(i != classIndex()) {
               while (indexRel < indicesRelevants.length - 1 &&
                       i > indicesRelevants[indexRel]) indexRel++;
               if (indicesRelevants[indexRel] != i){
                   indicesIrrelevants[index] = i;
                   index++;
               }
           }
       }
   }
 }
	package org.apache.samoa.instances;

	import java.io.InputStream;

	/*
	* #%L
	* SAMOA
	* %%
	* Copyright (C) 2014 - 2015 Apache Software Foundation
	* %%
	* Licensed under the Apache License, Version 2.0 (the "License");
	* you may not use this file except in compliance with the License.
	* You may obtain a copy of the License at
	*
	* http://www.apache.org/licenses/LICENSE-2.0
	*
	* Unless required by applicable law or agreed to in writing, software
	* distributed under the License is distributed on an "AS IS" BASIS,
	* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	* See the License for the specific language governing permissions and
	* limitations under the License.
	* #L%
	*/

	import java.io.Reader;
	import java.io.Serializable;
	import java.io.StringReader;
	import java.util.ArrayList;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Random;

	/**
	* Class Instances that stores a set of instances and their structure.
	*/
	public class Instances implements Serializable {

	/**
	* The keyword used to denote the start of an arff header
	*/
	public final static String ARFF_RELATION = "@relation";

	/**
	* The keyword used to denote the start of the arff data section
	*/
	public final static String ARFF_DATA = "@data";

	private static final long serialVersionUID = 8110510475535581577L;
	/**
	* The instance information.
	*/
	protected InstanceInformation instanceInformation;
	/**
	* The instances.
	*/
	protected List<Instance> instances;

	protected static enum AVRO_ENCODING_FORMAT {
	JSON, BINARY
	}

	protected int classAttribute;

	/**
	* A Hash that stores the indices of features.
	*/
	protected HashMap<String, Integer> hsAttributesIndices;

	transient protected Loader loader;

	/**
	* Indices of relevant features.
	*/
	protected int[] indicesRelevants;

	/**
	* Indices of irrelevant features.
	*/
	protected int[] indicesIrrelevants;

	/**
	* Instantiates a new instances.
	*
	* @param chunk the chunk
	*/
	public Instances(Instances chunk) {
	this(chunk, chunk.numInstances());
	chunk.copyInstances(0, this, chunk.numInstances());
	this.computeAttributesIndices();
	if(chunk.indicesRelevants != null) {
	this.indicesRelevants = chunk.indicesRelevants.clone();
	this.indicesIrrelevants = chunk.indicesIrrelevants.clone();
	}
	}

	/**
	* Instantiates a new instances.
	*/
	public Instances() {
	}

	/**
	* Instantiates a new instances.
	*
	* @param reader the reader
	* @param size the size
	* @param classAttribute the class attribute
	*/
	public Instances(Reader reader, int size, int classAttribute) {
	this.loader = new ArffLoader(reader, 0, classAttribute);
	this.instanceInformation = loader.getStructure();
	this.instances = new ArrayList<Instance>();
	this.computeAttributesIndices();
	}

	/**
	* Instantiates a new instances.
	*
	* @param reader the reader
	* @param range
	*/
	public Instances(Reader reader, Range range) {
	this.loader = new MultiTargetArffLoader(reader, range); //new ArffLoader(reader, 0, classAttribute);
	this.instanceInformation = loader.getStructure();
	this.instances = new ArrayList<Instance>();
	this.computeAttributesIndices();
	}

	public Instances(InputStream inputStream, int classAttribute, String encodingFormat) {
	this.classAttribute = classAttribute;

	if (encodingFormat.equalsIgnoreCase(AVRO_ENCODING_FORMAT.BINARY.toString()))
	loader = new AvroBinaryLoader(inputStream, classAttribute);
	else
	loader = new AvroJsonLoader(inputStream, classAttribute);

	this.instanceInformation = loader.getStructure();
	this.instances = new ArrayList<>();
	}

	/**
	* Instantiates a new instances.
	*
	* @param chunk the chunk
	* @param capacity the capacity
	*/
	public Instances(Instances chunk, int capacity) {
	this.instanceInformation = chunk.instanceInformation();
	if (capacity < 0) {
	capacity = 0;
	}
	this.instances = new ArrayList<Instance>(capacity);
	this.computeAttributesIndices();
	if(chunk.indicesRelevants != null) {
	this.indicesRelevants = chunk.indicesRelevants.clone();
	this.indicesIrrelevants = chunk.indicesIrrelevants.clone();
	}
	}

	/**
	* Instantiates a new instances.
	*
	* @param st the st
	* @param v the v
	* @param capacity the capacity
	*/
	public Instances(String st, Attribute[] v, int capacity) {
	this.instanceInformation = new InstanceInformation(st, v);
	this.instances = new ArrayList<Instance>(capacity);
	this.computeAttributesIndices();
	}

	/**
	* Instantiates a new instances.
	*
	* @param st the st
	* @param v the v
	* @param capacity the capacity
	*/
	public Instances(String st, List<Attribute> v, int capacity) {
	Attribute[] attributes = new Attribute[v.size()];
	for (int i = 0; i < v.size(); i++) {
	attributes[i]= v.get(i);
	}
	this.instanceInformation = new InstanceInformation(st, attributes);
	this.instances = new ArrayList<Instance>(capacity);
	this.computeAttributesIndices();
	}

	/**
	* Instantiates a new instances.
	*
	* @param chunk the chunk
	* @param first the first instance
	* @param toCopy the j
	*/
	public Instances(Instances chunk, int first, int toCopy) {

	this(chunk, toCopy);

	if ((first < 0) \|\| ((first + toCopy) > chunk.numInstances())) {
	throw new IllegalArgumentException("Parameters first and/or toCopy out "
	+ "of range");
	}
	chunk.copyInstances(first, this, toCopy);
	this.computeAttributesIndices();
	}

	/**
	* Instantiates a new instances.
	*
	* @param st the st
	* @param capacity the capacity
	*/
	public Instances(StringReader st, int capacity) {
	this.instances = new ArrayList<Instance>(capacity);
	this.computeAttributesIndices();
	}

	//Information Instances
	/**
	* Sets the relation name.
	*
	* @param string the new relation name
	*/
	public void setRelationName(String string) {
	this.instanceInformation.setRelationName(string);
	}

	/**
	* Gets the relation name.
	*
	* @return the relation name
	*/
	public String getRelationName() {
	return this.instanceInformation.getRelationName();
	}

	/**
	* Class index.
	*
	* @return the int
	*/
	public int classIndex() {
	return this.instanceInformation.classIndex();
	}

	/**
	* Sets the class index.
	*
	* @param classIndex the new class index
	*/
	public void setClassIndex(int classIndex) {
	this.instanceInformation.setClassIndex(classIndex);
	}

	/**
	* Class attribute.
	*
	* @return the attribute
	*/
	public Attribute classAttribute() {
	return this.instanceInformation.classAttribute();
	}

	/**
	* Num attributes.
	*
	* @return the int
	*/
	public int numAttributes() {
	return this.instanceInformation.numAttributes();
	}

	/**
	* Attribute.
	*
	* @param w the w
	* @return the attribute
	*/
	public Attribute attribute(int w) {
	return this.instanceInformation.attribute(w);
	}

	/**
	* Num classes.
	*
	* @return the int
	*/
	public int numClasses() {
	return this.instanceInformation.numClasses();
	}

	/**
	* Delete attribute at.
	*
	* @param integer the integer
	*/
	public void deleteAttributeAt(Integer integer) {
	this.instanceInformation.deleteAttributeAt(integer);
	for (int i = 0; i < numInstances(); i++) {
	instance(i).setDataset(null);
	instance(i).deleteAttributeAt(integer);
	instance(i).setDataset(this);
	}
	}

	/**
	* Insert attribute at.
	*
	* @param attribute the attribute
	* @param position the position
	*/
	public void insertAttributeAt(Attribute attribute, int position) {
	if (this.instanceInformation == null) {
	this.instanceInformation = new InstanceInformation();
	}
	this.instanceInformation.insertAttributeAt(attribute, position);
	for (int i = 0; i < numInstances(); i++) {
	instance(i).setDataset(null);
	instance(i).insertAttributeAt(i);
	instance(i).setDataset(this);
	}
	}


	//List of Instances
	/**
	* Instance.
	*
	* @param num the num
	* @return the instance
	*/
	public Instance instance(int num) {
	return this.instances.get(num);
	}

	/**
	* Num instances.
	*
	* @return the int
	*/
	public int numInstances() {
	return this.instances.size();
	}

	/**
	* Adds the.
	*
	* @param inst the inst
	*/
	public void add(Instance inst) {
	this.instances.add(inst);
	}

	/**
	* Randomize.
	*
	* @param random the random
	*/
	public void randomize(Random random) {
	for (int j = numInstances() - 1; j > 0; j--) {
	swap(j, random.nextInt(j + 1));
	}
	}

	/**
	* Stratify.
	*
	* @param numFolds the num folds
	*/
	public void stratify(int numFolds) {

	if (classAttribute().isNominal()) {

	// sort by class
	int index = 1;
	while (index < numInstances()) {
	Instance instance1 = instance(index - 1);
	for (int j = index; j < numInstances(); j++) {
	Instance instance2 = instance(j);
	if ((instance1.classValue() == instance2.classValue())
	\|\| (instance1.classIsMissing()
	&& instance2.classIsMissing())) {
	swap(index, j);
	index++;
	}
	}
	index++;
	}
	stratStep(numFolds);
	}
	}

	protected void stratStep(int numFolds) {
	ArrayList<Instance> newVec = new ArrayList<Instance>(this.instances.size());
	int start = 0, j;

	// create stratified batch
	while (newVec.size() < numInstances()) {
	j = start;
	while (j < numInstances()) {
	newVec.add(instance(j));
	j = j + numFolds;
	}
	start++;
	}
	this.instances = newVec;
	}

	/**
	* Train cv.
	*
	* @param numFolds the num folds
	* @param numFold
	* @param random the random
	* @return the instances
	*/
	public Instances trainCV(int numFolds, int numFold, Random random) {
	Instances train = trainCV(numFolds, numFold);
	train.randomize(random);
	return train;
	}

	public Instances trainCV(int numFolds, int numFold) {
	int numInstForFold, first, offset;
	Instances train;

	numInstForFold = numInstances() / numFolds;
	if (numFold < numInstances() % numFolds) {
	numInstForFold++;
	offset = numFold;
	} else {
	offset = numInstances() % numFolds;
	}
	train = new Instances(this, numInstances() - numInstForFold);
	first = numFold * (numInstances() / numFolds) + offset;
	copyInstances(0, train, first);
	copyInstances(first + numInstForFold, train,
	numInstances() - first - numInstForFold);
	return train;
	}

	protected void copyInstances(int from, Instances dest, int num) {
	for (int i = 0; i < num; i++) {
	dest.add(instance(from + i));
	}
	}

	/**
	* Test cv.
	*
	* @param numFolds the num folds
	* @param numFold the num fold
	* @return the instances
	*/
	public Instances testCV(int numFolds, int numFold) {

	int numInstForFold, first, offset;
	Instances test;

	numInstForFold = numInstances() / numFolds;
	if (numFold < numInstances() % numFolds) {
	numInstForFold++;
	offset = numFold;
	} else {
	offset = numInstances() % numFolds;
	}
	test = new Instances(this, numInstForFold);
	first = numFold * (numInstances() / numFolds) + offset;
	copyInstances(first, test, numInstForFold);
	return test;
	}

	/* public Instances dataset() {
	throw new UnsupportedOperationException("Not yet implemented");
	}*/
	/**
	* Mean or mode.
	*
	* @param j the j
	* @return the double
	*/
	public double meanOrMode(int j) {
	throw new UnsupportedOperationException("Not yet implemented"); //CobWeb
	}

	/**
	* Read instance.
	*
	* @param fileReader the file reader
	* @return true, if successful
	*/
	public boolean readInstance(Reader fileReader) {

	//ArffReader arff = new ArffReader(reader, this, m_Lines, 1);
	if (loader == null) {
	loader = new ArffLoader(fileReader, 0, this.classAttribute);
	}
	Instance inst = loader.readInstance();
	if (inst != null) {
	inst.setDataset(this);
	add(inst);
	return true;
	} else {
	return false;
	}
	}

	public boolean readInstance() {

	Instance inst = loader.readInstance();
	if (inst != null) {
	inst.setDataset(this);
	add(inst);
	return true;
	} else {
	return false;
	}
	}

	/**
	* Delete.
	*/
	public void delete() {
	this.instances = new ArrayList<Instance>();
	}

	/**
	* Delete.
	*/
	public void delete(int index) {
	this.instances.remove(index);
	}

	/**
	* Swap.
	*
	* @param i the i
	* @param j the j
	*/
	public void swap(int i, int j) {
	Instance in = instances.get(i);
	instances.set(i, instances.get(j));
	instances.set(j, in);
	}

	/**
	* Instance information.
	*
	* @return the instance information
	*/
	private InstanceInformation instanceInformation() {
	return this.instanceInformation;
	}

	public Attribute attribute(String name) {

	for (int i = 0; i < numAttributes(); i++) {
	if (attribute(i).name().equals(name)) {
	return attribute(i);
	}
	}
	return null;
	}

	public int size() {
	return this.numInstances();
	}

	public void set(int i, Instance inst) {
	this.instances.set(i, inst);
	}

	public Instance get(int k) {
	return this.instance(k);
	}

	public void setRangeOutputIndices(Range range) {
	this.instanceInformation.setRangeOutputIndices(range);

	}

	public void setAttributes(Attribute[] v) {
	if (this.instanceInformation == null) {
	this.instanceInformation = new InstanceInformation();
	}
	this.instanceInformation.setAttributes(v);
	}

	public void setAttributes(Attribute[] v, int[] indexValues) {
	if (this.instanceInformation == null) {
	this.instanceInformation = new InstanceInformation();
	}
	this.instanceInformation.setAttributes(v, indexValues);
	}

	public void setAttributes(List<Attribute> v, List<Integer> indexValues) {
	int[] ret = new int[indexValues.size()];
	for(int i = 0;i < ret.length;i++)
	ret[i] = indexValues.get(i);
	Attribute[] attributes = new Attribute[v.size()];
	for (int i = 0; i < v.size(); i++) {
	attributes[i]= v.get(i);
	}
	setAttributes(attributes, ret);
	}

	/**
	* Returns the dataset as a string in ARFF format. Strings are quoted if
	* they contain whitespace characters, or if they are a question mark.
	*
	* @return the dataset in ARFF format as a string
	*/
	public String toString() {

	StringBuffer text = new StringBuffer();

	text.append(ARFF_RELATION).append(" ").
	append(Utils.quote(this.instanceInformation.getRelationName())).append("\n\n");
	for (int i = 0; i < numAttributes(); i++) {
	text.append(attribute(i).toString()).append("\n");
	}
	text.append("\n").append(ARFF_DATA).append("\n");

	text.append(stringWithoutHeader());
	return text.toString();
	}

	/**
	* Returns the dataset as a string in ARFF format. Strings are quoted if
	* they contain whitespace characters, or if they are a question mark.
	*
	* @return the dataset in ARFF format as a string
	*/
	public String toStringArff() {

	StringBuffer text = new StringBuffer();

	text.append(ARFF_RELATION).append(" ").
	append(Utils.quote(this.instanceInformation.getRelationName())).append("\n\n");
	for (int i = 0; i < numAttributes(); i++) {
	text.append(attribute(i).toString()).append("\n");
	}
	text.append("\n").append(ARFF_DATA).append("\n");

	text.append(stringWithoutHeader());
	return text.toString();
	}

	/**
	* Returns the instances in the dataset as a string in ARFF format. Strings
	* are quoted if they contain whitespace characters, or if they are a
	* question mark.
	*
	* @return the dataset in ARFF format as a string
	*/
	protected String stringWithoutHeader() {

	StringBuffer text = new StringBuffer();

	for (int i = 0; i < numInstances(); i++) {
	text.append(instance(i));
	if (i < numInstances() - 1) {
	text.append('\n');
	}
	}
	return text.toString();

	}

	/**
	* Returns the index of an Attribute.
	*
	* @param att, the attribute.
	*/
	protected int indexOf(Attribute att) {
	if (this.hsAttributesIndices == null \|\| !this.hsAttributesIndices.containsKey(att.name)) {
	computeAttributesIndices();
	}

	return this.hsAttributesIndices.get(att.name());
	}

	/**
	* Completes the hashset with attributes indices.
	*/
	private void computeAttributesIndices() {
	this.hsAttributesIndices = new HashMap<String, Integer>();
	// iterates through all existing attributes
	// and sets an unique identifier for each one of them
	for (int i = 0; i < this.numAttributes(); i++) {
	hsAttributesIndices.put(this.attribute(i).name(), i);
	}
	}

	/**
	* Returns the indices of the relevant features indicesRelevants.
	* @return indicesRelevants
	*/
	public int[] getIndicesRelevants() {
	return indicesRelevants;
	}

	/**
	* Returns the indices of the irrelevant features indicesIrrelevants.
	* @return indicesIrrelevants
	*/
	public int[] getIndicesIrrelevants() {
	return indicesIrrelevants;
	}

	/**
	* Sets the indices of relevant features.
	* This method also sets the irrelevant ones since
	* it is the set complement.
	*
	* @param indicesRelevants
	*/
	public void setIndicesRelevants(int[] indicesRelevants) {
	this.indicesRelevants = indicesRelevants;
	// -1 to skip the class attribute
	int numIrrelevantFeatures = this.numAttributes() - this.indicesRelevants.length - 1;
	this.indicesIrrelevants = new int[numIrrelevantFeatures];

	// Infers and sets the set of irrelevant features
	int index = 0;
	int indexRel = 0;
	for(int i = 0; i < numAttributes(); i++){
	if(i != classIndex()) {
	while (indexRel < indicesRelevants.length - 1 &&
	i > indicesRelevants[indexRel]) indexRel++;
	if (indicesRelevants[indexRel] != i){
	indicesIrrelevants[index] = i;
	index++;
	}
	}
	}
	}
	}