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weka.attributeSelection.CheckAttributeSelection Maven / Gradle / Ivy

/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see .
 */

/*
 * CheckAttributeSelection.java
 * Copyright (C) 2006-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.attributeSelection;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;

import weka.core.Attribute;
import weka.core.CheckScheme;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SerializationHelper;
import weka.core.SerializedObject;
import weka.core.TestInstances;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;

/**
 * Class for examining the capabilities and finding problems with attribute
 * selection schemes. If you implement an attribute selection using the
 * WEKA.libraries, you should run the checks on it to ensure robustness and
 * correct operation. Passing all the tests of this object does not mean bugs in
 * the attribute selection don't exist, but this will help find some common
 * ones.
 * 

 * 
 * Typical usage:
 * 

 * java weka.attributeSelection.CheckAttributeSelection -W ASscheme_name 
 * -- ASscheme_options 
 * 

 * 
 * CheckAttributeSelection reports on the following:
 * 

 * 
Scheme abilities
 * 

 * 
Possible command line options to the scheme
 * 
Whether the scheme can predict nominal, numeric, string, date or
 * relational class attributes.
 * 
Whether the scheme can handle numeric predictor attributes
 * 
Whether the scheme can handle nominal predictor attributes
 * 
Whether the scheme can handle string predictor attributes
 * 
Whether the scheme can handle date predictor attributes
 * 
Whether the scheme can handle relational predictor attributes
 * 
Whether the scheme can handle multi-instance data
 * 
Whether the scheme can handle missing predictor values
 * 
Whether the scheme can handle missing class values
 * 
Whether a nominal scheme only handles 2 class problems
 * 
Whether the scheme can handle instance weights
 * 
 * 
 * 
Correct functioning
 * 

 * 
Correct initialisation during search (i.e. no result changes when search
 * is performed repeatedly)
 * 
Whether the scheme alters the data pased to it (number of instances,
 * instance order, instance weights, etc)
 * 
 * 
 * 
Degenerate cases
 * 

 * 
building scheme with zero instances
 * 
all but one predictor attribute values missing
 * 
all predictor attribute values missing
 * 
all but one class values missing
 * 
all class values missing
 * 
 * 
 * 
 * Running CheckAttributeSelection with the debug option set will output the
 * training dataset for any failed tests.
 * 

 * 
 * The weka.attributeSelection.AbstractAttributeSelectionTest uses
 * this class to test all the schemes. Any changes here, have to be checked in
 * that abstract test class, too.
 * 

 * 
 *  Valid options are:
 * 

 * 
 * 
 * -D
 *  Turn on debugging output.
 * 
 * 
 * 
 * -S
 *  Silent mode - prints nothing to stdout.
 * 
 * 
 * 
 * -N <num>
 *  The number of instances in the datasets (default 20).
 * 
 * 
 * 
 * -nominal <num>
 *  The number of nominal attributes (default 2).
 * 
 * 
 * 
 * -nominal-values <num>
 *  The number of values for nominal attributes (default 1).
 * 
 * 
 * 
 * -numeric <num>
 *  The number of numeric attributes (default 1).
 * 
 * 
 * 
 * -string <num>
 *  The number of string attributes (default 1).
 * 
 * 
 * 
 * -date <num>
 *  The number of date attributes (default 1).
 * 
 * 
 * 
 * -relational <num>
 *  The number of relational attributes (default 1).
 * 
 * 
 * 
 * -num-instances-relational <num>
 *  The number of instances in relational/bag attributes (default 10).
 * 
 * 
 * 
 * -words <comma-separated-list>
 *  The words to use in string attributes.
 * 
 * 
 * 
 * -word-separators <chars>
 *  The word separators to use in string attributes.
 * 
 * 
 * 
 * -eval name [options]
 *  Full name and options of the evaluator analyzed.
 *  eg: weka.attributeSelection.CfsSubsetEval
 * 
 * 
 * 
 * -search name [options]
 *  Full name and options of the search method analyzed.
 *  eg: weka.attributeSelection.Ranker
 * 
 * 
 * 
 * -test <eval|search>
 *  The scheme to test, either the evaluator or the search method.
 *  (Default: eval)
 * 
 * 
 * 
 * Options specific to evaluator weka.attributeSelection.CfsSubsetEval:
 * 
 * 
 * 
 * -M
 *  Treat missing values as a separate value.
 * 
 * 
 * 
 * -L
 *  Don't include locally predictive attributes.
 * 
 * 
 * 
 * Options specific to search method weka.attributeSelection.Ranker:
 * 
 * 
 * 
 * -P <start set>
 *  Specify a starting set of attributes.
 *  Eg. 1,3,5-7.
 *  Any starting attributes specified are
 *  ignored during the ranking.
 * 
 * 
 * 
 * -T <threshold>
 *  Specify a theshold by which attributes
 *  may be discarded from the ranking.
 * 
 * 
 * 
 * -N <num to select>
 *  Specify number of attributes to select
 * 
 * 
 * 
 * 
 * @author Len Trigg ([email protected])
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 15517 $
 * @see TestInstances
 */
public class CheckAttributeSelection extends CheckScheme {

  /*
   * Note about test methods: - methods return array of booleans - first index:
   * success or not - second index: acceptable or not (e.g., Exception is OK)
   * 
   * FracPete (fracpete at waikato dot ac dot nz)
   */

  /*** The evaluator to be examined */
  protected ASEvaluation m_Evaluator = new CfsSubsetEval();

  /*** The search method to be used */
  protected ASSearch m_Search = new Ranker();

  /** whether to test the evaluator (default) or the search method */
  protected boolean m_TestEvaluator = true;

  /**
   * Returns an enumeration describing the available options.
   * 
   * @return an enumeration of all the available options.
   */
  @Override
  public Enumeration listOptions() {
    Vector result = new Vector();

    result.add(new Option(
      "\tFull name and options of the evaluator analyzed.\n"
        + "\teg: weka.attributeSelection.CfsSubsetEval", "eval", 1,
      "-eval name [options]"));

    result.add(new Option(
      "\tFull name and options of the search method analyzed.\n"
        + "\teg: weka.attributeSelection.Ranker", "search", 1,
      "-search name [options]"));

    result.add(new Option(
      "\tThe scheme to test, either the evaluator or the search method.\n"
        + "\t(Default: eval)", "test", 1, "-test "));

    result.addAll(Collections.list(super.listOptions()));

    if ((m_Evaluator != null) && (m_Evaluator instanceof OptionHandler)) {
      result.add(new Option("", "", 0, "\nOptions specific to evaluator "
        + m_Evaluator.getClass().getName() + ":"));
      result.addAll(Collections.list(((OptionHandler) m_Evaluator)
        .listOptions()));
    }

    if ((m_Search != null) && (m_Search instanceof OptionHandler)) {
      result.add(new Option("", "", 0, "\nOptions specific to search method "
        + m_Search.getClass().getName() + ":"));
      result.addAll(Collections.list(((OptionHandler) m_Search).listOptions()));
    }

    return result.elements();
  }

  /**
   * Parses a given list of options.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -D
   *  Turn on debugging output.
   * 
   * 
   * 
   * -S
   *  Silent mode - prints nothing to stdout.
   * 
   * 
   * 
   * -N <num>
   *  The number of instances in the datasets (default 20).
   * 
   * 
   * 
   * -nominal <num>
   *  The number of nominal attributes (default 2).
   * 
   * 
   * 
   * -nominal-values <num>
   *  The number of values for nominal attributes (default 1).
   * 
   * 
   * 
   * -numeric <num>
   *  The number of numeric attributes (default 1).
   * 
   * 
   * 
   * -string <num>
   *  The number of string attributes (default 1).
   * 
   * 
   * 
   * -date <num>
   *  The number of date attributes (default 1).
   * 
   * 
   * 
   * -relational <num>
   *  The number of relational attributes (default 1).
   * 
   * 
   * 
   * -num-instances-relational <num>
   *  The number of instances in relational/bag attributes (default 10).
   * 
   * 
   * 
   * -words <comma-separated-list>
   *  The words to use in string attributes.
   * 
   * 
   * 
   * -word-separators <chars>
   *  The word separators to use in string attributes.
   * 
   * 
   * 
   * -eval name [options]
   *  Full name and options of the evaluator analyzed.
   *  eg: weka.attributeSelection.CfsSubsetEval
   * 
   * 
   * 
   * -search name [options]
   *  Full name and options of the search method analyzed.
   *  eg: weka.attributeSelection.Ranker
   * 
   * 
   * 
   * -test <eval|search>
   *  The scheme to test, either the evaluator or the search method.
   *  (Default: eval)
   * 
   * 
   * 
   * Options specific to evaluator weka.attributeSelection.CfsSubsetEval:
   * 
   * 
   * 
   * -M
   *  Treat missing values as a separate value.
   * 
   * 
   * 
   * -L
   *  Don't include locally predictive attributes.
   * 
   * 
   * 
   * Options specific to search method weka.attributeSelection.Ranker:
   * 
   * 
   * 
   * -P <start set>
   *  Specify a starting set of attributes.
   *  Eg. 1,3,5-7.
   *  Any starting attributes specified are
   *  ignored during the ranking.
   * 
   * 
   * 
   * -T <threshold>
   *  Specify a theshold by which attributes
   *  may be discarded from the ranking.
   * 
   * 
   * 
   * -N <num to select>
   *  Specify number of attributes to select
   * 
   * 
   * 
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {
    String tmpStr;
    String[] tmpOptions;

    super.setOptions(options);

    tmpStr = Utils.getOption("eval", options);
    tmpOptions = Utils.splitOptions(tmpStr);
    if (tmpOptions.length != 0) {
      tmpStr = tmpOptions[0];
      tmpOptions[0] = "";
      setEvaluator((ASEvaluation) forName("weka.attributeSelection",
        ASEvaluation.class, tmpStr, tmpOptions));
    }

    tmpStr = Utils.getOption("search", options);
    tmpOptions = Utils.splitOptions(tmpStr);
    if (tmpOptions.length != 0) {
      tmpStr = tmpOptions[0];
      tmpOptions[0] = "";
      setSearch((ASSearch) forName("weka.attributeSelection", ASSearch.class,
        tmpStr, tmpOptions));
    }

    tmpStr = Utils.getOption("test", options);
    setTestEvaluator(!tmpStr.equalsIgnoreCase("search"));
  }

  /**
   * Gets the current settings of the CheckAttributeSelection.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {
    Vector result = new Vector();

    Collections.addAll(result, super.getOptions());

    result.add("-eval");
    if (getEvaluator() instanceof OptionHandler) {
      result.add(getEvaluator().getClass().getName() + " "
        + Utils.joinOptions(((OptionHandler) getEvaluator()).getOptions()));
    } else {
      result.add(getEvaluator().getClass().getName());
    }

    result.add("-search");
    if (getSearch() instanceof OptionHandler) {
      result.add(getSearch().getClass().getName() + " "
        + Utils.joinOptions(((OptionHandler) getSearch()).getOptions()));
    } else {
      result.add(getSearch().getClass().getName());
    }

    result.add("-test");
    if (getTestEvaluator()) {
      result.add("eval");
    } else {
      result.add("search");
    }

    return result.toArray(new String[result.size()]);
  }

  /**
   * Begin the tests, reporting results to System.out
   */
  @Override
  public void doTests() {

    if (getTestObject() == null) {
      println("\n=== No scheme set ===");
      return;
    }
    println("\n=== Check on scheme: " + getTestObject().getClass().getName()
      + " ===\n");

    // Start tests
    m_ClasspathProblems = false;
    println("--> Checking for interfaces");
    canTakeOptions();
    boolean weightedInstancesHandler = weightedInstancesHandler()[0];
    boolean multiInstanceHandler = multiInstanceHandler()[0];
    println("--> Scheme tests");
    declaresSerialVersionUID();
    testsPerClassType(Attribute.NOMINAL, weightedInstancesHandler,
      multiInstanceHandler);
    testsPerClassType(Attribute.NUMERIC, weightedInstancesHandler,
      multiInstanceHandler);
    testsPerClassType(Attribute.DATE, weightedInstancesHandler,
      multiInstanceHandler);
    testsPerClassType(Attribute.STRING, weightedInstancesHandler,
      multiInstanceHandler);
    testsPerClassType(Attribute.RELATIONAL, weightedInstancesHandler,
      multiInstanceHandler);
  }

  /**
   * Set the evaluator to test.
   * 
   * @param value the evaluator to use.
   */
  public void setEvaluator(ASEvaluation value) {
    m_Evaluator = value;
  }

  /**
   * Get the current evaluator
   * 
   * @return the current evaluator
   */
  public ASEvaluation getEvaluator() {
    return m_Evaluator;
  }

  /**
   * Set the search method to test.
   * 
   * @param value the search method to use.
   */
  public void setSearch(ASSearch value) {
    m_Search = value;
  }

  /**
   * Get the current search method
   * 
   * @return the current search method
   */
  public ASSearch getSearch() {
    return m_Search;
  }

  /**
   * Sets whether the evaluator or the search method is being tested.
   * 
   * @param value if true then the evaluator will be tested
   */
  public void setTestEvaluator(boolean value) {
    m_TestEvaluator = value;
  }

  /**
   * Gets whether the evaluator is being tested or the search method.
   * 
   * @return true if the evaluator is being tested
   */
  public boolean getTestEvaluator() {
    return m_TestEvaluator;
  }

  /**
   * returns either the evaluator or the search method.
   * 
   * @return the object to be tested
   * @see #m_TestEvaluator
   */
  protected Object getTestObject() {
    if (getTestEvaluator()) {
      return getEvaluator();
    } else {
      return getSearch();
    }
  }

  /**
   * returns deep copies of the given object
   * 
   * @param obj the object to copy
   * @param num the number of copies
   * @return the deep copies
   * @throws Exception if copying fails
   */
  protected Object[] makeCopies(Object obj, int num) throws Exception {
    if (obj == null) {
      throw new Exception("No object set");
    }

    Object[] objs = new Object[num];
    SerializedObject so = new SerializedObject(obj);
    for (int i = 0; i < objs.length; i++) {
      objs[i] = so.getObject();
    }

    return objs;
  }

  /**
   * Performs a attribute selection with the given search and evaluation scheme
   * on the provided data. The generated AttributeSelection object is returned.
   * 
   * @param search the search scheme to use
   * @param eval the evaluator to use
   * @param data the data to work on
   * @return the used attribute selection object
   * @throws Exception if the attribute selection fails
   */
  protected AttributeSelection search(ASSearch search, ASEvaluation eval,
    Instances data) throws Exception {

    AttributeSelection result;

    result = new AttributeSelection();
    result.setSeed(42);
    result.setSearch(search);
    result.setEvaluator(eval);
    result.SelectAttributes(data);

    return result;
  }

  /**
   * Run a battery of tests for a given class attribute type
   * 
   * @param classType true if the class attribute should be numeric
   * @param weighted true if the scheme says it handles weights
   * @param multiInstance true if the scheme handles multi-instance data
   */
  protected void testsPerClassType(int classType, boolean weighted,
    boolean multiInstance) {

    boolean PNom = canPredict(true, false, false, false, false, multiInstance,
      classType)[0];
    boolean PNum = canPredict(false, true, false, false, false, multiInstance,
      classType)[0];
    boolean PStr = canPredict(false, false, true, false, false, multiInstance,
      classType)[0];
    boolean PDat = canPredict(false, false, false, true, false, multiInstance,
      classType)[0];
    boolean PRel;
    if (!multiInstance) {
      PRel = canPredict(false, false, false, false, true, multiInstance,
        classType)[0];
    } else {
      PRel = false;
    }

    if (PNom || PNum || PStr || PDat || PRel) {
      if (weighted) {
        instanceWeights(PNom, PNum, PStr, PDat, PRel, multiInstance, classType);
      }

      if (classType == Attribute.NOMINAL) {
        canHandleNClasses(PNom, PNum, PStr, PDat, PRel, multiInstance, 4);
      }

      if (!multiInstance) {
        canHandleClassAsNthAttribute(PNom, PNum, PStr, PDat, PRel,
          multiInstance, classType, 0);
        canHandleClassAsNthAttribute(PNom, PNum, PStr, PDat, PRel,
          multiInstance, classType, 1);
      }

      canHandleZeroTraining(PNom, PNum, PStr, PDat, PRel, multiInstance,
        classType);
      boolean handleMissingPredictors = canHandleMissing(PNom, PNum, PStr,
        PDat, PRel, multiInstance, classType, true, false, 20)[0];
      if (handleMissingPredictors) {
        canHandleMissing(PNom, PNum, PStr, PDat, PRel, multiInstance,
          classType, true, false, 100);
      }

      boolean handleMissingClass = canHandleMissing(PNom, PNum, PStr, PDat,
        PRel, multiInstance, classType, false, true, 20)[0];
      if (handleMissingClass) {
        canHandleMissing(PNom, PNum, PStr, PDat, PRel, multiInstance,
          classType, false, true, 100);
      }

      correctSearchInitialisation(PNom, PNum, PStr, PDat, PRel, multiInstance,
        classType);
      datasetIntegrity(PNom, PNum, PStr, PDat, PRel, multiInstance, classType,
        handleMissingPredictors, handleMissingClass);
    }
  }

  /**
   * Checks whether the scheme can take command line options.
   * 
   * @return index 0 is true if the scheme can take options
   */
  protected boolean[] canTakeOptions() {

    boolean[] result = new boolean[2];

    print("options...");
    if (getTestObject() instanceof OptionHandler) {
      println("yes");
      if (m_Debug) {
        println("\n=== Full report ===");
        Enumeration enu = ((OptionHandler) getTestObject())
          .listOptions();
        while (enu.hasMoreElements()) {
          Option option = enu.nextElement();
          print(option.synopsis() + "\n" + option.description() + "\n");
        }
        println("\n");
      }
      result[0] = true;
    } else {
      println("no");
      result[0] = false;
    }

    return result;
  }

  /**
   * Checks whether the scheme says it can handle instance weights.
   * 
   * @return true if the scheme handles instance weights
   */
  protected boolean[] weightedInstancesHandler() {

    boolean[] result = new boolean[2];

    print("weighted instances scheme...");
    if (getTestObject() instanceof WeightedInstancesHandler) {
      println("yes");
      result[0] = true;
    } else {
      println("no");
      result[0] = false;
    }

    return result;
  }

  /**
   * Checks whether the scheme handles multi-instance data.
   * 
   * @return true if the scheme handles multi-instance data
   */
  protected boolean[] multiInstanceHandler() {
    boolean[] result = new boolean[2];

    print("multi-instance scheme...");
    if (getTestObject() instanceof MultiInstanceCapabilitiesHandler) {
      println("yes");
      result[0] = true;
    } else {
      println("no");
      result[0] = false;
    }

    return result;
  }

  /**
   * tests for a serialVersionUID. Fails in case the schemes don't declare a UID
   * (both must!).
   * 
   * @return index 0 is true if the scheme declares a UID
   */
  protected boolean[] declaresSerialVersionUID() {
    boolean[] result = new boolean[2];
    boolean eval;
    boolean search;

    print("serialVersionUID...");

    eval = !SerializationHelper.needsUID(m_Evaluator.getClass());
    search = !SerializationHelper.needsUID(m_Search.getClass());

    result[0] = eval && search;

    if (result[0]) {
      println("yes");
    } else {
      println("no");
    }

    return result;
  }

  /**
   * Checks basic prediction of the scheme, for simple non-troublesome datasets.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NOMINAL, NUMERIC, etc.)
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] canPredict(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType) {

    print("basic predict");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    ArrayList accepts = new ArrayList();
    accepts.add("unary");
    accepts.add("binary");
    accepts.add("nominal");
    accepts.add("numeric");
    accepts.add("string");
    accepts.add("date");
    accepts.add("relational");
    accepts.add("multi-instance");
    accepts.add("not in classpath");
    int numTrain = getNumInstances(), numClasses = 2, missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType,
      missingLevel, predictorMissing, classMissing, numTrain, numClasses,
      accepts);
  }

  /**
   * Checks whether nominal schemes can handle more than two classes. If a
   * scheme is only designed for two-class problems it should throw an
   * appropriate exception for multi-class problems.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param numClasses the number of classes to test
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] canHandleNClasses(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int numClasses) {

    print("more than two class problems");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, Attribute.NOMINAL);
    print("...");
    ArrayList accepts = new ArrayList();
    accepts.add("number");
    accepts.add("class");
    int numTrain = getNumInstances(), missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, Attribute.NOMINAL,
      missingLevel, predictorMissing, classMissing, numTrain, numClasses,
      accepts);
  }

  /**
   * Checks whether the scheme can handle class attributes as Nth attribute.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param classIndex the index of the class attribute (0-based, -1 means last
   *          attribute)
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   * @see TestInstances#CLASS_IS_LAST
   */
  protected boolean[] canHandleClassAsNthAttribute(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType,
    int classIndex) {

    if (classIndex == TestInstances.CLASS_IS_LAST) {
      print("class attribute as last attribute");
    } else {
      print("class attribute as " + (classIndex + 1) + ". attribute");
    }
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    ArrayList accepts = new ArrayList();
    int numTrain = getNumInstances(), numClasses = 2, missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType, classIndex,
      missingLevel, predictorMissing, classMissing, numTrain, numClasses,
      accepts);
  }

  /**
   * Checks whether the scheme can handle zero training instances.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] canHandleZeroTraining(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType) {

    print("handle zero training instances");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    ArrayList accepts = new ArrayList();
    accepts.add("train");
    accepts.add("value");
    int numTrain = 0, numClasses = 2, missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType,
      missingLevel, predictorMissing, classMissing, numTrain, numClasses,
      accepts);
  }

  /**
   * Checks whether the scheme correctly initialises models when ASSearch.search
   * is called. This test calls search with one training dataset. ASSearch is
   * then called on a training set with different structure, and then again with
   * the original training set. If the equals method of the ASEvaluation class
   * returns false, this is noted as incorrect search initialisation.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @return index 0 is true if the test was passed, index 1 is always false
   */
  protected boolean[] correctSearchInitialisation(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType) {

    boolean[] result = new boolean[2];
    print("correct initialisation during search");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    int numTrain = getNumInstances(), numClasses = 2, missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    Instances train1 = null;
    Instances train2 = null;
    ASSearch search = null;
    ASEvaluation evaluation1A = null;
    ASEvaluation evaluation1B = null;
    ASEvaluation evaluation2 = null;
    AttributeSelection attsel1A = null;
    AttributeSelection attsel1B = null;
    int stage = 0;
    try {

      // Make two train sets with different numbers of attributes
      train1 = makeTestDataset(42, numTrain, nominalPredictor ? getNumNominal()
        : 0, numericPredictor ? getNumNumeric() : 0,
        stringPredictor ? getNumString() : 0, datePredictor ? getNumDate() : 0,
        relationalPredictor ? getNumRelational() : 0, numClasses, classType,
        multiInstance);
      train2 = makeTestDataset(84, numTrain,
        nominalPredictor ? getNumNominal() + 1 : 0,
        numericPredictor ? getNumNumeric() + 1 : 0,
        stringPredictor ? getNumString() : 0, datePredictor ? getNumDate() : 0,
        relationalPredictor ? getNumRelational() : 0, numClasses, classType,
        multiInstance);
      if (missingLevel > 0) {
        addMissing(train1, missingLevel, predictorMissing, classMissing);
        addMissing(train2, missingLevel, predictorMissing, classMissing);
      }

      search = ASSearch.makeCopies(getSearch(), 1)[0];
      evaluation1A = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
      evaluation1B = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
      evaluation2 = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
    } catch (Exception ex) {
      throw new Error("Error setting up for tests: " + ex.getMessage());
    }
    try {
      stage = 0;
      attsel1A = search(search, evaluation1A, train1);

      stage = 1;
      search(search, evaluation2, train2);

      stage = 2;
      attsel1B = search(search, evaluation1B, train1);

      stage = 3;
      if (!attsel1A.toResultsString().equals(attsel1B.toResultsString())) {
        if (m_Debug) {
          println("\n=== Full report ===\n" + "\nFirst search\n"
            + attsel1A.toResultsString() + "\n\n");
          println("\nSecond search\n" + attsel1B.toResultsString() + "\n\n");
        }
        throw new Exception("Results differ between search calls");
      }
      println("yes");
      result[0] = true;
    } catch (Exception ex) {
      println("no");
      result[0] = false;
      if (m_Debug) {
        println("\n=== Full Report ===");
        print("Problem during  training");
        switch (stage) {
        case 0:
          print(" of dataset 1");
          break;
        case 1:
          print(" of dataset 2");
          break;
        case 2:
          print(" of dataset 1 (2nd build)");
          break;
        case 3:
          print(", comparing results from builds of dataset 1");
          break;
        }
        println(": " + ex.getMessage() + "\n");
        println("here are the datasets:\n");
        println("=== Train1 Dataset ===\n" + train1.toString() + "\n");
        println("=== Train2 Dataset ===\n" + train2.toString() + "\n");
      }
    }

    return result;
  }

  /**
   * Checks basic missing value handling of the scheme. If the missing values
   * cause an exception to be thrown by the scheme, this will be recorded.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param predictorMissing true if the missing values may be in the predictors
   * @param classMissing true if the missing values may be in the class
   * @param missingLevel the percentage of missing values
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] canHandleMissing(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType,
    boolean predictorMissing, boolean classMissing, int missingLevel) {

    if (missingLevel == 100) {
      print("100% ");
    }
    print("missing");
    if (predictorMissing) {
      print(" predictor");
      if (classMissing) {
        print(" and");
      }
    }
    if (classMissing) {
      print(" class");
    }
    print(" values");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    ArrayList accepts = new ArrayList();
    accepts.add("missing");
    accepts.add("value");
    accepts.add("train");
    accepts.add("no attributes");
    int numTrain = getNumInstances(), numClasses = 2;

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType,
      missingLevel, predictorMissing, classMissing, numTrain, numClasses,
      accepts);
  }

  /**
   * Checks whether the scheme can handle instance weights. This test compares
   * the scheme performance on two datasets that are identical except for the
   * training weights. If the results change, then the scheme must be using the
   * weights. It may be possible to get a false positive from this test if the
   * weight changes aren't significant enough to induce a change in scheme
   * performance (but the weights are chosen to minimize the likelihood of
   * this).
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @return index 0 true if the test was passed
   */
  protected boolean[] instanceWeights(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType) {

    print("scheme uses instance weights");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    int numTrain = 2 * getNumInstances(), numClasses = 2, missingLevel = 0;
    boolean predictorMissing = false, classMissing = false;

    boolean[] result = new boolean[2];
    Instances train = null;
    ASSearch[] search = null;
    ASEvaluation evaluationB = null;
    ASEvaluation evaluationI = null;
    AttributeSelection attselB = null;
    AttributeSelection attselI = null;
    boolean evalFail = false;
    try {
      train = makeTestDataset(42, numTrain,
        nominalPredictor ? getNumNominal() + 1 : 0,
        numericPredictor ? getNumNumeric() + 1 : 0,
        stringPredictor ? getNumString() : 0, datePredictor ? getNumDate() : 0,
        relationalPredictor ? getNumRelational() : 0, numClasses, classType,
        multiInstance);
      if (missingLevel > 0) {
        addMissing(train, missingLevel, predictorMissing, classMissing);
      }
      search = ASSearch.makeCopies(getSearch(), 2);
      evaluationB = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
      evaluationI = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
      attselB = search(search[0], evaluationB, train);
    } catch (Exception ex) {
      throw new Error("Error setting up for tests: " + ex.getMessage());
    }
    try {

      // Now modify instance weights and re-built/test
      for (int i = 0; i < train.numInstances(); i++) {
        train.instance(i).setWeight(0);
      }
      Random random = new Random(1);
      for (int i = 0; i < train.numInstances() / 2; i++) {
        int inst = random.nextInt(train.numInstances());
        int weight = random.nextInt(10) + 1;
        train.instance(inst).setWeight(weight);
      }
      attselI = search(search[1], evaluationI, train);
      if (attselB.toResultsString().equals(attselI.toResultsString())) {
        // println("no");
        evalFail = true;
        throw new Exception("evalFail");
      }

      println("yes");
      result[0] = true;
    } catch (Exception ex) {
      println("no");
      result[0] = false;

      if (m_Debug) {
        println("\n=== Full Report ===");

        if (evalFail) {
          println("Results don't differ between non-weighted and "
            + "weighted instance models.");
          println("Here are the results:\n");
          println("\nboth methods\n");
          println(evaluationB.toString());
        } else {
          print("Problem during training");
          println(": " + ex.getMessage() + "\n");
        }
        println("Here is the dataset:\n");
        println("=== Train Dataset ===\n" + train.toString() + "\n");
        println("=== Train Weights ===\n");
        for (int i = 0; i < train.numInstances(); i++) {
          println(" " + (i + 1) + "    " + train.instance(i).weight());
        }
      }
    }

    return result;
  }

  /**
   * Checks whether the scheme alters the training dataset during training. If
   * the scheme needs to modify the training data it should take a copy of the
   * training data. Currently checks for changes to header structure, number of
   * instances, order of instances, instance weights.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param predictorMissing true if we know the scheme can handle (at least)
   *          moderate missing predictor values
   * @param classMissing true if we know the scheme can handle (at least)
   *          moderate missing class values
   * @return index 0 is true if the test was passed
   */
  protected boolean[] datasetIntegrity(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType,
    boolean predictorMissing, boolean classMissing) {

    print("scheme doesn't alter original datasets");
    printAttributeSummary(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType);
    print("...");
    int numTrain = getNumInstances(), numClasses = 2, missingLevel = 20;

    boolean[] result = new boolean[2];
    Instances train = null;
    Instances trainCopy = null;
    ASSearch search = null;
    ASEvaluation evaluation = null;
    try {
      train = makeTestDataset(42, numTrain, nominalPredictor ? getNumNominal()
        : 0, numericPredictor ? getNumNumeric() : 0,
        stringPredictor ? getNumString() : 0, datePredictor ? getNumDate() : 0,
        relationalPredictor ? getNumRelational() : 0, numClasses, classType,
        multiInstance);
      if (missingLevel > 0) {
        addMissing(train, missingLevel, predictorMissing, classMissing);
      }
      search = ASSearch.makeCopies(getSearch(), 1)[0];
      evaluation = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
      trainCopy = new Instances(train);
    } catch (Exception ex) {
      throw new Error("Error setting up for tests: " + ex.getMessage());
    }
    try {
      search(search, evaluation, trainCopy);
      compareDatasets(train, trainCopy);

      println("yes");
      result[0] = true;
    } catch (Exception ex) {
      println("no");
      result[0] = false;

      if (m_Debug) {
        println("\n=== Full Report ===");
        print("Problem during training");
        println(": " + ex.getMessage() + "\n");
        println("Here are the datasets:\n");
        println("=== Train Dataset (original) ===\n" + trainCopy.toString()
          + "\n");
        println("=== Train Dataset ===\n" + train.toString() + "\n");
      }
    }

    return result;
  }

  /**
   * Runs a text on the datasets with the given characteristics.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param missingLevel the percentage of missing values
   * @param predictorMissing true if the missing values may be in the predictors
   * @param classMissing true if the missing values may be in the class
   * @param numTrain the number of instances in the training set
   * @param numClasses the number of classes
   * @param accepts the acceptable string in an exception
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] runBasicTest(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType,
    int missingLevel, boolean predictorMissing, boolean classMissing,
    int numTrain, int numClasses, ArrayList accepts) {

    return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
      datePredictor, relationalPredictor, multiInstance, classType,
      TestInstances.CLASS_IS_LAST, missingLevel, predictorMissing,
      classMissing, numTrain, numClasses, accepts);
  }

  /**
   * Runs a text on the datasets with the given characteristics.
   * 
   * @param nominalPredictor if true use nominal predictor attributes
   * @param numericPredictor if true use numeric predictor attributes
   * @param stringPredictor if true use string predictor attributes
   * @param datePredictor if true use date predictor attributes
   * @param relationalPredictor if true use relational predictor attributes
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param classIndex the attribute index of the class
   * @param missingLevel the percentage of missing values
   * @param predictorMissing true if the missing values may be in the predictors
   * @param classMissing true if the missing values may be in the class
   * @param numTrain the number of instances in the training set
   * @param numClasses the number of classes
   * @param accepts the acceptable string in an exception
   * @return index 0 is true if the test was passed, index 1 is true if test was
   *         acceptable
   */
  protected boolean[] runBasicTest(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType,
    int classIndex, int missingLevel, boolean predictorMissing,
    boolean classMissing, int numTrain, int numClasses,
    ArrayList accepts) {

    boolean[] result = new boolean[2];
    Instances train = null;
    ASSearch search = null;
    ASEvaluation evaluation = null;
    try {
      train = makeTestDataset(42, numTrain, nominalPredictor ? getNumNominal()
        : 0, numericPredictor ? getNumNumeric() : 0,
        stringPredictor ? getNumString() : 0, datePredictor ? getNumDate() : 0,
        relationalPredictor ? getNumRelational() : 0, numClasses, classType,
        classIndex, multiInstance);
      if (missingLevel > 0) {
        addMissing(train, missingLevel, predictorMissing, classMissing);
      }
      search = ASSearch.makeCopies(getSearch(), 1)[0];
      evaluation = ASEvaluation.makeCopies(getEvaluator(), 1)[0];
    } catch (Exception ex) {
      ex.printStackTrace();
      throw new Error("Error setting up for tests: " + ex.getMessage());
    }
    try {
      search(search, evaluation, train);
      println("yes");
      result[0] = true;
    } catch (Exception ex) {
      boolean acceptable = false;
      String msg;
      if (ex.getMessage() == null) {
        msg = "";
      } else {
        msg = ex.getMessage().toLowerCase();
      }
      if (msg.indexOf("not in classpath") > -1) {
        m_ClasspathProblems = true;
      }
      for (int i = 0; i < accepts.size(); i++) {
        if (msg.indexOf(accepts.get(i)) >= 0) {
          acceptable = true;
        }
      }

      println("no" + (acceptable ? " (OK error message)" : ""));
      result[1] = acceptable;

      if (m_Debug) {
        println("\n=== Full Report ===");
        print("Problem during training");
        println(": " + ex.getMessage() + "\n");
        if (!acceptable) {
          if (accepts.size() > 0) {
            print("Error message doesn't mention ");
            for (int i = 0; i < accepts.size(); i++) {
              if (i != 0) {
                print(" or ");
              }
              print('"' + accepts.get(i) + '"');
            }
          }
          println("here is the dataset:\n");
          println("=== Train Dataset ===\n" + train.toString() + "\n");
        }
      }
    }

    return result;
  }

  /**
   * Make a simple set of instances, which can later be modified for use in
   * specific tests.
   * 
   * @param seed the random number seed
   * @param numInstances the number of instances to generate
   * @param numNominal the number of nominal attributes
   * @param numNumeric the number of numeric attributes
   * @param numString the number of string attributes
   * @param numDate the number of date attributes
   * @param numRelational the number of relational attributes
   * @param numClasses the number of classes (if nominal class)
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param multiInstance whether the dataset should a multi-instance dataset
   * @return the test dataset
   * @throws Exception if the dataset couldn't be generated
   * @see #process(Instances)
   */
  protected Instances makeTestDataset(int seed, int numInstances,
    int numNominal, int numNumeric, int numString, int numDate,
    int numRelational, int numClasses, int classType, boolean multiInstance)
    throws Exception {

    return makeTestDataset(seed, numInstances, numNominal, numNumeric,
      numString, numDate, numRelational, numClasses, classType,
      TestInstances.CLASS_IS_LAST, multiInstance);
  }

  /**
   * Make a simple set of instances with variable position of the class
   * attribute, which can later be modified for use in specific tests.
   * 
   * @param seed the random number seed
   * @param numInstances the number of instances to generate
   * @param numNominal the number of nominal attributes
   * @param numNumeric the number of numeric attributes
   * @param numString the number of string attributes
   * @param numDate the number of date attributes
   * @param numRelational the number of relational attributes
   * @param numClasses the number of classes (if nominal class)
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   * @param classIndex the index of the class (0-based, -1 as last)
   * @param multiInstance whether the dataset should a multi-instance dataset
   * @return the test dataset
   * @throws Exception if the dataset couldn't be generated
   * @see TestInstances#CLASS_IS_LAST
   * @see #process(Instances)
   */
  protected Instances makeTestDataset(int seed, int numInstances,
    int numNominal, int numNumeric, int numString, int numDate,
    int numRelational, int numClasses, int classType, int classIndex,
    boolean multiInstance) throws Exception {

    TestInstances dataset = new TestInstances();

    dataset.setSeed(seed);
    dataset.setNumInstances(numInstances);
    dataset.setNumNominal(numNominal);
    dataset.setNumNumeric(numNumeric);
    dataset.setNumString(numString);
    dataset.setNumDate(numDate);
    dataset.setNumRelational(numRelational);
    dataset.setNumClasses(numClasses);
    dataset.setClassType(classType);
    dataset.setClassIndex(classIndex);
    dataset.setNumClasses(numClasses);
    dataset.setMultiInstance(multiInstance);
    dataset.setWords(getWords());
    dataset.setWordSeparators(getWordSeparators());

    return process(dataset.generate());
  }

  /**
   * Print out a short summary string for the dataset characteristics
   * 
   * @param nominalPredictor true if nominal predictor attributes are present
   * @param numericPredictor true if numeric predictor attributes are present
   * @param stringPredictor true if string predictor attributes are present
   * @param datePredictor true if date predictor attributes are present
   * @param relationalPredictor true if relational predictor attributes are
   *          present
   * @param multiInstance whether multi-instance is needed
   * @param classType the class type (NUMERIC, NOMINAL, etc.)
   */
  protected void printAttributeSummary(boolean nominalPredictor,
    boolean numericPredictor, boolean stringPredictor, boolean datePredictor,
    boolean relationalPredictor, boolean multiInstance, int classType) {

    String str = "";

    if (numericPredictor) {
      str += " numeric";
    }

    if (nominalPredictor) {
      if (str.length() > 0) {
        str += " &";
      }
      str += " nominal";
    }

    if (stringPredictor) {
      if (str.length() > 0) {
        str += " &";
      }
      str += " string";
    }

    if (datePredictor) {
      if (str.length() > 0) {
        str += " &";
      }
      str += " date";
    }

    if (relationalPredictor) {
      if (str.length() > 0) {
        str += " &";
      }
      str += " relational";
    }

    str += " predictors)";

    switch (classType) {
    case Attribute.NUMERIC:
      str = " (numeric class," + str;
      break;
    case Attribute.NOMINAL:
      str = " (nominal class," + str;
      break;
    case Attribute.STRING:
      str = " (string class," + str;
      break;
    case Attribute.DATE:
      str = " (date class," + str;
      break;
    case Attribute.RELATIONAL:
      str = " (relational class," + str;
      break;
    }

    print(str);
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 15517 $");
  }

  /**
   * Test method for this class
   * 
   * @param args the commandline parameters
   */
  public static void main(String[] args) {
    runCheck(new CheckAttributeSelection(), args);
  }
}