content: /*
   *    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 2 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, write to the Free Software
   *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
   */
  
  /*
   *    Copy.java
   *    Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
   *
   */
  
  
  package weka.filters.unsupervised.attribute;
  
  import weka.core.Attribute;
  import weka.core.Capabilities;
  import weka.core.Instance; 
  import weka.core.DenseInstance;
  import weka.core.Instances;
  import weka.core.Option;
  import weka.core.OptionHandler;
  import weka.core.Range;
  import weka.core.RevisionUtils;
  import weka.core.SparseInstance;
  import weka.core.Utils;
  import weka.core.Capabilities.Capability;
  import weka.filters.Filter;
  import weka.filters.StreamableFilter;
  import weka.filters.UnsupervisedFilter;
  
  import java.util.Enumeration;
  import java.util.Vector;
  
  /** 
   <!-- globalinfo-start -->
   * An instance filter that copies a range of attributes in the dataset. This is used in conjunction with other filters that overwrite attribute values during the course of their operation -- this filter allows the original attributes to be kept as well as the new attributes.
   * <p/>
   <!-- globalinfo-end -->
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -R &lt;index1,index2-index4,...&gt;
   *  Specify list of columns to copy. First and last are valid
   *  indexes. (default none)</pre>
   * 
   * <pre> -V
   *  Invert matching sense (i.e. copy all non-specified columns)</pre>
   * 
   <!-- options-end -->
   *
   * @author Len Trigg (trigg@cs.waikato.ac.nz)
   * @version $Revision: 6997 $
   */
  public class Copy 
    extends Filter 
    implements UnsupervisedFilter, StreamableFilter, OptionHandler {
    
    /** for serialization */
    static final long serialVersionUID = -8543707493627441566L;
  
    /** Stores which columns to copy */
    protected Range m_CopyCols = new Range();
  
    /**
     * Stores the indexes of the selected attributes in order, once the
     * dataset is seen
     */
    protected int [] m_SelectedAttributes;
  
    /**
     * Returns an enumeration describing the available options.
     *
     * @return an enumeration of all the available options.
     */
    public Enumeration listOptions() {
  
      Vector newVector = new Vector(2);
  
      newVector.addElement(new Option(
                "\tSpecify list of columns to copy. First and last are valid\n"
  	      +"\tindexes. (default none)",
                "R", 1, "-R <index1,index2-index4,...>"));
      newVector.addElement(new Option(
  	      "\tInvert matching sense (i.e. copy all non-specified columns)",
                "V", 0, "-V"));
  
      return newVector.elements();
    }
  
    /**
     * Parses a given list of options. <p/>
     * 
     <!-- options-start -->
     * Valid options are: <p/>
     * 
     * <pre> -R &lt;index1,index2-index4,...&gt;
     *  Specify list of columns to copy. First and last are valid
     *  indexes. (default none)</pre>
     * 
     * <pre> -V
     *  Invert matching sense (i.e. copy all non-specified columns)</pre>
     * 
     <!-- options-end -->
     *
     * @param options the list of options as an array of strings
     * @throws Exception if an option is not supported
     */
    public void setOptions(String[] options) throws Exception {
  
      String copyList = Utils.getOption('R', options);
      if (copyList.length() != 0) {
        setAttributeIndices(copyList);
      }
      setInvertSelection(Utils.getFlag('V', options));
      
      if (getInputFormat() != null) {
        setInputFormat(getInputFormat());
      }
    }
  
    /**
     * Gets the current settings of the filter.
     *
     * @return an array of strings suitable for passing to setOptions
     */
    public String [] getOptions() {
  
      String [] options = new String [3];
      int current = 0;
  
      if (getInvertSelection()) {
        options[current++] = "-V";
      }
      if (!getAttributeIndices().equals("")) {
        options[current++] = "-R"; options[current++] = getAttributeIndices();
      }
  
      while (current < options.length) {
        options[current++] = "";
      }
      return options;
    }
  
    /** 
     * Returns the Capabilities of this filter.
     *
     * @return            the capabilities of this object
     * @see               Capabilities
     */
    public Capabilities getCapabilities() {
      Capabilities result = super.getCapabilities();
      result.disableAll();
  
      // attributes
      result.enableAllAttributes();
      result.enable(Capability.MISSING_VALUES);
      
      // class
      result.enableAllClasses();
      result.enable(Capability.MISSING_CLASS_VALUES);
      result.enable(Capability.NO_CLASS);
      
      return result;
    }
  
    /**
     * Sets the format of the input instances.
     *
     * @param instanceInfo an Instances object containing the input instance
     * structure (any instances contained in the object are ignored - only the
     * structure is required).
     * @return true if the outputFormat may be collected immediately
     * @throws Exception if a problem occurs setting the input format
     */
    public boolean setInputFormat(Instances instanceInfo) throws Exception {
  
      super.setInputFormat(instanceInfo);
      
      m_CopyCols.setUpper(instanceInfo.numAttributes() - 1);
  
      // Create the output buffer
      Instances outputFormat = new Instances(instanceInfo, 0); 
      m_SelectedAttributes = m_CopyCols.getSelection();
      for (int i = 0; i < m_SelectedAttributes.length; i++) {
        int current = m_SelectedAttributes[i];
        // Create a copy of the attribute with a different name
        Attribute origAttribute = instanceInfo.attribute(current);
        outputFormat.insertAttributeAt((Attribute)origAttribute.copy("Copy of " + origAttribute.name()),
  				     outputFormat.numAttributes());
  
      }
  
      // adapt locators
      int[] newIndices = new int[instanceInfo.numAttributes() + m_SelectedAttributes.length];
      for (int i = 0; i < instanceInfo.numAttributes(); i++)
        newIndices[i] = i;
      for (int i = 0; i < m_SelectedAttributes.length; i++)
        newIndices[instanceInfo.numAttributes() + i] = m_SelectedAttributes[i];
      initInputLocators(instanceInfo, newIndices);
  
      setOutputFormat(outputFormat);
      
      return true;
    }
    
  
    /**
     * Input an instance for filtering. Ordinarily the instance is processed
     * and made available for output immediately. Some filters require all
     * instances be read before producing output.
     *
     * @param instance the input instance
     * @return true if the filtered instance may now be
     * collected with output().
     * @throws IllegalStateException if no input format has been defined.
     */
    public boolean input(Instance instance) {
  
      if (getInputFormat() == null) {
        throw new IllegalStateException("No input instance format defined");
      }
      if (m_NewBatch) {
        resetQueue();
        m_NewBatch = false;
      }
  
      double[] vals = new double[outputFormatPeek().numAttributes()];
      for(int i = 0; i < getInputFormat().numAttributes(); i++) {
        vals[i] = instance.value(i);
      }
      int j = getInputFormat().numAttributes();
      for (int i = 0; i < m_SelectedAttributes.length; i++) {
        int current = m_SelectedAttributes[i];
        vals[i + j] = instance.value(current);
      }
      Instance inst = null;
      if (instance instanceof SparseInstance) {
        inst = new SparseInstance(instance.weight(), vals);
      } else {
        inst = new DenseInstance(instance.weight(), vals);
      }
      
      inst.setDataset(getOutputFormat());
      copyValues(inst, false, instance.dataset(), getOutputFormat());
      inst.setDataset(getOutputFormat());
      push(inst);
      return true;
    }
  
    /**
     * Returns a string describing this filter
     *
     * @return a description of the filter suitable for
     * displaying in the explorer/experimenter gui
     */
    public String globalInfo() {
  
      return "An instance filter that copies a range of attributes in the"
        + " dataset. This is used in conjunction with other filters that"
        + " overwrite attribute values during the course of their operation --"
        + " this filter allows the original attributes to be kept as well"
        + " as the new attributes.";
    }
  
    /**
     * Returns the tip text for this property
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String invertSelectionTipText() {
      return "Sets copy selected vs unselected action."
        + " If set to false, only the specified attributes will be copied;"
        + " If set to true, non-specified attributes will be copied.";
    }
  
    /**
     * Get whether the supplied columns are to be removed or kept
     *
     * @return true if the supplied columns will be kept
     */
    public boolean getInvertSelection() {
  
      return m_CopyCols.getInvert();
    }
  
    /**
     * Set whether selected columns should be removed or kept. If true the 
     * selected columns are kept and unselected columns are copied. If false
     * selected columns are copied and unselected columns are kept. <br>
     * Note: use this method before you call 
     * <code>setInputFormat(Instances)</code>, since the output format is
     * determined in that method.
     *
     * @param invert the new invert setting
     */
    public void setInvertSelection(boolean invert) {
  
      m_CopyCols.setInvert(invert);
    }
  
    /**
     * Get the current range selection
     *
     * @return a string containing a comma separated list of ranges
     */
    public String getAttributeIndices() {
  
      return m_CopyCols.getRanges();
    }
  
    /**
     * Returns the tip text for this property
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String attributeIndicesTipText() {
      return "Specify range of attributes to act on."
        + " This is a comma separated list of attribute indices, with"
        + " \"first\" and \"last\" valid values. Specify an inclusive"
        + " range with \"-\". E.g: \"first-3,5,6-10,last\".";
    }
  
    /**
     * Set which attributes are to be copied (or kept if invert is true)
     *
     * @param rangeList a string representing the list of attributes.  Since
     * the string will typically come from a user, attributes are indexed from
     * 1. <br>
     * eg: first-3,5,6-last<br>
     * Note: use this method before you call 
     * <code>setInputFormat(Instances)</code>, since the output format is
     * determined in that method.
     * @throws Exception if an invalid range list is supplied
     */
    public void setAttributeIndices(String rangeList) throws Exception {
  
      m_CopyCols.setRanges(rangeList);
    }
  
    /**
     * Set which attributes are to be copied (or kept if invert is true)
     *
     * @param attributes an array containing indexes of attributes to select.
     * Since the array will typically come from a program, attributes are indexed
     * from 0.<br>
     * Note: use this method before you call 
     * <code>setInputFormat(Instances)</code>, since the output format is
     * determined in that method.
     * @throws Exception if an invalid set of ranges is supplied
     */
    public void setAttributeIndicesArray(int [] attributes) throws Exception {
  
      setAttributeIndices(Range.indicesToRangeList(attributes));
    }
    
    /**
     * Returns the revision string.
     * 
     * @return		the revision
     */
    public String getRevision() {
      return RevisionUtils.extract("$Revision: 6997 $");
    }
  
    /**
     * Main method for testing this class.
     *
     * @param argv should contain arguments to the filter: use -h for help
     */
    public static void main(String [] argv) {
      runFilter(new Copy(), argv);
    }
  }
  