/*
* 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.
*/
/*
* FromFile.java
* Copyright (C) 2004 University of Waikato, Hamilton, New Zealand
*
*/
package weka.classifiers.bayes.net.search.fixed;
import weka.classifiers.bayes.BayesNet;
import weka.classifiers.bayes.net.BIFReader;
import weka.classifiers.bayes.net.ParentSet;
import weka.classifiers.bayes.net.search.SearchAlgorithm;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.Utils;
import java.util.Enumeration;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* The FromFile reads the structure of a Bayes net from a file in BIFF format.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -B <BIF File>
* Name of file containing network structure in BIF format
* </pre>
*
<!-- options-end -->
*
* @author Remco Bouckaert
* @version $Revision: 1.8 $
*/
public class FromFile
extends SearchAlgorithm {
/** for serialization */
static final long serialVersionUID = 7334358169507619525L;
/** name of file to read structure from **/
String m_sBIFFile = "";
/**
* Returns a string describing this object
* @return a description of the classifier suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return
"The FromFile reads the structure of a Bayes net from a file "
+ "in BIFF format.";
}
/**
*
* @param bayesNet
* @param instances the instances to work with
* @throws Exception if attribute from BIF file could not be found
*/
public void buildStructure (BayesNet bayesNet, Instances instances) throws Exception {
// read network structure in BIF format
BIFReader bifReader = new BIFReader();
bifReader.processFile(m_sBIFFile);
// copy parent sets
for (int iAttribute = 0; iAttribute < instances.numAttributes(); iAttribute++) {
int iBIFAttribute = bifReader.getNode(bayesNet.getNodeName(iAttribute));
ParentSet bifParentSet = bifReader.getParentSet(iBIFAttribute);
for (int iBIFParent = 0; iBIFParent < bifParentSet.getNrOfParents(); iBIFParent++) {
String sParent = bifReader.getNodeName(bifParentSet.getParent(iBIFParent));
int iParent = 0;
while (iParent < instances.numAttributes() && !bayesNet.getNodeName(iParent).equals(sParent)) {
iParent++;
}
if (iParent >= instances.numAttributes()) {
throw new Exception("Could not find attribute " + sParent + " from BIF file in data");
}
bayesNet.getParentSet(iAttribute).addParent(iParent, instances);
}
}
} // buildStructure
/**
* Set name of network in BIF file to read structure from
*
* @param sBIFFile the name of the BIF file
*/
public void setBIFFile(String sBIFFile) {
m_sBIFFile = sBIFFile;
}
/**
* Get name of network in BIF file to read structure from
* @return BIF file name
*/
public String getBIFFile() {
return m_sBIFFile;
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector();
newVector.addElement(new Option("\tName of file containing network structure in BIF format\n",
"B", 1, "-B <BIF File>"));
Enumeration en = super.listOptions();
while (en.hasMoreElements())
newVector.addElement(en.nextElement());
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -B <BIF File>
* Name of file containing network structure in BIF format
* </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 {
setBIFFile( Utils.getOption('B', options));
super.setOptions(options);
}
/**
* Gets the current settings of the search algorithm.
*
* @return an array of strings suitable for passing to setOptions
*/
public String [] getOptions() {
String[] superOptions = super.getOptions();
String [] options = new String [2 + superOptions.length];
int current = 0;
options[current++] = "-B";
options[current++] = "" + getBIFFile();
// insert options from parent class
for (int iOption = 0; iOption < superOptions.length; iOption++) {
options[current++] = superOptions[iOption];
}
// Fill up rest with empty strings, not nulls!
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.8 $");
}
} // class FromFile