bifparser.java

MacroWeka扩展了著名数据挖掘工具weka

/*
 *    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.
 */

/*
 *    BIFParser.java
 *    Copyright (C) 2003 Ashraf M. Kibriya
 *
 */
package weka.gui.graphvisualizer;

import java.io.InputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringReader;
import java.util.StringTokenizer;

import weka.core.FastVector;

import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
import org.w3c.dom.Element;


/**
 * This class parses an inputstream or a string in
 * XMLBIF ver. 0.3 format, and builds the datastructures
 * that are passed to it through the constructor.
 *
 * @author Ashraf M. Kibriya ([e-mail])
 * @version $Revision: 1.1 $ - 24 Apr 2003 - Initial version (Ashraf M. Kibriya)
 */
public class BIFParser implements GraphConstants {
  
  /** These holds the nodes and edges of the graph */
  protected FastVector m_nodes, m_edges;
  /**  This holds the name of the graph (i.e. the name of network tag in XMLBIF
   * input)
   */
  protected String graphName;
  /** This holds the string to be parsed */
  protected String inString;
  /** This holds the InputStream to be parsed */
  protected InputStream inStream;
  
  
  /**
   * Constructor (if our input is a String)
   *
   * @param input the string to be parsed (should not be null)
   * @param nodes vector containing GraphNode objects (should be empty)
   * @param edges vector containing GraphEdge objects (should be empty)
   */
  public BIFParser(String input, FastVector nodes, FastVector edges) {
    m_nodes = nodes; m_edges = edges; inString = input;
  }
  
  
  /**
   * Constructor (if our input is an InputStream)
   *
   * @param instream the InputStream to be parsed (should not be null)
   * @param nodes vector containing GraphNode objects (should be empty)
   * @param edges vector containing GraphEdge objects (should be empty)
   */
  public BIFParser(InputStream instream, FastVector nodes, FastVector edges) {
    m_nodes = nodes; m_edges = edges; inStream = instream;
  }
  
  
  /**
   * This method parses the string or the InputStream that we
   * passed in through the constructor and builds up the
   * m_nodes and m_edges vectors
   * @exception - Exception if both the inString and inStream are
   *              null, i.e. no input has been provided
   * @exception - BIFFormatException if there is format of the
   *              input is not correct. The format should conform to
   *              XMLBIF version 0.3
   * @exception - NumberFormatException if there is an invalid
   *              char in the probability table of a node.
   * @return    - returns the name of the graph
   */
  public String parse() throws Exception {
    Document dc=null;
    
    javax.xml.parsers.DocumentBuilderFactory dbf =
    javax.xml.parsers.DocumentBuilderFactory.newInstance();
    dbf.setIgnoringElementContentWhitespace(true);
    javax.xml.parsers.DocumentBuilder db = dbf.newDocumentBuilder();
    
    if(inStream!=null)
      dc = db.parse(inStream);
    else if(inString!=null)
      dc = db.parse(new org.xml.sax.InputSource(new StringReader(inString)));
    else
    { throw new Exception("No input given"); }
    
    NodeList nl = dc.getElementsByTagName( "NETWORK" );
    
    if(nl.getLength()==0) {
      throw new BIFFormatException( "NETWORK tag not found" );
    }
    
    //take only the first network node
    NodeList templist = ((Element)nl.item(0)).getElementsByTagName( "NAME" );
    graphName = templist.item(0).getFirstChild().getNodeValue();
    //System.out.println("The name of the network is "+
    //templist.item(0).getFirstChild().getNodeValue());
    
    //Get all the variables
    nl = dc.getElementsByTagName("VARIABLE");
    for(int i=0; i<nl.getLength(); i++) {
      
      templist = ((Element)nl.item(i)).getElementsByTagName("NAME");
      if(templist.getLength()>1)
        throw new BIFFormatException("More than one name tags found for "+
        "variable no. "+(i+1));
      
      String nodename =
      ((org.w3c.dom.Node)templist.item(0)).getFirstChild().getNodeValue();
      GraphNode n = new GraphNode( nodename, nodename, GraphNode.NORMAL );
      m_nodes.addElement(n);
      //getting nodes position
      templist = ((Element)nl.item(i)).getElementsByTagName("PROPERTY");
      for(int j=0; j<templist.getLength(); j++) {
        if( ((org.w3c.dom.Node)templist.item(j)).getFirstChild()
        .getNodeValue().startsWith("position") ) {
          String xy = templist.item(j).getFirstChild().getNodeValue();
          //System.out.println("x: "+
          //                   xy.substring(xy.indexOf('(')+1, xy.indexOf(','))+
          //                   " y: "+
          //                   xy.substring(xy.indexOf(',')+1, xy.indexOf(')'))
          //                  );
          n.x = Integer.parseInt( xy.substring(xy.indexOf('(')+
          1, xy.indexOf(',')).trim() );
          n.y = Integer.parseInt( xy.substring(xy.indexOf(',')+
          1, xy.indexOf(')')).trim() );
          break;
        }
      }
      //getting all the outcomes of the node
      templist = ((Element)nl.item(i)).getElementsByTagName("OUTCOME");
      n.outcomes = new String[templist.getLength()];
      for(int j=0; j<templist.getLength(); j++) {
        n.outcomes[j] = templist.item(j).getFirstChild().getNodeValue();
        //System.out.println("Outcome["+j+"]: "+n.outcomes[j]);
      }
    } //end for (for variables)
    
    //Get all the edges and probability tables by getting all the definitions
    nl = dc.getElementsByTagName("DEFINITION");
    for(int i=0; i<nl.getLength(); i++) {
      
      templist = ((Element)nl.item(i)).getElementsByTagName("FOR");
      //the Label of the node the edges are coming into
      String nid = templist.item(0).getFirstChild().getNodeValue();
      
      //getting the GraphNode object with the above label
      GraphNode n = (GraphNode)m_nodes.elementAt(0);
      for(int j=1; j<m_nodes.size() && !n.ID.equals(nid); j++)
        n = (GraphNode)m_nodes.elementAt(j);
      
      
      templist = ((Element)nl.item(i)).getElementsByTagName("GIVEN");
      int parntOutcomes = 1; //for creating the probability table later on
      //creating all the edges coming into the node
      for(int j=0; j<templist.getLength(); j++) {
        nid = templist.item(j).getFirstChild().getNodeValue();
        
        GraphNode n2 = (GraphNode)m_nodes.elementAt(0);
        for(int k=1; k<m_nodes.size() && !n2.ID.equals(nid); k++)
          n2 = (GraphNode)m_nodes.elementAt(k);
        m_edges.addElement( new GraphEdge(m_nodes.indexOf(n2),
        m_nodes.indexOf(n), 1) );
        
        parntOutcomes *= n2.outcomes.length;
      }
      
      //creating the probability table for the node
      templist = ((Element)nl.item(i)).getElementsByTagName("TABLE");
      if(templist.getLength()>1)
        throw new BIFFormatException("More than one Probability Table for "+
        n.ID);
      
      String probs = templist.item(0).getFirstChild().getNodeValue();
      StringTokenizer tk = new StringTokenizer(probs, " \n\t");
      
      if(parntOutcomes*n.outcomes.length > tk.countTokens())