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    The Waikato Environment for Knowledge Analysis (WEKA), a machine learning workbench. This version represents the developer version, the "bleeding edge" of development, you could say. New functionality gets added to this version.

    There is a newer version: 3.9.6
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    /*
 *   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 .
 */

/*
 * XMLBeans.java
 * Copyright (C) 2005-2012 University of Waikato, Hamilton, New Zealand
 */

package weka.gui.beans.xml;

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Point;
import java.beans.BeanInfo;
import java.beans.EventSetDescriptor;
import java.beans.Introspector;
import java.beans.beancontext.BeanContextSupport;
import java.io.File;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;

import javax.swing.JComponent;
import javax.swing.JPanel;
import javax.swing.plaf.ColorUIResource;
import javax.swing.plaf.FontUIResource;

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

import weka.core.Environment;
import weka.core.EnvironmentHandler;
import weka.core.WekaPackageClassLoaderManager;
import weka.core.converters.ConverterUtils;
import weka.core.xml.XMLBasicSerialization;
import weka.core.xml.XMLDocument;
import weka.gui.beans.BeanCommon;
import weka.gui.beans.BeanConnection;
import weka.gui.beans.BeanInstance;
import weka.gui.beans.BeanVisual;
import weka.gui.beans.MetaBean;
import weka.gui.beans.Visible;

/**
 * This class serializes and deserializes a KnowledgeFlow setup to and fro XML. 
    
 * 
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 13476 $
 */
public class XMLBeans extends XMLBasicSerialization {

  /** the value of the id property */
  public final static String VAL_ID = "id";

  /** the value of the x property */
  public final static String VAL_X = "x";

  /** the value of the y property */
  public final static String VAL_Y = "y";

  /** the value of the bean property */
  public final static String VAL_BEAN = "bean";

  /** the value of the customName property */
  public final static String VAL_CUSTOM_NAME = "custom_name";

  /** the value of the source property */
  public final static String VAL_SOURCEID = "source_id";

  /** the value of the target property */
  public final static String VAL_TARGETID = "target_id";

  /** the value of the eventname property */
  public final static String VAL_EVENTNAME = "eventname";

  /** the value of the hidden property */
  public final static String VAL_HIDDEN = "hidden";

  /** the value of the file property */
  public final static String VAL_FILE = "file";

  /** the value of the dir property */
  public final static String VAL_DIR = "dir";

  /** the value of the prefix property */
  public final static String VAL_PREFIX = "prefix";

  public final static String VAL_RELATIVE_PATH = "useRelativePath";

  /** the value of the options property */
  public final static String VAL_OPTIONS = "options";

  /** the value of the saver property */
  public final static String VAL_SAVER = "wrappedAlgorithm";

  /** the value of the loader property */
  public final static String VAL_LOADER = "wrappedAlgorithm";

  /** the value of the text property */
  public final static String VAL_TEXT = "text";

  /** the value of the beanContext property */
  public final static String VAL_BEANCONTEXT = "beanContext";

  /** the value of the width property */
  public final static String VAL_WIDTH = "width";

  /** the value of the height property */
  public final static String VAL_HEIGHT = "height";

  /** the value of the red property */
  public final static String VAL_RED = "red";

  /** the value of the green property */
  public final static String VAL_GREEN = "green";

  /** the value of the blue property */
  public final static String VAL_BLUE = "blue";

  /** the value of the value property */
  public final static String VAL_NAME = "name";

  /** the value of the style property */
  public final static String VAL_STYLE = "style";

  /** the value of the location property */
  public final static String VAL_LOCATION = "location";

  /** the value of the size property */
  public final static String VAL_SIZE = "size";

  /** the value of the color property */
  public final static String VAL_COLOR = "color";

  /** the value of the font property */
  public final static String VAL_FONT = "font";

  /** the value of the iconpath property */
  public final static String VAL_ICONPATH = "iconPath";

  /** the value of the animatedIconPath property */
  public final static String VAL_ANIMATEDICONPATH = "animatedIconPath";

  /** the value of the associatedConnections property */
  public final static String VAL_ASSOCIATEDCONNECTIONS = "associatedConnections";

  /** the value of the input property */
  public final static String VAL_INPUTS = "inputs";

  /** the value of the input id property */
  public final static String VAL_INPUTSID = "inputs_id";

  /** the value of the outputs id property */
  public final static String VAL_OUTPUTS = "outputs";

  /** the value of the outputs property */
  public final static String VAL_OUTPUTSID = "outputs_id";

  /** the value of the subFlow property */
  public final static String VAL_SUBFLOW = "subFlow";

  /** the value of the originalCoords property */
  public final static String VAL_ORIGINALCOORDS = "originalCoords";

  /** the value of the relationNameForFilename property (Saver) */
  public final static String VAL_RELATIONNAMEFORFILENAME = "relationNameForFilename";

  /**
   * the index in the Vector, where the BeanInstances are stored (Instances and
   * Connections are stored in a Vector and then serialized)
   */
  public final static int INDEX_BEANINSTANCES = 0;

  /**
   * the index in the Vector, where the BeanConnections are stored (Instances
   * and Connections are stored in a Vector and then serialized)
   */
  public final static int INDEX_BEANCONNECTIONS = 1;

  /** the component that manages the layout of the beans */
  protected JComponent m_BeanLayout;

  /** keeps track of the BeanInstances read so far, used for the BeanConnections */
  protected Vector m_BeanInstances;

  /** keeps track of the BeanInstances read so far, used for the BeanConnections */
  protected Vector m_BeanInstancesID;

  /** whether to ignore the BeanConnection */
  protected boolean m_IgnoreBeanConnections;

  /** the current MetaBean (for the BeanConnections) */
  protected MetaBean m_CurrentMetaBean;

  /** the identifier for regular BeanConnections */
  protected final static String REGULAR_CONNECTION = "regular_connection";

  /**
   * the relation between Bean and connection, MetaBean BeanConnections are
   * stored under the reference of the MetaBean, regular connections are stored
   * under REGULAR_CONNECTION. The relation has the following format (is a
   * string): sourcePos,targetPos,event,hidden
   * 
   * @see #REGULAR_CONNECTION
   */
  protected Hashtable> m_BeanConnectionRelation;

  /**
   * the data that is about to be read/written contains a complete layout
   * 
   * @see #m_DataType
   */
  public final static int DATATYPE_LAYOUT = 0;

  /**
   * the data that is about to be read/written contains user-components, i.e.,
   * Metabeans
   * 
   * @see #m_DataType
   */
  public final static int DATATYPE_USERCOMPONENTS = 1;

  /**
   * the type of data that is be read/written
   * 
   * @see #DATATYPE_LAYOUT
   * @see #DATATYPE_USERCOMPONENTS
   */
  protected int m_DataType = DATATYPE_LAYOUT;

  /**
   * the beancontext to use for loading from XML and the beancontext is null in
   * the bean
   */
  protected BeanContextSupport m_BeanContextSupport = null;

  /**
   * The index of the vector of bean instances or connections to use. this
   * corresponds to a tab in the main KnowledgeFlow UI
   */
  protected int m_vectorIndex = 0;

  /**
   * initializes the serialization for layouts
   * 
   * @param layout the component that manages the layout
   * @param context the bean context support to use
   * @param tab the index of the vector of bean instances or connections to use
   *          (this corresponds to a visible tab in the main KnowledgeFlow UI)
   * @throws Exception if initialization fails
   */
  public XMLBeans(JComponent layout, BeanContextSupport context, int tab) throws Exception {
    this(layout, context, DATATYPE_LAYOUT, tab);
  }

  /**
   * initializes the serialization for different types of data
   * 
   * @param layout the component that manages the layout
   * @param context the bean context support to use
   * @param datatype the type of data to read/write
   * @throws Exception if initialization fails
   */
  public XMLBeans(JComponent layout, BeanContextSupport context, int datatype,
    int tab) throws Exception {
    super();

    m_vectorIndex = tab;
    m_BeanLayout = layout;
    m_BeanContextSupport = context;
    setDataType(datatype);
  }

  /**
   * sets what kind of data is to be read/written
   * 
   * @param value the type of data
   * @see #m_DataType
   */
  public void setDataType(int value) {
    if (value == DATATYPE_LAYOUT) {
      m_DataType = value;
    } else if (value == DATATYPE_USERCOMPONENTS) {
      m_DataType = value;
    } else {
      System.out.println("DataType '" + value + "' is unknown!");
    }
  }

  /**
   * returns the type of data that is to be read/written
   * 
   * @return the type of data
   * @see #m_DataType
   */
  public int getDataType() {
    return m_DataType;
  }

  /**
   * generates internally a new XML document and clears also the IgnoreList and
   * the mappings for the Read/Write-Methods
   * 
   * @throws Exception if something goes wrong
   */
  @Override
  public void clear() throws Exception {
    Vector classnames;
    int i;

    super.clear();

    // ignore: suppress unnecessary GUI stuff
    // needs to be checked for new Java versions (might introduce new
    // properties)
    // - works with Java 1.5
    m_Properties.addIgnored("UI");
    m_Properties.addIgnored("actionMap");
    m_Properties.addIgnored("alignmentX");
    m_Properties.addIgnored("alignmentY");
    m_Properties.addIgnored("autoscrolls");
    m_Properties.addIgnored("background");
    m_Properties.addIgnored("border");
    m_Properties.addIgnored("componentPopupMenu");
    m_Properties.addIgnored("debugGraphicsOptions");
    m_Properties.addIgnored("doubleBuffered");
    m_Properties.addIgnored("enabled");
    m_Properties.addIgnored("focusCycleRoot");
    m_Properties.addIgnored("focusTraversalPolicy");
    m_Properties.addIgnored("focusTraversalPolicyProvider");
    m_Properties.addIgnored("focusable");
    m_Properties.addIgnored("font");
    m_Properties.addIgnored("foreground");
    m_Properties.addIgnored("inheritsPopupMenu");
    m_Properties.addIgnored("inputVerifier");
    m_Properties.addIgnored("layout");
    m_Properties.addIgnored("locale");
    m_Properties.addIgnored("maximumSize");
    m_Properties.addIgnored("minimumSize");
    m_Properties.addIgnored("nextFocusableComponent");
    m_Properties.addIgnored("opaque");
    m_Properties.addIgnored("preferredSize");
    m_Properties.addIgnored("requestFocusEnabled");
    m_Properties.addIgnored("toolTipText");
    m_Properties.addIgnored("transferHandler");
    m_Properties.addIgnored("verifyInputWhenFocusTarget");
    m_Properties.addIgnored("visible");

    // special ignore
    m_Properties.addIgnored("size"); // otherwise you get an endless loop with
                                     // Dimension!
    m_Properties.addIgnored("location"); // otherwise you get an endless loop
                                         // with Point!

    // allow
    m_Properties.addAllowed(weka.gui.beans.BeanInstance.class, "x");
    m_Properties.addAllowed(weka.gui.beans.BeanInstance.class, "y");
    m_Properties.addAllowed(weka.gui.beans.BeanInstance.class, "bean");
    m_Properties.addAllowed(weka.gui.beans.Saver.class, "wrappedAlgorithm");
    m_Properties.addAllowed(weka.gui.beans.Loader.class, "wrappedAlgorithm");
    m_Properties.addAllowed(weka.gui.beans.Saver.class,
      "relationNameForFilename");
    if (getDataType() == DATATYPE_LAYOUT) {
      m_Properties.addAllowed(weka.gui.beans.Loader.class, "beanContext");
    } else {
      m_Properties.addIgnored(weka.gui.beans.Loader.class, "beanContext"); // TODO:
                                                                           // more
                                                                           // classes???
    }
    m_Properties.addAllowed(weka.gui.beans.Filter.class, "filter");
    m_Properties.addAllowed(weka.gui.beans.Associator.class, "associator");
    m_Properties
      .addAllowed(weka.gui.beans.Classifier.class, "wrappedAlgorithm");
    m_Properties.addAllowed(weka.gui.beans.Clusterer.class, "wrappedAlgorithm");
    m_Properties.addAllowed(weka.gui.beans.Classifier.class, "executionSlots");
    m_Properties.addAllowed(weka.gui.beans.Classifier.class, "blockOnLastFold");
    m_Properties.addAllowed(weka.gui.beans.Classifier.class,
      "resetIncrementalClassifier");
    m_Properties.addAllowed(weka.gui.beans.Classifier.class,
      "updateIncrementalClassifier");
    m_Properties.addAllowed(weka.gui.beans.Classifier.class,
      "loadClassifierFileName");

    m_Properties.addAllowed(weka.classifiers.Classifier.class, "debug");
    m_Properties.addAllowed(weka.classifiers.Classifier.class, "options");
    m_Properties.addAllowed(weka.associations.Associator.class, "options");
    m_Properties.addAllowed(weka.clusterers.Clusterer.class, "options");
    m_Properties.addAllowed(weka.filters.Filter.class, "options");
    m_Properties.addAllowed(weka.core.converters.Saver.class, "options");
    m_Properties.addAllowed(weka.core.converters.Loader.class, "options");

    m_Properties
      .addAllowed(weka.core.converters.DatabaseSaver.class, "options");
    m_Properties.addAllowed(weka.core.converters.DatabaseLoader.class,
      "options");
    m_Properties.addAllowed(weka.core.converters.TextDirectoryLoader.class,
      "options");

    // we assume that classes implementing SplitEvaluator also implement
    // OptionHandler
    m_Properties.addAllowed(weka.experiment.SplitEvaluator.class, "options");
    // we assume that classes implementing ResultProducer also implement
    // OptionHandler
    m_Properties.addAllowed(weka.experiment.ResultProducer.class, "options");

    // read/write methods
    m_CustomMethods.register(this, Color.class, "Color");
    m_CustomMethods.register(this, Dimension.class, "Dimension");
    m_CustomMethods.register(this, Font.class, "Font");
    m_CustomMethods.register(this, Point.class, "Point");
    m_CustomMethods.register(this, ColorUIResource.class, "ColorUIResource");
    m_CustomMethods.register(this, FontUIResource.class, "FontUIResource");

    m_CustomMethods.register(this, weka.gui.beans.BeanInstance.class,
      "BeanInstance");
    m_CustomMethods.register(this, weka.gui.beans.BeanConnection.class,
      "BeanConnection");
    m_CustomMethods.register(this, weka.gui.beans.BeanVisual.class,
      "BeanVisual");
    m_CustomMethods.register(this, weka.gui.beans.Saver.class, "BeanSaver");
    m_CustomMethods.register(this, weka.gui.beans.MetaBean.class, "MetaBean");

    classnames = ConverterUtils.getFileLoaders();
    for (i = 0; i < classnames.size(); i++) {
      m_CustomMethods
        .register(this, WekaPackageClassLoaderManager.forName(classnames.get(i)), "Loader");
    }
    classnames = ConverterUtils.getFileSavers();
    for (i = 0; i < classnames.size(); i++) {
      m_CustomMethods.register(this, WekaPackageClassLoaderManager.forName(classnames.get(i)), "Saver");
    }

    // other variables
    m_BeanInstances = null;
    m_BeanInstancesID = null;
    m_CurrentMetaBean = null;
    m_IgnoreBeanConnections = true;
    m_BeanConnectionRelation = null;
  }

  /**
   * traverses over all BeanInstances (or MetaBeans) and stores them in a vector
   * (recurses into MetaBeans, since the sub-BeanInstances are not visible)
   * 
   * @param list the BeanInstances/MetaBeans to traverse
   */
  protected void addBeanInstances(Vector list) {
    int i;
    BeanInstance beaninst;

    for (i = 0; i < list.size(); i++) {
      if (list.get(i) instanceof BeanInstance) {
        beaninst = (BeanInstance) list.get(i);

        m_BeanInstancesID.add(new Integer(m_BeanInstances.size()));
        m_BeanInstances.add(beaninst);

        if (beaninst.getBean() instanceof MetaBean) {
          addBeanInstances(((MetaBean) beaninst.getBean()).getBeansInSubFlow());
        }
      } else if (list.get(i) instanceof MetaBean) {
        addBeanInstances(((MetaBean) list.get(i)).getBeansInSubFlow());
      } else {
        System.out
          .println("addBeanInstances does not support Vectors of class '"
            + list.get(i) + "'!");
      }
    }
  }

  /**
   * enables derived classes to due some pre-processing on the objects, that's
   * about to be serialized. Right now it only returns the object.
   * 
   * @param o the object that is serialized into XML
   * @return the possibly altered object
   * @throws Exception if post-processing fails
   */
  @Override
  @SuppressWarnings("unchecked")
  protected Object writePreProcess(Object o) throws Exception {
    o = super.writePreProcess(o);

    // gather all BeanInstances, also the ones in MetaBeans
    m_BeanInstances = new Vector();
    m_BeanInstancesID = new Vector();

    switch (getDataType()) {
    case DATATYPE_LAYOUT:
      addBeanInstances(BeanInstance.getBeanInstances(m_vectorIndex));
      break;

    case DATATYPE_USERCOMPONENTS:
      addBeanInstances((Vector) o);
      break;

    default:
      System.out.println("writePreProcess: data type '" + getDataType()
        + "' is not recognized!");
      break;
    }

    return o;
  }

  /**
   * enables derived classes to add other properties to the DOM tree, e.g. ones
   * that do not apply to the get/set convention of beans. only implemented with
   * empty method body.
   * 
   * @param o the object that is serialized into XML
   * @throws Exception if post-processing fails
   */
  @Override
  protected void writePostProcess(Object o) throws Exception {
    Element root;
    NodeList list;
    Element conns;
    Element child;
    int i;

    // since not all BeanConnections get saved to XML (e.g., MetaBeans in the
    // UserToolBar) if one saves a layout, the numbering in the Vector of the
    // BeanConnections is not correct. The "name" attribute of the nodes has
    // to be modified
    if (getDataType() == DATATYPE_LAYOUT) {
      root = m_Document.getDocument().getDocumentElement();
      conns = (Element) root.getChildNodes().item(INDEX_BEANCONNECTIONS);
      list = conns.getChildNodes();
      for (i = 0; i < list.getLength(); i++) {
        child = (Element) list.item(i);
        child.setAttribute(ATT_NAME, "" + i);
      }
    }
  }

  /**
   * additional pre-processing can happen in derived classes before the actual
   * reading from XML (working on the raw XML). right now it does nothing with
   * the document, only empties the help-vector for the BeanInstances and reads
   * the IDs for the BeanInstances, s.t. the correct references can be set again
   * 
   * @param document the document to pre-process
   * @return the processed object
   * @throws Exception if post-processing fails
   * @see #m_BeanInstances
   */
  @Override
  protected Document readPreProcess(Document document) throws Exception {
    NodeList list;
    int i;
    Element node;
    String clsName;
    Vector children;
    int id;
    int n;
    Element child;

    m_BeanInstances = new Vector();
    m_BeanInstancesID = new Vector();

    // get all BeanInstance nodes
    list = document.getElementsByTagName("*");
    clsName = BeanInstance.class.getName();
    for (i = 0; i < list.getLength(); i++) {
      node = (Element) list.item(i);

      // is it a BeanInstance?
      if (node.getAttribute(ATT_CLASS).equals(clsName)) {
        children = XMLDocument.getChildTags(node);
        id = m_BeanInstancesID.size();

        // get id-tag (if available)
        for (n = 0; n < children.size(); n++) {
          child = children.get(n);
          if (child.getAttribute(ATT_NAME).equals(VAL_ID)) {
            id = readIntFromXML(child);
          }
        }

        m_BeanInstancesID.add(new Integer(id));
      }
    }

    m_BeanInstances.setSize(m_BeanInstancesID.size());

    // set MetaBean to null
    m_CurrentMetaBean = null;

    // no BeanConnections -> see readPostProcess(Object)
    m_IgnoreBeanConnections = true;

    // reset BeanConnection-Relations
    m_BeanConnectionRelation = new Hashtable>();

    return document;
  }

  /**
   * puts the given BeanConnection onto the next null in the given Vector, or at
   * the end of the list, if no null is found. (during the de-serializing, no
   * BeanConnections are set, only nulls)
   * 
   * @param conn the connection to add to the list
   * @param list the list to add the BeanConnection to
   */
  protected void setBeanConnection(BeanConnection conn,
    Vector list) {
    int i;
    boolean added;

    added = false;
    for (i = 0; i < list.size(); i++) {
      if (list.get(i) == null) {
        list.set(i, conn);
        added = true;
        break;
      }
    }

    if (!added) {
      list.add(conn);
    }
  }

  /**
   * generates a connection based on the given parameters
   * 
   * @param sourcePos the source position in the m_BeanInstances vector
   * @param targetPos the target position in the m_BeanInstances vector
   * @param event the name of the event, i.e., the connection
   * @param hidden true if the connection is hidden
   * @return the generated BeanConnection
   * @throws Exception if something goes wrong
   */
  protected BeanConnection createBeanConnection(int sourcePos, int targetPos,
    String event, boolean hidden) throws Exception {
    BeanConnection result;
    BeanInfo compInfo;
    EventSetDescriptor[] esds;
    int i;
    BeanInstance instSource;
    BeanInstance instTarget;

    result = null;

    // was there a connection?
    if ((sourcePos == -1) || (targetPos == -1)) {
      return result;
    }

    instSource = (BeanInstance) m_BeanInstances.get(sourcePos);
    instTarget = (BeanInstance) m_BeanInstances.get(targetPos);

    compInfo = Introspector.getBeanInfo(((BeanInstance) m_BeanInstances
      .get(sourcePos)).getBean().getClass());
    esds = compInfo.getEventSetDescriptors();

    for (i = 0; i < esds.length; i++) {
      if (esds[i].getName().equals(event)) {
        result = new BeanConnection(instSource, instTarget, esds[i],
          m_vectorIndex);
        result.setHidden(hidden);
        break;
      }
    }

    return result;
  }

  /**
   * rebuilds all the connections for a certain key in the hashtable. for the
   * ones being part of a MetaBean, no new instance is built, but only the
   * reference to the actual BeanConnection set.
   * 
   * @param deserialized the deserialized knowledgeflow
   * @param key the key of the hashtable to rebuild all connections for
   * @throws Exception if something goes wrong
   */
  @SuppressWarnings("unchecked")
  protected void rebuildBeanConnections(Vector> deserialized,
    Object key) throws Exception {
    int i;
    int n;
    int sourcePos;
    int targetPos;
    String event;
    boolean hidden;
    Vector conns;
    BeanConnection conn;
    StringTokenizer tok;
    Vector beanconns;

    conns = m_BeanConnectionRelation.get(key);

    // no connections?
    if (conns == null) {
      return;
    }

    for (n = 0; n < conns.size(); n++) {
      tok = new StringTokenizer(conns.get(n).toString(), ",");
      conn = null;
      sourcePos = Integer.parseInt(tok.nextToken());
      targetPos = Integer.parseInt(tok.nextToken());
      event = tok.nextToken();
      hidden = stringToBoolean(tok.nextToken());

      // regular connection? -> new instance
      // or MetaBean from user toolbar
      if ((!(key instanceof MetaBean))
        || (getDataType() == DATATYPE_USERCOMPONENTS)) {
        conn = createBeanConnection(sourcePos, targetPos, event, hidden);
      }
      // MetaBean? -> find BeanConnection
      else {
        beanconns = BeanConnection.getConnections(m_vectorIndex);

        for (i = 0; i < beanconns.size(); i++) {
          conn = beanconns.get(i);
          if ((conn.getSource() == m_BeanInstances.get(sourcePos))
            && (conn.getTarget() == m_BeanInstances.get(targetPos))
            && (conn.getEventName().equals(event))) {
            break;
          }
          conn = null;
        }
      }

      // add the connection to the corresponding list/MetaBean
      if (key instanceof MetaBean) {
        setBeanConnection(conn, ((MetaBean) key).getAssociatedConnections());
      } else {
        setBeanConnection(conn,
          (Vector) deserialized.get(INDEX_BEANCONNECTIONS));
      }
    }
  }

  /**
   * removes the given meta beans from the layout, since they're only listed in
   * the user toolbar
   * 
   * @param metabeans the list of MetaBeans in the user toolbar
   */
  protected void removeUserToolBarBeans(Vector metabeans) {
    int i;
    int n;
    MetaBean meta;
    Vector subflow;
    BeanInstance beaninst;

    for (i = 0; i < metabeans.size(); i++) {
      meta = (MetaBean) metabeans.get(i);
      subflow = meta.getSubFlow();

      for (n = 0; n < subflow.size(); n++) {
        beaninst = (BeanInstance) subflow.get(n);
        beaninst.removeBean(m_BeanLayout);
      }
    }
  }

  /**
   * additional post-processing can happen in derived classes after reading from
   * XML. re-builds the BeanConnections.
   * 
   * @param o the object to perform some additional processing on
   * @return the processed object
   * @throws Exception if post-processing fails
   */
  @SuppressWarnings("unchecked")
  @Override
  protected Object readPostProcess(Object o) throws Exception {
    Enumeration enm;
    Vector> deserialized;
    Object key;

    deserialized = (Vector>) super.readPostProcess(o);

    // rebuild the actual connections
    rebuildBeanConnections(deserialized, REGULAR_CONNECTION);

    // rebuild the references in the MetaBeans
    enm = m_BeanConnectionRelation.keys();
    while (enm.hasMoreElements()) {
      key = enm.nextElement();

      // skip the regular connections
      if (!(key instanceof MetaBean)) {
        continue;
      }

      rebuildBeanConnections(deserialized, key);
    }

    // remove MetaBean and subflow from BeanInstance (not part of the flow!)
    if (getDataType() == DATATYPE_USERCOMPONENTS) {
      removeUserToolBarBeans(deserialized);
    }

    return deserialized;
  }

  /**
   * returns the relation for the given MetaBean, for the regular connections,
   * null has to be used
   * 
   * @param meta the MetaBean (or null for regular connections) to retrieve the
   *          connections for
   * @return the associated connections
   * @see #REGULAR_CONNECTION
   */
  protected Vector getBeanConnectionRelation(MetaBean meta) {
    Vector result;
    Object key;

    if (meta == null) {
      key = REGULAR_CONNECTION;
    } else {
      key = meta;
    }

    // not yet in there?
    if (!m_BeanConnectionRelation.containsKey(key)) {
      m_BeanConnectionRelation.put(key, new Vector());
    }

    result = m_BeanConnectionRelation.get(key);

    return result;
  }

  /**
   * adds the given connection-relation for the specified MetaBean (or null in
   * case of regular connections)
   * 
   * @param meta the MetaBean (or null for regular connections) to add the
   *          relationship for
   * @param connection the connection relation to add
   */
  protected void addBeanConnectionRelation(MetaBean meta, String connection) {
    Vector relations;
    Object key;

    relations = getBeanConnectionRelation(meta);

    // add relation
    relations.add(connection);

    // update
    if (meta == null) {
      key = REGULAR_CONNECTION;
    } else {
      key = meta;
    }
    m_BeanConnectionRelation.put(key, relations);
  }

  /**
   * adds the given Color to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeColor(Element parent, Object o, String name)
    throws Exception {

    Element node;
    Color color;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    color = (Color) o;
    node = addElement(parent, name, color.getClass().getName(), false);

    writeIntToXML(node, color.getRed(), VAL_RED);
    writeIntToXML(node, color.getGreen(), VAL_GREEN);
    writeIntToXML(node, color.getBlue(), VAL_BLUE);

    return node;
  }

  /**
   * builds the Color from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readColor(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    int red;
    int green;
    int blue;
    String name;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    red = 0;
    green = 0;
    blue = 0;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_RED)) {
        red = readIntFromXML(child);
      } else if (name.equals(VAL_GREEN)) {
        green = readIntFromXML(child);
      } else if (name.equals(VAL_BLUE)) {
        blue = readIntFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new Color(red, green, blue);

    return result;
  }

  /**
   * adds the given Dimension to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeDimension(Element parent, Object o, String name)
    throws Exception {

    Element node;
    Dimension dim;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    dim = (Dimension) o;
    node = addElement(parent, name, dim.getClass().getName(), false);

    writeDoubleToXML(node, dim.getWidth(), VAL_WIDTH);
    writeDoubleToXML(node, dim.getHeight(), VAL_HEIGHT);

    return node;
  }

  /**
   * builds the Dimension from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readDimension(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    double width;
    double height;
    String name;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    width = 0;
    height = 0;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_WIDTH)) {
        width = readDoubleFromXML(child);
      } else if (name.equals(VAL_HEIGHT)) {
        height = readDoubleFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new Dimension();
    ((Dimension) result).setSize(width, height);

    return result;
  }

  /**
   * adds the given Font to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeFont(Element parent, Object o, String name)
    throws Exception {

    Element node;
    Font font;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    font = (Font) o;
    node = addElement(parent, name, font.getClass().getName(), false);

    invokeWriteToXML(node, font.getName(), VAL_NAME);
    writeIntToXML(node, font.getStyle(), VAL_STYLE);
    writeIntToXML(node, font.getSize(), VAL_SIZE);

    return node;
  }

  /**
   * builds the Font from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readFont(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    int style;
    int size;
    String name;
    String fontname;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    fontname = "";
    style = 0;
    size = 0;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_NAME)) {
        name = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_STYLE)) {
        style = readIntFromXML(child);
      } else if (name.equals(VAL_SIZE)) {
        size = readIntFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new Font(fontname, style, size);

    return result;
  }

  /**
   * adds the given Point to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writePoint(Element parent, Object o, String name)
    throws Exception {

    Element node;
    Point p;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    p = (Point) o;
    node = addElement(parent, name, p.getClass().getName(), false);

    writeDoubleToXML(node, p.getX(), VAL_X);
    writeDoubleToXML(node, p.getY(), VAL_Y);

    return node;
  }

  /**
   * builds the Point from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readPoint(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    double x;
    double y;
    String name;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    x = 0;
    y = 0;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_X)) {
        x = readDoubleFromXML(child);
      } else if (name.equals(VAL_Y)) {
        y = readDoubleFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new Point();
    ((Point) result).setLocation(x, y);

    return result;
  }

  /**
   * adds the given ColorUIResource to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeColorUIResource(Element parent, Object o, String name)
    throws Exception {

    Element node;
    ColorUIResource resource;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    resource = (ColorUIResource) o;
    node = addElement(parent, name, resource.getClass().getName(), false);
    invokeWriteToXML(node, new Color(resource.getRGB()), VAL_COLOR);

    return node;
  }

  /**
   * builds the ColorUIResource from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readColorUIResource(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    Color color;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    color = null;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_COLOR)) {
        color = (Color) invokeReadFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new ColorUIResource(color);

    return result;
  }

  /**
   * adds the given FontUIResource to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeFontUIResource(Element parent, Object o, String name)
    throws Exception {

    Element node;
    FontUIResource resource;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    resource = (FontUIResource) o;
    node = addElement(parent, name, resource.getClass().getName(), false);
    invokeWriteToXML(node, new Font(resource.getName(), resource.getStyle(),
      resource.getSize()), VAL_COLOR);

    return node;
  }

  /**
   * builds the FontUIResource from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readFontUIResource(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    Font font;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    font = null;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_FONT)) {
        font = (Font) invokeReadFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new FontUIResource(font);

    return result;
  }

  /**
   * adds the given BeanInstance to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeBeanInstance(Element parent, Object o, String name)
    throws Exception {

    Element node;
    BeanInstance beaninst;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    beaninst = (BeanInstance) o;
    node = addElement(parent, name, beaninst.getClass().getName(), false);

    writeIntToXML(node, m_BeanInstances.indexOf(beaninst), VAL_ID);
    int w = beaninst.getWidth() / 2;
    int h = beaninst.getHeight() / 2;
    // If a bean instance doesn't have dimensions (0 widht/height) then it means
    // that it hasn't been rendered (yet). In this case we'll
    // use half the known width/height of the icons so that the
    // position does not change
    if (w == 0 && h == 0) {
      w = 28;
      h = 28;
    }
    writeIntToXML(node, beaninst.getX() + w, VAL_X); // x is thought to be in
                                                     // the center?
    writeIntToXML(node, beaninst.getY() + h, VAL_Y); // y is thought to be in
                                                     // the center?
    if (beaninst.getBean() instanceof BeanCommon) {
      // write the custom name of this bean
      String custName = ((BeanCommon) beaninst.getBean()).getCustomName();
      invokeWriteToXML(node, custName, VAL_CUSTOM_NAME);
    }
    invokeWriteToXML(node, beaninst.getBean(), VAL_BEAN);

    return node;
  }

  /**
   * builds the BeanInstance from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readBeanInstance(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    String name;
    int i;
    int x;
    int y;
    int id;
    Object bean;
    BeanVisual visual;
    BeanInstance beaninst;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    id = -1;
    x = 0;
    y = 0;
    bean = null;
    String customName = null;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_ID)) {
        id = readIntFromXML(child);
      } else if (name.equals(VAL_X)) {
        x = readIntFromXML(child);
      } else if (name.equals(VAL_Y)) {
        y = readIntFromXML(child);
      } else if (name.equals(VAL_CUSTOM_NAME)) {
        customName = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_BEAN)) {
        bean = invokeReadFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    result = new BeanInstance(m_BeanLayout, bean, x, y, m_vectorIndex);
    beaninst = (BeanInstance) result;

    // set parent of BeanVisual
    if (beaninst.getBean() instanceof weka.gui.beans.Visible) {
      visual = ((Visible) beaninst.getBean()).getVisual();
      visual.setSize(visual.getPreferredSize());
      if (visual.getParent() == null) {
        ((JPanel) beaninst.getBean()).add(visual);
      }
    }

    if (beaninst.getBean() instanceof BeanCommon && customName != null) {
      ((BeanCommon) beaninst.getBean()).setCustomName(customName);
    }

    // no IDs -> get next null position
    if (id == -1) {
      for (i = 0; i < m_BeanInstances.size(); i++) {
        if (m_BeanInstances.get(i) == null) {
          id = m_BeanInstancesID.get(i).intValue();
          break;
        }
      }
    }
    // get position for id
    i = m_BeanInstancesID.indexOf(new Integer(id));

    // keep track of the BeanInstances for reading the connections later on
    m_BeanInstances.set(i, result);

    // no current MetaBean
    m_CurrentMetaBean = null;

    return result;
  }

  /**
   * adds the given BeanConncetion to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeBeanConnection(Element parent, Object o, String name)
    throws Exception {

    Element node;
    BeanConnection beanconn;
    int source;
    int target;
    int sourcePos;
    int targetPos;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    beanconn = (BeanConnection) o;
    node = null;

    // get position
    sourcePos = m_BeanInstances.indexOf(beanconn.getSource());
    targetPos = m_BeanInstances.indexOf(beanconn.getTarget());

    // get id (if Connection is from a Bean in the UserToolBar, it's not listed!
    // -> ignore it)
    if ((sourcePos > -1) && (targetPos > -1)) {
      source = m_BeanInstancesID.get(sourcePos).intValue();
      target = m_BeanInstancesID.get(targetPos).intValue();
    } else {
      source = -1;
      target = -1;
    }

    // connection exists in the layout?
    if ((source > -1) && (target > -1)) {
      node = addElement(parent, name, beanconn.getClass().getName(), false);

      writeIntToXML(node, source, VAL_SOURCEID);
      writeIntToXML(node, target, VAL_TARGETID);
      invokeWriteToXML(node, beanconn.getEventName(), VAL_EVENTNAME);
      writeBooleanToXML(node, beanconn.isHidden(), VAL_HIDDEN);
    }

    return node;
  }

  /**
   * builds the BeanConnection from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readBeanConnection(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    String name;
    int i;
    int source;
    int target;
    int sourcePos;
    int targetPos;
    String event;
    boolean hidden;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    source = 0;
    target = 0;
    event = "";
    hidden = false;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_SOURCEID)) {
        source = readIntFromXML(child);
      } else if (name.equals(VAL_TARGETID)) {
        target = readIntFromXML(child);
      } else if (name.equals(VAL_EVENTNAME)) {
        event = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_HIDDEN)) {
        hidden = readBooleanFromXML(child);
      } else {
        System.out.println("WARNING: '" + name
          + "' is not a recognized name for " + node.getAttribute(ATT_NAME)
          + "!");
      }
    }

    // get position of id
    sourcePos = m_BeanInstancesID.indexOf(new Integer(source));
    targetPos = m_BeanInstancesID.indexOf(new Integer(target));

    // do we currently ignore the connections?
    // Note: necessary because of the MetaBeans
    if (m_IgnoreBeanConnections) {
      addBeanConnectionRelation(m_CurrentMetaBean, sourcePos + "," + targetPos
        + "," + event + "," + hidden);
      return result;
    }

    // generate it normally
    result = createBeanConnection(sourcePos, targetPos, event, hidden);

    return result;
  }

  /**
   * adds the given Loader (a bean) to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeBeanLoader(Element parent, Object o, String name)
    throws Exception {

    Element node;
    weka.gui.beans.Loader loader;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    loader = (weka.gui.beans.Loader) o;
    node = addElement(parent, name, loader.getClass().getName(), false);

    invokeWriteToXML(node, loader.getLoader(), VAL_LOADER);
    invokeWriteToXML(node, loader.getBeanContext(), VAL_BEANCONTEXT);

    return node;
  }

  /**
   * adds the given Saver (a bean) to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeBeanSaver(Element parent, Object o, String name)
    throws Exception {

    Element node;
    weka.gui.beans.Saver saver;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    saver = (weka.gui.beans.Saver) o;
    node = addElement(parent, name, saver.getClass().getName(), false);
    invokeWriteToXML(node, saver.getRelationNameForFilename(),
      VAL_RELATIONNAMEFORFILENAME);

    invokeWriteToXML(node, saver.getSaverTemplate(), VAL_SAVER);

    return node;
  }

  /**
   * adds the given Loader to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeLoader(Element parent, Object o, String name)
    throws Exception {

    Element node;
    weka.core.converters.Loader loader;
    File file;
    boolean known;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    loader = (weka.core.converters.Loader) o;
    node = addElement(parent, name, loader.getClass().getName(), false);
    known = true;
    file = null;

    // file
    if (loader instanceof weka.core.converters.AbstractFileLoader) {
      file = ((weka.core.converters.AbstractFileLoader) loader).retrieveFile();
    } else {
      known = false;
    }

    if (!known) {
      System.out.println("WARNING: unknown loader class '"
        + loader.getClass().getName() + "' - cannot retrieve file!");
    }

    Boolean relativeB = null;
    if (loader instanceof weka.core.converters.FileSourcedConverter) {
      boolean relative = ((weka.core.converters.FileSourcedConverter) loader)
        .getUseRelativePath();
      relativeB = new Boolean(relative);
    }

    // only save it, if it's a real file!
    if ((file == null) || (file.isDirectory())) {
      invokeWriteToXML(node, "", VAL_FILE);
    } else {
      String withResourceSeparators = file.getPath().replace(
        File.pathSeparatorChar, '/');
      boolean notAbsolute = (((weka.core.converters.AbstractFileLoader) loader)
        .getUseRelativePath()
        || (loader instanceof EnvironmentHandler && Environment
          .containsEnvVariables(file.getPath()))
        || this.getClass().getClassLoader().getResource(withResourceSeparators) != null || !file
        .exists());

      String path = (notAbsolute) ? file.getPath() : file.getAbsolutePath();
      // Replace any windows file separators with forward slashes (Java under
      // windows can
      // read paths with forward slashes (apparantly)
      path = path.replace('\\', '/');
      invokeWriteToXML(node, path, VAL_FILE);
    }
    if (relativeB != null) {
      invokeWriteToXML(node, relativeB.toString(), VAL_RELATIVE_PATH);
    }

    if (loader instanceof weka.core.OptionHandler) {
      String[] opts = ((weka.core.OptionHandler) loader).getOptions();
      invokeWriteToXML(node, opts, VAL_OPTIONS);
    }

    return node;
  }

  /**
   * builds the Loader from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readLoader(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    String file;
    File fl;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = Class.forName(node.getAttribute(ATT_CLASS)).newInstance();
    children = XMLDocument.getChildTags(node);
    file = "";
    Object relativeB = null;
    boolean relative = false;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_FILE)) {
        file = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_RELATIVE_PATH)) {
        relativeB = readFromXML(child);
        if (relativeB instanceof Boolean) {
          relative = ((Boolean) relativeB).booleanValue();
        }
      } else {
        readFromXML(result, name, child);
      }
    }

    if (result instanceof weka.core.converters.FileSourcedConverter) {
      ((weka.core.converters.FileSourcedConverter) result)
        .setUseRelativePath(relative);
    }

    if (file.equals("")) {
      file = null;
    }

    // set file only, if it exists
    if (file != null) {
      String tempFile = file;

      boolean containsEnv = false;
      containsEnv = Environment.containsEnvVariables(file);

      fl = new File(file);
      // only test for existence if the path does not contain environment vars
      // (trust that after they are resolved that everything is hunky dory).
      // Also
      // don't test if the file can be found as a resource in the classath
      if (containsEnv || fl.exists()
        || this.getClass().getClassLoader().getResource(file) != null) {
        ((weka.core.converters.AbstractFileLoader) result).setSource(new File(
          file));
      } else {
        System.out.println("WARNING: The file '" + tempFile
          + "' does not exist!");
      }
    }

    return result;
  }

  /**
   * adds the given Saver to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeSaver(Element parent, Object o, String name)
    throws Exception {

    Element node;
    weka.core.converters.Saver saver;
    String prefix;
    String dir;
    boolean known;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    saver = (weka.core.converters.Saver) o;
    node = addElement(parent, name, saver.getClass().getName(), false);
    known = true;
    prefix = "";
    dir = "";

    // file
    if (saver instanceof weka.core.converters.AbstractFileSaver) {
      ((weka.core.converters.AbstractFileSaver) saver).retrieveFile();
      prefix = ((weka.core.converters.AbstractFileSaver) saver).filePrefix();
      dir = ((weka.core.converters.AbstractFileSaver) saver).retrieveDir();
      // Replace any windows file separators with forward slashes (Java under
      // windows can
      // read paths with forward slashes (apparantly)
      dir = dir.replace('\\', '/');
    } else {
      known = false;
    }

    if (!known) {
      System.out.println("WARNING: unknown saver class '"
        + saver.getClass().getName() + "' - cannot retrieve file!");
    }

    Boolean relativeB = null;
    if (saver instanceof weka.core.converters.FileSourcedConverter) {
      boolean relative = ((weka.core.converters.FileSourcedConverter) saver)
        .getUseRelativePath();
      relativeB = new Boolean(relative);
    }

    // if ( (file == null) || (file.isDirectory()) ) {
    invokeWriteToXML(node, "", VAL_FILE);
    invokeWriteToXML(node, dir, VAL_DIR);
    invokeWriteToXML(node, prefix, VAL_PREFIX);
    /*
     * } else { String path = (((weka.core.converters.FileSourcedConverter)
     * saver).getUseRelativePath()) ? file.getPath() : file.getAbsolutePath();
     * // Replace any windows file separators with forward slashes (Java under
     * windows can // read paths with forward slashes (apparantly) path =
     * path.replace('\\', '/'); invokeWriteToXML(node, path, VAL_FILE);
     * invokeWriteToXML(node, dir, VAL_DIR); invokeWriteToXML(node, prefix,
     * VAL_PREFIX); }
     */

    if (relativeB != null) {
      invokeWriteToXML(node, relativeB.toString(), VAL_RELATIVE_PATH);
    }

    if (saver instanceof weka.core.OptionHandler) {
      String[] opts = ((weka.core.OptionHandler) saver).getOptions();
      invokeWriteToXML(node, opts, VAL_OPTIONS);
    }

    return node;
  }

  /**
   * builds the Saver from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readSaver(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    String file;
    String dir;
    String prefix;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = Class.forName(node.getAttribute(ATT_CLASS)).newInstance();
    children = XMLDocument.getChildTags(node);
    file = null;
    dir = null;
    prefix = null;

    Object relativeB = null;
    boolean relative = false;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_FILE)) {
        file = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_DIR)) {
        dir = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_PREFIX)) {
        prefix = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_RELATIVE_PATH)) {
        relativeB = readFromXML(child);
        if (relativeB instanceof Boolean) {
          relative = ((Boolean) relativeB).booleanValue();
        }
      } else {
        readFromXML(result, name, child);
      }
    }

    if ((file != null) && (file.length() == 0)) {
      file = null;
    }

    // savers only get directory and prefix, not file (KnowledgeFlow sets the
    // file/destination based on the relation, dir and prefix)
    if ((dir != null) && (prefix != null)) {
      ((weka.core.converters.AbstractFileSaver) result).setDir(dir);
      ((weka.core.converters.AbstractFileSaver) result).setFilePrefix(prefix);
    }

    if (result instanceof weka.core.converters.FileSourcedConverter) {
      ((weka.core.converters.FileSourcedConverter) result)
        .setUseRelativePath(relative);
    }

    return result;
  }

  /**
   * adds the given BeanVisual to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeBeanVisual(Element parent, Object o, String name)
    throws Exception {

    Element node;
    BeanVisual visual;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    visual = (BeanVisual) o;
    node = writeToXML(parent, o, name);

    // add icon paths
    invokeWriteToXML(node, visual.getIconPath(), VAL_ICONPATH);
    invokeWriteToXML(node, visual.getAnimatedIconPath(), VAL_ANIMATEDICONPATH);

    return node;
  }

  /**
   * builds the BeanVisual from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  public Object readBeanVisual(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    String text;
    String iconPath;
    String animIconPath;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = null;
    children = XMLDocument.getChildTags(node);
    text = "";
    iconPath = "";
    animIconPath = "";

    // find text
    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_TEXT)) {
        text = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_ICONPATH)) {
        iconPath = (String) invokeReadFromXML(child);
      } else if (name.equals(VAL_ANIMATEDICONPATH)) {
        animIconPath = (String) invokeReadFromXML(child);
      }
    }

    result = new BeanVisual(text, iconPath, animIconPath);

    // set rest of properties
    for (i = 0; i < children.size(); i++) {
      readFromXML(result, node.getAttribute(ATT_NAME), children.get(i));
    }

    return result;
  }

  /**
   * returns the IDs for the given BeanInstances, i.e., the stored IDs in
   * m_BeanInstancesID, based on m_BeanInstances
   * 
   * @param beans the beans to retrieve the IDs for
   * @return the IDs for the given BeanInstances
   * @see #m_BeanInstances
   * @see #m_BeanInstancesID
   */
  protected Vector getIDsForBeanInstances(Vector beans) {
    Vector result;
    int i;
    int pos;

    result = new Vector();

    for (i = 0; i < beans.size(); i++) {
      pos = m_BeanInstances.indexOf(beans.get(i));
      result.add(m_BeanInstancesID.get(pos));
    }

    return result;
  }

  /**
   * adds the given MetaBean to a DOM structure.
   * 
   * @param parent the parent of this object, e.g. the class this object is a
   *          member of
   * @param o the Object to describe in XML
   * @param name the name of the object
   * @return the node that was created
   * @throws Exception if the DOM creation fails
   */
  public Element writeMetaBean(Element parent, Object o, String name)
    throws Exception {

    Element node;
    MetaBean meta;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), name);
    }

    m_CurrentNode = parent;

    meta = (MetaBean) o;
    node = writeToXML(parent, o, name);

    invokeWriteToXML(node, getIDsForBeanInstances(meta.getBeansInInputs()),
      VAL_INPUTSID);
    invokeWriteToXML(node, getIDsForBeanInstances(meta.getBeansInOutputs()),
      VAL_OUTPUTSID);

    return node;
  }

  /**
   * returns a vector with references to BeanInstances according to the IDs in
   * the given Vector.
   * 
   * @param ids contains the IDs of the BeanInstances
   * @return the corresponding BeanInstances
   * @see #m_BeanInstances
   * @see #m_BeanInstancesID
   */
  protected Vector getBeanInstancesForIDs(Vector ids) {
    Vector result;
    int i;
    int pos;

    result = new Vector();

    for (i = 0; i < ids.size(); i++) {
      pos = m_BeanInstancesID.indexOf(ids.get(i));
      result.add(m_BeanInstances.get(pos));
    }

    return result;
  }

  /**
   * builds the MetaBean from the given DOM node.
   * 
   * @param node the associated XML node
   * @return the instance created from the XML description
   * @throws Exception if instantiation fails
   */
  @SuppressWarnings("unchecked")
  public Object readMetaBean(Element node) throws Exception {
    Object result;
    Vector children;
    Element child;
    int i;
    String name;
    Vector inputs;
    Vector outputs;
    Vector coords;
    MetaBean bean;

    // for debugging only
    if (DEBUG) {
      trace(new Throwable(), node.getAttribute(ATT_NAME));
    }

    m_CurrentNode = node;

    result = new MetaBean();
    children = XMLDocument.getChildTags(node);
    inputs = new Vector();
    outputs = new Vector();
    coords = new Vector();

    // the current MetaBean
    m_CurrentMetaBean = (MetaBean) result;

    for (i = 0; i < children.size(); i++) {
      child = children.get(i);
      name = child.getAttribute(ATT_NAME);

      if (name.equals(VAL_ASSOCIATEDCONNECTIONS)) {
        ((MetaBean) result)
          .setAssociatedConnections((Vector) invokeReadFromXML(child));
      } else if (name.equals(VAL_INPUTSID)) {
        inputs = (Vector) invokeReadFromXML(child);
      } else if (name.equals(VAL_OUTPUTSID)) {
        outputs = (Vector) invokeReadFromXML(child);
      } else if (name.equals(VAL_SUBFLOW)) {
        ((MetaBean) result)
          .setSubFlow((Vector) invokeReadFromXML(child));
      } else if (name.equals(VAL_ORIGINALCOORDS)) {
        coords = (Vector) invokeReadFromXML(child);
      } else if (name.equals(VAL_INPUTS)) {
        System.out.println("INFO: '" + name + "' will be restored later.");
      } else if (name.equals(VAL_OUTPUTS)) {
        System.out.println("INFO: '" + name + "' will be restored later.");
      } else {
        readFromXML(result, name, child);
      }
    }

    bean = (MetaBean) result;

    // set inputs and outputs, after the beans have been instantiated
    bean.setInputs(getBeanInstancesForIDs(inputs));
    bean.setOutputs(getBeanInstancesForIDs(outputs));
    bean.setOriginalCoords(coords);

    return result;
  }
}
    
    
    
    

    




    
    
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