RubyGems - toxtree - Versions diffs - 0.0.1 - Mend

toxtree 0.0.1

Files changed (1384) hide show

data/Toxtree-v2.6.13/src/toxtree/ui/actions/package.html ADDED

@@ -0,0 +1,16 @@
+<HTML><HEAD><TITLE>toxTree.tree classes</TITLE>
+<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
+</SCRIPT>
+<META NAME="Description" CONTENT="toxTree application">
+<META NAME="Keywords" CONTENT="source,decision tree,TTC,java">
+<!--  -->
+<body bgColor="#FFFFFF" link="#428EFF">
+Actions (derived from {@link javax.swing.AbstractAction}
+used in {@link toxTree.apps.ToxTreeApp}  main menu.
+</body></HTML>

data/Toxtree-v2.6.13/src/toxtree/ui/batch/AbstractJobProcessingDialog.java ADDED

@@ -0,0 +1,308 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+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.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.batch;
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.GraphicsConfiguration;
+import java.awt.HeadlessException;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+/**
+ * A dialog with start, pause and cancel buttons.
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-5
+ */
+public abstract class AbstractJobProcessingDialog extends JDialog {
+	protected JButton cancelButton, okButton, pauseButton;
+	protected boolean pausePressed = false;
+	protected boolean okPressed = false;
+	protected boolean cancelPressed = false;
+	protected int result;
+	protected JPanel buttonPane, mainPanel;
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = -5641683445720590852L;
+	/**
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog() throws HeadlessException {
+		super();
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Dialog owner) throws HeadlessException {
+		super(owner);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param modal
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Dialog owner, boolean modal)
+			throws HeadlessException {
+		super(owner, modal);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Frame owner) throws HeadlessException {
+		super(owner);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param modal
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Frame owner, boolean modal)
+			throws HeadlessException {
+		super(owner, modal);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Dialog owner, String title)
+			throws HeadlessException {
+		super(owner, title);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Dialog owner, String title, boolean modal)
+			throws HeadlessException {
+		super(owner, title, modal);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Frame owner, String title)
+			throws HeadlessException {
+		super(owner, title);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Frame owner, String title, boolean modal)
+			throws HeadlessException {
+		super(owner, title, modal);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @param gc
+	 * @throws java.awt.HeadlessException
+	 */
+	public AbstractJobProcessingDialog(Dialog owner, String title, boolean modal,
+			GraphicsConfiguration gc) throws HeadlessException {
+		super(owner, title, modal, gc);
+		addWidgets();
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @param gc
+	 */
+	public AbstractJobProcessingDialog(Frame owner, String title, boolean modal,
+			GraphicsConfiguration gc) {
+		super(owner, title, modal, gc);
+		addWidgets();
+	}
+	protected void addWidgets() {
+		int minW = 400; int minH = 200;
+		cancelButton = new JButton("Cancel");
+		okButton = new JButton("OK");
+		pauseButton = new JButton("Pause");
+		pauseButton.setVisible(false);
+		pauseButton.addActionListener(new ActionListener() {
+			 public void actionPerformed(ActionEvent e) {
+			 	pauseAction();
+			 }
+			});
+		cancelButton.addActionListener(new ActionListener() {
+		 public void actionPerformed(ActionEvent e) {
+		 	cancelAction();
+		 }
+		});
+		okButton.addActionListener(new ActionListener() {
+		 public void actionPerformed(ActionEvent e) {
+		     okAction();
+		 }
+		});
+		getRootPane().setDefaultButton(okButton);
+//		Lay out the buttons from left to right.
+		buttonPane = new JPanel();
+		buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.X_AXIS));
+		buttonPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+		buttonPane.add(Box.createHorizontalGlue());
+		buttonPane.add(okButton);
+		buttonPane.add(Box.createRigidArea(new Dimension(10, 0)));
+		buttonPane.add(pauseButton);
+		buttonPane.add(Box.createRigidArea(new Dimension(10, 0)));
+		buttonPane.add(cancelButton);
+		buttonPane.setPreferredSize(new Dimension(minW,48));
+		buttonPane.setMinimumSize(new Dimension(minW,48));
+//		Put everything together, using the content pane's BorderLayout.
+		Container contentPane = getContentPane();
+		JPanel panel = new JPanel();
+		panel.setLayout(new BorderLayout());
+		//panel.setPreferredSize(new Dimension(300,300));
+		panel.setMinimumSize(new Dimension(minW,minH));
+		panel.add(buttonPane, BorderLayout.SOUTH);
+		mainPanel = createMainPanel();
+		panel.add(mainPanel, BorderLayout.CENTER);
+		contentPane.add(panel);
+		pack();
+	}
+	protected abstract JPanel createMainPanel();
+	protected  void cancelAction() {
+		cancelPressed = true;
+	    result = JOptionPane.CANCEL_OPTION;
+		setVisible(false);
+	}
+	protected void okAction() {
+		cancelPressed = false;
+		pausePressed = false;
+		okButton.setVisible(false);
+		pauseButton.setVisible(true);
+		cancelButton.setVisible(true);
+	}
+	/*
+		result = JOptionPane.OK_OPTION;
+		setVisible(false);
+	}
+		*/
+	protected void pauseAction() {
+		pausePressed = ! pausePressed;
+	}
+	/**
+	 * @return Returns the result.
+	 */
+	public synchronized int getResult() {
+		return result;
+	}
+	/**
+	 * @param result The result to set.
+	 */
+	public synchronized void setResult(int result) {
+		this.result = result;
+	}
+	/*
+//	 centers the dialog within the parent container [1.1]
+	public void centerParent () {
+	  int x;
+	  int y;
+	  // Find out our parent
+	  Container myParent = getParent();
+	  Point topLeft = myParent.getLocationOnScreen();
+	  Dimension parentSize = myParent.getSize();
+	  Dimension mySize = getSize();
+	  if (parentSize.width > mySize.width)
+	    x = ((parentSize.width - mySize.width)/2) + topLeft.x;
+	  else
+	    x = topLeft.x;
+	  if (parentSize.height > mySize.height)
+	    y = ((parentSize.height - mySize.height)/2) + topLeft.y;
+	  else
+	    y = topLeft.y;
+	  setLocation (x, y);
+	  }
+*/
+	public void centerScreen() {
+		  Dimension dim = java.awt.Toolkit.getDefaultToolkit().getScreenSize();
+		  Rectangle abounds = this.getBounds();
+		  this.setLocation((dim.width - abounds.width) / 2,
+		      (dim.height - abounds.height) / 2);
+	}
+	public abstract void enableDataControls(boolean enable);
+}

data/Toxtree-v2.6.13/src/toxtree/ui/batch/BatchProcessingDialog.java ADDED

@@ -0,0 +1,725 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+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.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.batch;
+import java.awt.BorderLayout;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.Frame;
+import java.awt.GraphicsConfiguration;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.HeadlessException;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.Locale;
+import java.util.Observable;
+import java.util.Observer;
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JFormattedTextField;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.SwingWorker;
+import toxTree.core.IDecisionMethod;
+import toxTree.io.batch.BatchFactory;
+import toxTree.io.batch.BatchProcessing;
+import toxTree.io.batch.BatchProcessingException;
+import toxTree.io.batch.ChemObjectBatchProcessing;
+import toxTree.io.batch.IBatchProcessing;
+import toxTree.io.batch.ToxTreeBatchProcessing;
+import toxtree.data.ToxTreeActions;
+/**
+ * UI for batch processing {@link toxTree.io.batch.IBatchProcessing}
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-5
+ */
+public class BatchProcessingDialog extends AbstractJobProcessingDialog implements Observer {
+    JLabel batchTitle;
+	JFormattedTextField inputField, outputField;
+	JButton b1, b2;
+	File openFile =null; File saveFile = null;
+	JLabel  stateLabel, progressLabel, loadBatch, saveBatch, configLabel;
+	JProgressBar progressBar;
+	IBatchProcessing batch;
+	IDecisionMethod decisionMethod = null;
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = 3314347684369161157L;
+	/**
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch) throws HeadlessException {
+		super();
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch, Dialog owner) throws HeadlessException {
+		super(owner);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param modal
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Dialog owner, boolean modal)
+			throws HeadlessException {
+		super(owner, modal);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Frame owner) throws HeadlessException {
+		super(owner);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param modal
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Frame owner, boolean modal)
+			throws HeadlessException {
+		super(owner, modal);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Dialog owner, String title)
+			throws HeadlessException {
+		super(owner, title);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Dialog owner, String title, boolean modal)
+			throws HeadlessException {
+		super(owner, title, modal);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Frame owner, String title)
+			throws HeadlessException {
+		super(owner, title);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Frame owner, String title, boolean modal)
+			throws HeadlessException {
+		super(owner, title, modal);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @param gc
+	 * @throws HeadlessException
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Dialog owner, String title, boolean modal,
+			GraphicsConfiguration gc) throws HeadlessException {
+		super(owner, title, modal, gc);
+		setBatch(batch);
+	}
+	/**
+	 * @param owner
+	 * @param title
+	 * @param modal
+	 * @param gc
+	 */
+	public BatchProcessingDialog(IBatchProcessing batch,Frame owner, String title, boolean modal,
+			GraphicsConfiguration gc) {
+		super(owner, title, modal, gc);
+		setBatch(batch);
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.ui.AbstractJobProcessingDialog#createMainPanel()
+	 */
+	@Override
+	protected JPanel createMainPanel() {
+		JPanel main = new JPanel();
+		main.setLayout(new BorderLayout());
+		JPanel p = new JPanel();
+		p.setBorder(BorderFactory.createTitledBorder("Batch processing options"));
+		Dimension d = new Dimension(400,170);
+		p.setPreferredSize(d);
+		p.setMinimumSize(d);
+		GridBagLayout g = new GridBagLayout();
+		p.setLayout(g);
+		GridBagConstraints c = new GridBagConstraints();
+		c.weightx = 1;
+		c.weighty = 1;
+		c.gridwidth = GridBagConstraints.REMAINDER;
+		c.anchor = GridBagConstraints.WEST;
+		Insets insets = new Insets(1,3,1,3);
+		c.insets = insets;
+		c.fill = GridBagConstraints.BOTH;
+		d = new Dimension(Integer.MAX_VALUE,24);
+        batchTitle = new JLabel("");
+        if ((batch !=null) && (batch instanceof ToxTreeBatchProcessing)) {
+            batchTitle.setText(((ToxTreeBatchProcessing)batch).getDecisionMethod().toString());
+        }
+		JLabel l1 = new JLabel("Process file");
+		l1.setAlignmentX(LEFT_ALIGNMENT);
+		l1.setPreferredSize(d);
+		l1.setMinimumSize(d);
+		inputField = new JFormattedTextField("");
+		inputField.setEditable(false);
+		inputField.setMinimumSize(d);
+		inputField.setMaximumSize(d);
+		inputField.setPreferredSize(d);
+		b1 = new JButton(new  AbstractAction("Browse") {
+			/**
+			 * Comment for <code>serialVersionUID</code>
+			 */
+			private static final long serialVersionUID = -8159958269747554023L;
+			/* (non-Javadoc)
+			 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+			 */
+			public void actionPerformed(ActionEvent e) {
+				//String[] ext = {".sdf",".smi",".csv"};
+				update((Observable)batch,null);
+				File f = ToxTreeActions.selectFile(null,
+						ChemObjectBatchProcessing.extensions,ChemObjectBatchProcessing.extensions_descr, true);
+				if (f !=null) {
+					openFile = f;
+					inputField.setText(openFile.getAbsolutePath());
+					okButton.setText("Start");
+					batch = null;
+				}
+			}
+		});
+		JLabel l2 = new JLabel("Store results in");
+		l2.setAlignmentX(LEFT_ALIGNMENT);
+		l2.setPreferredSize(d);
+		l2.setMinimumSize(d);
+		l2.setMaximumSize(d);
+		outputField = new JFormattedTextField("");
+		outputField.setEditable(false);
+		outputField.setMinimumSize(d);
+		outputField.setMaximumSize(d);
+		outputField.setPreferredSize(d);
+		b2 = new JButton(new  AbstractAction("Browse") {
+			/**
+			 * Comment for <code>serialVersionUID</code>
+			 */
+			private static final long serialVersionUID = -767018500263991989L;
+			/* (non-Javadoc)
+			 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+			 */
+			public void actionPerformed(ActionEvent e) {
+				update((Observable)batch,null);
+				File f = ToxTreeActions.selectFile(null, ChemObjectBatchProcessing.extensions,ChemObjectBatchProcessing.extensions_descr, false);
+				setOutputFile(f);
+			}
+		});
+		b2.setMaximumSize(d);
+        loadBatch = new JLabel("<html><u>Load batch configuration</u></html>");
+        loadBatch.setOpaque(true);
+        loadBatch.setPreferredSize(new Dimension(120,32));
+        loadBatch.setAlignmentX(CENTER_ALIGNMENT);
+		loadBatch.addMouseListener(new MouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			if ((batch !=null) && batch.isRunning()) {
+	   				progressLabel.setText("Can't load batch configuration while batch is running!");
+	   				return;
+	   			}
+	   			File f = ToxTreeActions.selectFile(null, new String[] {".batch"}, new String[] {"toxTree batch files"}, true);
+	   			if (f != null)
+	   				try {
+	   					cleanPausedBatch();
+	   					ToxTreeBatchProcessing b = (ToxTreeBatchProcessing) BatchFactory.createFromConfig(f);
+	   					batch = b;
+                        if (b.getDecisionMethod() == null)
+                            batchTitle.setText("No decision method assigned!");
+                        else batchTitle.setText(b.getDecisionMethod().toString());
+	   					openFile = b.getInputFile().getFile();
+	   					inputField.setText(openFile.getAbsolutePath());
+	   					saveFile = b.getOutputFile().getFile();
+	   					outputField.setText(saveFile.getAbsolutePath());
+	   					update((Observable)batch,null);
+	   					if (batch.isPaused()) {
+	   						okButton.setVisible(true);
+	   						okButton.setText("Continue");
+	   						pauseButton.setVisible(false);
+	   						cancelButton.setVisible(true);
+	   					}
+	   					//statusLabel.setText(batch.toString());
+	   				} catch (BatchProcessingException x) {
+	   					setErrorMessage(x);
+	   					ToxTreeActions.showMsg(f.getAbsolutePath(),"Error on loading batch configuration");
+	   					batch = null;
+	   				}
+	   		}
+	    });
+        saveBatch = new JLabel("<html><u>Save batch configuration</u></html>");
+        saveBatch.setOpaque(true);
+        saveBatch.setPreferredSize(new Dimension(120,32));
+        saveBatch.setAlignmentX(CENTER_ALIGNMENT);
+        saveBatch.addMouseListener(new MouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			if ((batch !=null) && batch.isRunning()) {
+	   				progressLabel.setText("Can't save while batch is running! Pause batch to save!");
+	   				return;
+	   			}
+	   			if ((openFile == null) || (saveFile == null)) {
+	   				setErrorMessage(new BatchProcessingException("Empty input or output file!"));
+	   				return;
+	   			}
+	   			File f = ToxTreeActions.selectFile(null,  new String[] {".batch"}, new String[] {"toxTree batch files"}, false);
+	   			setVisible(true);
+	   			if (f != null)
+	   				try {
+	   					if (batch == null) {
+	   						ToxTreeBatchProcessing b = new ToxTreeBatchProcessing(openFile,saveFile);
+	   						b.setDecisionMethod(decisionMethod);
+	   						batch = b;
+	   					}
+	   					if (batch != null) {
+	   						batch.setConfigFile(f);
+	   						batch.saveConfig();
+	   						update((Observable) batch,null);
+	   					} else setErrorMessage(new BatchProcessingException("Can't save batch configuration!"));
+	   				} catch (BatchProcessingException x) {
+	   					batch = null;
+	   					x.printStackTrace();
+	   					setErrorMessage(x);
+	   					ToxTreeActions.showMsg(f.getAbsolutePath(),"Error on loading batch configuration");
+	   				}
+	   		}
+	    });
+        configLabel = new JLabel("");
+        configLabel.setOpaque(true);
+        configLabel.setPreferredSize(d);
+        configLabel.setAlignmentX(LEFT_ALIGNMENT);
+        g.setConstraints(batchTitle,c);         p.add(batchTitle);
+        g.setConstraints(l1,c);         p.add(l1);
+        c.gridwidth = GridBagConstraints.RELATIVE;
+        c.weightx = Integer.MAX_VALUE;
+        g.setConstraints(inputField,c);
+        p.add(inputField);
+        c.weightx = 0.2;
+        c.gridwidth = GridBagConstraints.REMAINDER;
+        g.setConstraints(b1,c);
+        p.add(b1);
+        c.weightx = 1;
+        g.setConstraints(l2,c);        p.add(l2);
+        c.gridwidth = GridBagConstraints.RELATIVE;
+        c.weightx = Integer.MAX_VALUE;
+        c.weightx = 0.2;
+        g.setConstraints(outputField,c);
+        p.add(outputField);
+        c.gridwidth = GridBagConstraints.REMAINDER;
+        g.setConstraints(b2,c);
+        p.add(b2);
+        JPanel bp = new JPanel();
+        bp.setLayout(new BoxLayout(bp,BoxLayout.LINE_AXIS));
+        bp.add(loadBatch);bp.add(saveBatch);
+        bp.setPreferredSize(new Dimension(Integer.MAX_VALUE,24));
+        c.gridwidth = GridBagConstraints.REMAINDER;
+        g.setConstraints(bp,c);
+        p.add(bp);
+        c.gridwidth = GridBagConstraints.REMAINDER;
+        g.setConstraints(configLabel,c);
+        p.add(configLabel);
+        JPanel progressPanel = new JPanel();
+        progressPanel.setBorder(BorderFactory.createTitledBorder("Batch status"));
+        progressPanel.setLayout(new BorderLayout());
+        Dimension d1 = new Dimension(200,24);
+        stateLabel = new JLabel("");
+        stateLabel.setMinimumSize(d1);
+        stateLabel.setPreferredSize(d1);
+        stateLabel.setVisible(true);
+        progressLabel = new JLabel("");
+        progressLabel.setMinimumSize(d1);
+        progressLabel.setPreferredSize(d1);
+        progressLabel.setVisible(true);
+        JPanel topPanel = new JPanel();
+        topPanel.setLayout(new BorderLayout());
+        topPanel.add(stateLabel,BorderLayout.WEST);
+        topPanel.add(progressLabel,BorderLayout.CENTER);
+        topPanel.setMinimumSize(new Dimension(400,24));
+        topPanel.setPreferredSize(new Dimension(400,24));
+        progressPanel.add(topPanel,BorderLayout.CENTER);
+        progressBar = new JProgressBar();
+        progressPanel.add(progressBar,BorderLayout.SOUTH);
+        progressBar.setIndeterminate(false);
+        progressBar.setVisible(false);
+        main.add(p,BorderLayout.CENTER);
+        main.add(progressPanel,BorderLayout.SOUTH);
+		return main;
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.ui.AbstractJobProcessingDialog#cancelAction()
+	 */
+	@Override
+	protected void cancelAction() {
+		try {
+			if (batch != null) {
+				batch.cancel();
+				if (batch instanceof Observable)
+					((Observable)batch).deleteObservers();
+				ToxTreeActions.showMsg(batch.toString(),"Batch processing aborted!");
+			}
+		} catch (BatchProcessingException x) {
+			ToxTreeActions.showMsg("Batch processing aborted!",x.getMessage());
+			x.printStackTrace();
+		}
+		super.cancelAction();
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.ui.AbstractJobProcessingDialog#okAction()
+	 */
+	@Override
+	protected void okAction() {
+		super.okAction();
+		pauseButton.setEnabled(true);
+		enableDataControls(false);
+        batch();
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.ui.AbstractJobProcessingDialog#pauseAction()
+	 */
+	@Override
+	protected void pauseAction() {
+		try {
+			pauseButton.setEnabled(false);
+			batch.pause();
+			super.pauseAction();
+		} catch (BatchProcessingException x) {
+			x.printStackTrace();
+		}
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.ui.AbstractJobProcessingDialog#addWidgets()
+	 */
+	@Override
+	protected void addWidgets() {
+		super.addWidgets();
+		okButton.setText("Start");
+	}
+	/**
+	 * @return Returns the decisionMethod.
+	 */
+	public synchronized IDecisionMethod getDecisionMethod() {
+		return decisionMethod;
+	}
+	/**
+	 * @param decisionMethod The decisionMethod to set.
+	 */
+	public synchronized void setDecisionMethod(IDecisionMethod decisionMethod) {
+		this.decisionMethod = decisionMethod;
+	}
+	protected void batch() {
+		try {
+			if (batch == null) {
+				ToxTreeBatchProcessing b = new ToxTreeBatchProcessing(openFile,saveFile);
+				b.setDecisionMethod(decisionMethod);
+				this.batch = b;
+			} else if (batch instanceof Observable) ((Observable) batch).deleteObservers();
+			if (batch instanceof Observable) ((Observable)batch).addObserver(this);
+		} catch (BatchProcessingException x) {
+			batch  = null;
+			jobFinished(x);
+			setErrorMessage(x);
+			return;
+		}
+    	new SwingWorker<IBatchProcessing, Object>() {
+  	       @Override
+  	       public IBatchProcessing doInBackground() {
+	           	try {
+	        		setErrorMessage(null);
+	        		batch.start();
+	        	} catch (BatchProcessingException x) {
+	        		batch  = null;
+	        		jobFinished(x);
+	        		setErrorMessage(x);
+	        		ToxTreeActions.showMsg(x.getMessage(),"Error on batch processing");
+	        	}
+	            return batch;
+  	       }
+  	       @Override
+  	       protected void done() {
+	           	try {
+	        		if (batch != null)
+	        			batch.close();
+	        		jobFinished(null);
+	        	} catch (BatchProcessingException x) {
+	        		ToxTreeActions.showMsg(x.getMessage(),"Error on batch processing");
+	        	}
+  	       }
+  	   }.execute();
+	}
+	protected void jobFinished(Exception x) {
+		if ((x == null) && (batch != null)) {
+			if (batch.isPaused()) {
+				okButton.setVisible(true);
+				okButton.setText("Continue");
+				pauseButton.setVisible(false);
+				cancelButton.setVisible(true);
+			} else {
+				if (batch instanceof Observable) ((Observable)batch).deleteObservers();
+				okButton.setVisible(true);
+				pauseButton.setVisible(false);
+				cancelButton.setVisible(false);
+				result = JOptionPane.OK_OPTION;
+				if (!batch.isCancelled())
+					JOptionPane.showMessageDialog(getParent(),
+							"Batch completed!",
+							batch.toString(),
+						    JOptionPane.INFORMATION_MESSAGE);
+				setVisible(false);
+			}
+		} else { //stopped because of exception
+			if (batch != null) {
+				if (batch instanceof Observable) ((Observable)batch).deleteObservers();
+				batch = null;
+			}
+			enableDataControls(true);
+			okButton.setVisible(true);
+			pauseButton.setVisible(false);
+			cancelButton.setVisible(true);
+		}
+	}
+	/* (non-Javadoc)
+	 * @see java.util.Observer#update(java.util.Observable, java.lang.Object)
+	 */
+	public void update(final Observable o, Object arg) {
+		if (batch == null) return;
+		if (o instanceof BatchProcessing)
+	        EventQueue.invokeLater(new Runnable() {
+	            public void run() {
+	    			BatchProcessing b = (BatchProcessing) o;
+	    			boolean running = (b.isStatus(BatchProcessing.STATUS_RUNNING));
+	                if ((b !=null) && (b instanceof ToxTreeBatchProcessing)) {
+	                    batchTitle.setText(((ToxTreeBatchProcessing)b).getDecisionMethod().toString());
+	                }
+	    			progressBar.setIndeterminate(running);
+	    			progressBar.setVisible(running || b.isStatus(BatchProcessing.STATUS_PAUSED));
+	    			stateLabel.setText(b.toString());
+	    			progressLabel.setToolTipText("");
+	    			progressLabel.setText("Records processed " + b.getWrittenRecordsCount());
+	    			pauseButton.setVisible(running || b.isStatus(BatchProcessing.STATUS_PAUSED));
+	    			if (b.getConfigFile() != null)
+	    			configLabel.setText("Batch configuration: " +
+	    					new SimpleDateFormat("M/d/y,H:m",Locale.US).format(b.getDateLastProcessed()) +
+	    					" " + b.getConfigFile().getName());
+	            }
+	        });
+	}
+	/**
+	 * @return Returns the batch.
+	 */
+	public synchronized IBatchProcessing getBatch() {
+		return batch;
+	}
+	/**
+	 * @param batch The batch to set.
+	 */
+	public synchronized void setBatch(IBatchProcessing batch) {
+		this.batch = batch;
+		if (batch != null)
+			if (batch instanceof ToxTreeBatchProcessing) {
+				    ToxTreeBatchProcessing b = (ToxTreeBatchProcessing) batch;
+					cleanPausedBatch();
+   					this.batch = b;
+                    if (b.getDecisionMethod() == null)
+                        batchTitle.setText("No decision method assigned!");
+                    else batchTitle.setText(b.getDecisionMethod().toString());
+   					openFile = b.getInputFile().getFile();
+   					inputField.setText(openFile.getAbsolutePath());
+   					saveFile = b.getOutputFile().getFile();
+   					outputField.setText(saveFile.getAbsolutePath());
+   					update((Observable)batch,null);
+   					if (batch.isPaused()) {
+   						okButton.setVisible(true);
+   						okButton.setText("Continue");
+   						pauseButton.setVisible(false);
+   						cancelButton.setVisible(true);
+   					}
+			}
+	}
+	@Override
+	public void enableDataControls(boolean enable) {
+		inputField.setEnabled(enable);
+		outputField.setEnabled(enable);
+		b1.setEnabled(enable);
+		b2.setEnabled(enable);
+		loadBatch.setEnabled(enable);
+		saveBatch.setEnabled(enable);
+	}
+	protected void cleanPausedBatch() {
+		if ((batch !=null) && (batch.isPaused())) {
+			try {
+				batch.cancel();
+				batch.close();
+			} catch (BatchProcessingException x) {
+				setErrorMessage(x);
+				x.printStackTrace();
+				batch = null;
+			}
+		}
+	}
+	protected void setErrorMessage(BatchProcessingException x) {
+		if (x != null) {
+			stateLabel.setText("Error");
+			progressLabel.setText(x.getMessage());
+			progressLabel.setToolTipText(x.getMessage());
+		} else {
+			stateLabel.setText("");
+			progressLabel.setText("");
+			progressLabel.setToolTipText("");
+		}
+	}
+	protected void setOutputFile(File f) {
+		if (f != null) {
+			saveFile = f;
+			outputField.setText(saveFile.getAbsolutePath());
+			okButton.setText("Start");
+			batch = null;
+		}
+	}
+}