import java.io.*;
import java.util.*;
import java.util.zip.DataFormatException;
import javax.swing.*;
import javax.swing.table.*;
import java.awt.Insets;
import java.awt.Component;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.app.swing.CySwingAppAdapter;
import org.cytoscape.work.Task;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.cytoscape.work.swing.PanelTaskManager;
import org.cytoscape.work.TaskIterator;
import org.osgi.framework.FrameworkUtil;

public class AlignmentPanel extends JPanel implements CytoPanelComponent
{
	private CySwingAppAdapter adapter;
	private NetworksData netData=new NetworksData();
	private JFileChooser fileChooser = new JFileChooser();
        private JFileChooser dirChooser = new JFileChooser();
        private JScrollPane scrollPane = new JScrollPane();
        private JPanel pane = new JPanel();
        private JPanel settingsPane = new JPanel();
        private JLabel iterSeedLabel = new JLabel();
        private JLabel iterExtentedLabel = new JLabel();
        private JLabel sigmaLabel = new JLabel();
        private JTextField iterSeedText = new JTextField();
        private JTextField iterExtendText = new JTextField();
        private JTextField sigmaText = new JTextField();
	private JButton iterSeedTip = new JButton();
        private JButton iterExtendTip = new JButton();
        private JButton sigmaTip = new JButton();
        private JButton allignButton = new JButton();
        private JPanel optionalSettingsPane = new JPanel();
        private JLabel overlapLabel = new JLabel();
        private JLabel refineLabel = new JLabel();
        private JLabel minComplexSizeLabel = new JLabel();
        private JCheckBox activeOptionalCheck = new JCheckBox();
        private JTextField overlapText = new JTextField();
        private JTextField refineText = new JTextField();
        private JTextField minComplexSizeText = new JTextField();
	private JButton overlapTip = new JButton();
        private JButton refineTip = new JButton();
        private JButton minComplexSizeTip = new JButton();
        private JPanel networksPane = new JPanel();
	private JTable tabNet=new JTable();
	private Vector<String> listPath=new Vector<String>();
	private Vector<String> listNet=new Vector<String>();
        private JButton addNetButton = new JButton();
	private JButton removeNetButton = new JButton();
	private JButton clearAllNetButton = new JButton();
        private JPanel filesPane = new JPanel();
	private JRadioButton homologyType = new JRadioButton("BLAST Bit scores",true);
	private JRadioButton COGType = new JRadioButton("COG groups", false);
        private JLabel homologyFileLabel = new JLabel();
        private JLabel destFolderLabel = new JLabel();
        private JTextField homologyFileText = new JTextField();
        private JTextField destFolderText = new JTextField();
	private JButton homologyTip=new JButton();
	private JButton destFolderTip=new JButton();
        private JPanel ontologiesPane = new JPanel();
        private JButton addOntButton = new JButton();
        private JButton removeOntButton = new JButton();
	private JButton clearAllOntButton = new JButton();
	private JTable tabOnt=new JTable();
	private Vector<String> ontFiles=new Vector<String>();
	private JPanel outputPane=new JPanel();
	
    public AlignmentPanel(CySwingAppAdapter adapter) 
    {
        initComponents();
	this.adapter=adapter;
    }

	public Component getComponent() 
	{
		return this;
	}
	public CytoPanelName getCytoPanelName() 
	{
		return CytoPanelName.WEST;
	}
	public String getTitle() 
	{
		return "Gasoline";
	}
	public Icon getIcon() 
	{
		return null;
	}
	
    private void initComponents() 
    {
        scrollPane.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
        settingsPane.setBorder(javax.swing.BorderFactory.createTitledBorder(javax.swing.BorderFactory.createTitledBorder(""), "Parameters setting"));

        iterSeedLabel.setText("Iter Seed: ");
        iterExtentedLabel.setText("Iter Extend: ");
        sigmaLabel.setText("Sigma: ");

	iterSeedTip.setText("?");
	iterSeedTip.setToolTipText("Number of iterations of Gibbs sampling in the initial phase");
	iterSeedTip.setMargin(new Insets(0,0,0,0));
	iterSeedTip.setEnabled(false);
	iterExtendTip.setText("?");
	iterExtendTip.setToolTipText("Number of iterations of Gibbs sampling in each extension step of the iterative phase");
	iterExtendTip.setMargin(new Insets(0,0,0,0));
	iterExtendTip.setEnabled(false);
	sigmaTip.setText("?");
	sigmaTip.setToolTipText("Minimum degree of nodes that can be potential seeds in the initial phase");
	sigmaTip.setMargin(new Insets(0,0,0,0));
	sigmaTip.setEnabled(false);
	
        iterSeedText.setText("200");
        iterExtendText.setText("200");
        sigmaText.setText("7");

        javax.swing.GroupLayout settingsPaneLayout = new javax.swing.GroupLayout(settingsPane);
        settingsPane.setLayout(settingsPaneLayout);
        settingsPaneLayout.setHorizontalGroup(
            settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, settingsPaneLayout.createSequentialGroup()
                .addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
			.addComponent(sigmaLabel)
			.addComponent(iterExtentedLabel)
			.addComponent(iterSeedLabel))
		.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
		.addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
			.addComponent(sigmaText, javax.swing.GroupLayout.PREFERRED_SIZE, 43, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addComponent(iterSeedText, javax.swing.GroupLayout.PREFERRED_SIZE, 43, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addComponent(iterExtendText, javax.swing.GroupLayout.PREFERRED_SIZE, 43, javax.swing.GroupLayout.PREFERRED_SIZE))
		.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
		.addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
			.addComponent(sigmaTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addComponent(iterSeedTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addComponent(iterExtendTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(55, 55, 55))
        );
        settingsPaneLayout.setVerticalGroup(
            settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(settingsPaneLayout.createSequentialGroup()
                .addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(iterSeedText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(iterSeedLabel)
		    .addComponent(iterSeedTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(iterExtentedLabel)
                    .addComponent(iterExtendText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
		    .addComponent(iterExtendTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(settingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(sigmaText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(sigmaLabel)
		    .addComponent(sigmaTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(8, 8, 8))
        );

        allignButton.setText("Align");
        allignButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                allignButtonActionPerformed(evt);
            }
        });

        optionalSettingsPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Optional parameters setting"));

        overlapLabel.setText("Overlap: ");
        refineLabel.setText("Refine: ");
        minComplexSizeLabel.setText("Min Complex Size: ");
	
	overlapTip.setText("?");
	overlapTip.setToolTipText("Maximum allowed percentage of common nodes between two alignments, in order to be cosidered distinct");
	overlapTip.setMargin(new Insets(0,0,0,0));
	overlapTip.setEnabled(false);
	refineTip.setText("?");
	refineTip.setToolTipText("Number of extensions followed by removal steps in the iterative phase");
	refineTip.setMargin(new Insets(0,0,0,0));
	refineTip.setEnabled(false);
	minComplexSizeTip.setText("?");
	minComplexSizeTip.setToolTipText("Minimum size of complexes in the final set of local alignments");
	minComplexSizeTip.setMargin(new Insets(0,0,0,0));
	minComplexSizeTip.setEnabled(false);
	
        activeOptionalCheck.setText("Active optional settings");
        activeOptionalCheck.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                activeOptionalCheckActionPerformed(evt);
            }
        });

        overlapText.setText("0.5");
        overlapText.setEnabled(false);

        refineText.setText("10");
        refineText.setEnabled(false);

        minComplexSizeText.setText("5");
        minComplexSizeText.setEnabled(false);

        javax.swing.GroupLayout optionalSettingsPaneLayout = new javax.swing.GroupLayout(optionalSettingsPane);
        optionalSettingsPane.setLayout(optionalSettingsPaneLayout);
        optionalSettingsPaneLayout.setHorizontalGroup(
            optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(optionalSettingsPaneLayout.createSequentialGroup()
                .addComponent(activeOptionalCheck)
                .addContainerGap())
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, optionalSettingsPaneLayout.createSequentialGroup()
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(overlapLabel)
                    .addComponent(refineLabel)
                    .addComponent(minComplexSizeLabel))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                    .addComponent(refineText, javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(overlapText, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 39, Short.MAX_VALUE)
                    .addComponent(minComplexSizeText))
		.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                    .addComponent(refineTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(overlapTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(minComplexSizeTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(50, 50, 50))
        );
        optionalSettingsPaneLayout.setVerticalGroup(
            optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(optionalSettingsPaneLayout.createSequentialGroup()
                .addComponent(activeOptionalCheck, javax.swing.GroupLayout.PREFERRED_SIZE, 22, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addGap(12, 12, 12)
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(overlapLabel)
                    .addComponent(overlapText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
		    .addComponent(overlapTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(8, 8, 8)
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(refineText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(refineLabel)
		    .addComponent(refineTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(optionalSettingsPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(minComplexSizeText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(minComplexSizeLabel)
		    .addComponent(minComplexSizeTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        networksPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Networks"));
	
	String[] columns={"Networks"};
        Object[][] rows= {};
	DefaultTableModel dm = new DefaultTableModel(rows, columns) {
			public boolean isCellEditable(int row, int col) {
				return false;
			}
		};
        tabNet.setModel(dm);
        tabNet.setRowSorter(new TableRowSorter(dm));
        TableColumnModel cm=tabNet.getColumnModel();
        TableColumn tc1=cm.getColumn(0);
        tc1.setPreferredWidth(105);
        javax.swing.JScrollPane netScrollPane = new javax.swing.JScrollPane(tabNet);

        addNetButton.setText("Add");
        addNetButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                addNetButtonActionPerformed(evt);
            }
        });
	
	removeNetButton.setText("Remove selected");
        removeNetButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                removeNetButtonActionPerformed(evt);
            }
        });
	
	clearAllNetButton.setText("Clear all");
        clearAllNetButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                clearAllNetButtonActionPerformed(evt);
            }
        });
	
        javax.swing.GroupLayout networksPaneLayout = new javax.swing.GroupLayout(networksPane);
        networksPane.setLayout(networksPaneLayout);
        networksPaneLayout.setHorizontalGroup(
	networksPaneLayout.createSequentialGroup()
            .addGroup(networksPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
		.addGroup(javax.swing.GroupLayout.Alignment.LEADING, networksPaneLayout.createSequentialGroup()
			.addComponent(addNetButton)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
			.addComponent(removeNetButton)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
			.addComponent(clearAllNetButton))
		.addGap(15,15,15)
		.addComponent(netScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 130, javax.swing.GroupLayout.DEFAULT_SIZE)
                .addGap(20,20,20))
        );
        networksPaneLayout.setVerticalGroup(
            networksPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(javax.swing.GroupLayout.Alignment.LEADING, networksPaneLayout.createSequentialGroup()
		.addGroup(networksPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
			.addComponent(addNetButton)
			.addGap(10,10,10)
			.addComponent(removeNetButton)
			.addGap(10,10,10)
			.addComponent(clearAllNetButton))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(netScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 120, Short.MAX_VALUE))
        );

        filesPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Similarity information"));
	
	javax.swing.ButtonGroup bg=new javax.swing.ButtonGroup();
        bg.add(homologyType);
        bg.add(COGType);
	
        homologyFileLabel.setText("Similarity file: ");
	homologyTip.setText("?");
	homologyTip.setToolTipText("Orthology data text file");
	homologyTip.setMargin(new Insets(0,0,0,0));
	homologyTip.setEnabled(false);
        homologyFileText.addMouseListener(new java.awt.event.MouseAdapter() {
            public void mouseClicked(java.awt.event.MouseEvent evt) {
                homologyFileTextMouseClicked(evt);
            }
        });

        javax.swing.GroupLayout filesPaneLayout = new javax.swing.GroupLayout(filesPane);
        filesPane.setLayout(filesPaneLayout);
        filesPaneLayout.setHorizontalGroup(
		filesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
		.addGroup(filesPaneLayout.createSequentialGroup()
                    .addComponent(homologyType)
                    .addComponent(COGType))
                .addGap(10)
                .addGroup(filesPaneLayout.createSequentialGroup()
		     .addComponent(homologyFileLabel)
		     .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
		     .addComponent(homologyFileText, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
		     .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
		     .addComponent(homologyTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
		     .addGap(18,18,18))
        );
        filesPaneLayout.setVerticalGroup(
		filesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
		.addGroup(filesPaneLayout.createSequentialGroup()
			.addGroup(filesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
				.addComponent(homologyType)
				.addComponent(COGType))
			.addGap(10,10,10)
			.addGroup(filesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
				.addComponent(homologyFileLabel)
				.addComponent(homologyFileText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
				.addComponent(homologyTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE))
			.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        ontologiesPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Ontologies (Optional)"));
	
	String[] columns2={"Gene Ontologies"};
        Object[][] rows2= {};
	DefaultTableModel dm2 = new DefaultTableModel(rows2, columns2) {
			public boolean isCellEditable(int row, int col) {
				return false;
			}
		};
        tabOnt.setModel(dm2);
        tabOnt.setRowSorter(new TableRowSorter(dm2));
        TableColumnModel cm2=tabOnt.getColumnModel();
        TableColumn tc2=cm2.getColumn(0);
        tc2.setPreferredWidth(105);
        JScrollPane ontoScrollPane = new JScrollPane(tabOnt);
	
        addOntButton.setText("Add");
        addOntButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                addOntButtonActionPerformed(evt);
            }
        });

	removeOntButton.setText("Remove selected");
        removeOntButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                removeOntButtonActionPerformed(evt);
            }
        });
	
	clearAllOntButton.setText("Clear all");
        clearAllOntButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                clearAllOntButtonActionPerformed(evt);
            }
        });

        javax.swing.GroupLayout ontologiesPaneLayout = new javax.swing.GroupLayout(ontologiesPane);
        ontologiesPane.setLayout(ontologiesPaneLayout);
        ontologiesPaneLayout.setHorizontalGroup(
		ontologiesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
		.addGroup(javax.swing.GroupLayout.Alignment.LEADING, ontologiesPaneLayout.createSequentialGroup()
			.addComponent(addOntButton)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
			.addComponent(removeOntButton)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
			.addComponent(clearAllOntButton))
		.addGap(15,15,15)
		.addComponent(ontoScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 130, javax.swing.GroupLayout.DEFAULT_SIZE)
                .addGap(20,20,20)
        );
        ontologiesPaneLayout.setVerticalGroup(
		ontologiesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
		.addGroup(javax.swing.GroupLayout.Alignment.LEADING, ontologiesPaneLayout.createSequentialGroup()
		.addGroup(ontologiesPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
			.addComponent(addOntButton)
			.addGap(10,10,10)
			.addComponent(removeOntButton)
			.addGap(10,10,10)
			.addComponent(clearAllOntButton))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(ontoScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 120, Short.MAX_VALUE))
        );
	
	outputPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Output"));
	
	destFolderLabel.setText("Output folder: ");
	destFolderTip.setText("?");
	destFolderTip.setToolTipText("Folder where final alignments will be saved");
	destFolderTip.setMargin(new Insets(0,0,0,0));
	destFolderTip.setEnabled(false);
	destFolderText.setText(System.getProperty("user.dir"));
        destFolderText.addMouseListener(new java.awt.event.MouseAdapter() {
            public void mouseClicked(java.awt.event.MouseEvent evt) {
                destFolderTextMouseClicked(evt);
            }
        });
	
	javax.swing.GroupLayout outputPaneLayout = new javax.swing.GroupLayout(outputPane);
        outputPane.setLayout(outputPaneLayout);
        outputPaneLayout.setHorizontalGroup(
		outputPaneLayout.createSequentialGroup()
			.addComponent(destFolderLabel)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
			.addComponent(destFolderText, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
			.addComponent(destFolderTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addGap(10,10,10)
        );
        outputPaneLayout.setVerticalGroup(
		outputPaneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
			.addComponent(destFolderText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addComponent(destFolderLabel)
			.addComponent(destFolderTip, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
			.addGap(18,18,18)
        );
	
        javax.swing.GroupLayout paneLayout = new javax.swing.GroupLayout(pane);
        pane.setLayout(paneLayout);
        paneLayout.setHorizontalGroup(
            paneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(paneLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(paneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(paneLayout.createSequentialGroup()
                        .addGroup(paneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                            .addComponent(ontologiesPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                            .addComponent(settingsPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                            .addComponent(optionalSettingsPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
			    .addComponent(outputPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
			    .addComponent(filesPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                          .addComponent(networksPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
			    .addComponent(allignButton, javax.swing.GroupLayout.Alignment.CENTER, 80, 80, 80))
                        .addGap(0, 0, Short.MAX_VALUE))))
        );
        paneLayout.setVerticalGroup(
            paneLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(paneLayout.createSequentialGroup()
                .addGap(15, 15, 15)
                .addComponent(filesPane, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(networksPane, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(settingsPane, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(optionalSettingsPane, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(ontologiesPane, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
		.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(outputPane, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addGap(15, 15, 15)
		.addComponent(allignButton)
                .addGap(20, 20, 20))
        );

        scrollPane.setViewportView(pane);

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
        this.setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(scrollPane)
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(scrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 933, Short.MAX_VALUE)
        );
    }

	private void allignButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		String homologyFileName=homologyFileText.getText();
		String destFolderName=destFolderText.getText();
		boolean pairScores=true;
		if(COGType.isSelected())
			pairScores=false;
		int iterSeed;
		int iterExtend;
		double sigma;
		int refine;
		int minComplexSize;
		double overlap;
		try
		{
			iterSeed=Integer.parseInt(iterSeedText.getText());
			iterExtend=Integer.parseInt(iterExtendText.getText());
			sigma=Double.parseDouble(sigmaText.getText());
			refine=Integer.parseInt(refineText.getText());
			minComplexSize=Integer.parseInt(minComplexSizeText.getText());
			overlap=Double.parseDouble(overlapText.getText());
		}
		catch(NumberFormatException nfe)
		{
			JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), "Please configure correctly all settings");
			return;
		}
        
		DefaultTableModel tm=(DefaultTableModel)tabNet.getModel();
		int numRows=tm.getRowCount();
		if(numRows<2)
		{
			JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), "Please import at least two networks");
			return;
		}
        
		if(homologyFileText.getText().isEmpty() || destFolderText.getText().isEmpty() || iterSeed<=0 || iterExtend<=0 || sigma<0)
		{
			JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), "Please configure all necessary settings");
			return;
		}
		if(minComplexSize<=0 || overlap<0 || refine<0)
		{
			JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), "Please configure all necessary settings");
			return;
		}
		
		allignButton.setEnabled(false);
		addNetButton.setEnabled(false);
		removeNetButton.setEnabled(false);
		clearAllNetButton.setEnabled(false);
		addOntButton.setEnabled(false);
		removeOntButton.setEnabled(false);
		clearAllOntButton.setEnabled(false);
		homologyFileText.setEnabled(false);
		destFolderText.setEnabled(false);
		iterSeedText.setEnabled(false);
		iterExtendText.setEnabled(false);
		sigmaText.setEnabled(false);
		overlapText.setEnabled(false);
		refineText.setEnabled(false);
		minComplexSizeText.setEnabled(false);
		activeOptionalCheck.setSelected(false);
        
		//Caricamento delle reti in Cytoscape
		netData.deleteAll();
		int i=0;
		CyServiceRegistrar csr=adapter.getCyServiceRegistrar();
		PanelTaskManager ptm=csr.getService(PanelTaskManager.class);
		TaskIterator taskIt=new TaskIterator();
		for(i=0;i<listNet.size();i++)
		{
			ImportNetTask task = new ImportNetTask(netData, listPath.get(i), listNet.get(i));
			taskIt.append(task);
		}
		
		//Esecuzione dell'algoritmo
		AlignmentTask task = new AlignmentTask (sigma, iterExtend, iterSeed, overlap, refine, minComplexSize, pairScores, homologyFileName, netData, destFolderName, this, ontFiles, adapter);
		taskIt.append(task);
		ptm.execute(taskIt);
	}

	public void enable()
	{
		allignButton.setEnabled(true);
		addNetButton.setEnabled(true);
		removeNetButton.setEnabled(true);
		clearAllNetButton.setEnabled(true);
		addOntButton.setEnabled(true);
		removeOntButton.setEnabled(true);
		clearAllOntButton.setEnabled(true);
		homologyFileText.setEnabled(true);
		destFolderText.setEnabled(true);
		iterSeedText.setEnabled(true);
		iterExtendText.setEnabled(true);
		sigmaText.setEnabled(true);
	}
	
	private void activeOptionalCheckActionPerformed(java.awt.event.ActionEvent evt) 
	{
		if(activeOptionalCheck.isSelected())
		{
			overlapText.setEnabled(true);
			refineText.setEnabled(true);
			minComplexSizeText.setEnabled(true);
		}
		else if(!activeOptionalCheck.isSelected())
		{
			overlapText.setEnabled(false);
			refineText.setEnabled(false);
			minComplexSizeText.setEnabled(false);
		}
	}

	private void homologyFileTextMouseClicked(java.awt.event.MouseEvent evt) 
	{
		fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
		fileChooser.setMultiSelectionEnabled(false);
		int response = fileChooser.showOpenDialog(adapter.getCySwingApplication().getJFrame()); 
		String fname = homologyFileText.getText();
		File file=null;
		if(response==JFileChooser.APPROVE_OPTION) 
		{ 
			int line=0;
			file = fileChooser.getSelectedFile(); 
			fname=file.getAbsolutePath();
				
			//Controllo formato
			String header=null;
			String regex=null;
			if(homologyType.isSelected())
			{
				header="Similarity_scores";
				regex=".*[ \t]+.*[ \t]+[0-9]+(\\.[0-9]+)?";
			}
			else
				regex=".*[ \t]+\\[[^,]+(, [^,]+)*\\]";
			FileFormatTask task = new FileFormatTask(file, header, regex);
			CyServiceRegistrar csr=adapter.getCyServiceRegistrar();
			PanelTaskManager ptm=csr.getService(PanelTaskManager.class);
			TaskIterator taskIt=new TaskIterator(task);
			ptm.execute(taskIt);
			if(task.getError()!=null)
			{
				JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), task.getError());
				return;
			}
		}
		homologyFileText.setText(fname);
	}

	private void addNetButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int i=0;
		fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
		fileChooser.setMultiSelectionEnabled(true);
		int response = fileChooser.showOpenDialog(adapter.getCySwingApplication().getJFrame()); 
		if(response==JFileChooser.APPROVE_OPTION) 
		{ 
			File[] list=fileChooser.getSelectedFiles();
			DefaultTableModel tm=(DefaultTableModel)tabNet.getModel();
			for(i=0;i<list.length;i++)
			{
				//Controllo formato file
				FileFormatTask task = new FileFormatTask(list[i], null, ".*[ \t]+.*[ \t]+[0-9]+(\\.[0-9]+)?");
				CyServiceRegistrar csr=adapter.getCyServiceRegistrar();
				PanelTaskManager ptm=csr.getService(PanelTaskManager.class);
				TaskIterator taskIt=new TaskIterator(task);
				ptm.execute(taskIt);
				if(task.getError()!=null)
				{
					JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), task.getError());
					continue;
				}
					
				//Aggiunta della rete, se non gia' presente
				if(!listPath.contains(list[i].getAbsolutePath()))
				{
					Vector row=new Vector();
					row.add(list[i].getName());
					tm.addRow(row);
					listPath.add(list[i].getAbsolutePath());
					listNet.add(list[i].getName());
				}
			}
		} 
	}
	
	private void removeNetButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int row=0;
		DefaultTableModel tm=(DefaultTableModel)tabNet.getModel();
		while((row=tabNet.getSelectedRow())!=-1)
		{
			tm.removeRow(row);
			listNet.remove(row);
			listPath.remove(row);
		}
	}
	
	private void clearAllNetButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int i=0;
		DefaultTableModel tm=(DefaultTableModel)tabNet.getModel();
		int numRows=tm.getRowCount();
		for(i=0;i<numRows;i++)
			tm.removeRow(0);
		listNet.removeAllElements();
		listPath.removeAllElements();
	}
	
	private void destFolderTextMouseClicked(java.awt.event.MouseEvent evt) 
	{
		dirChooser.setCurrentDirectory(new File(destFolderText.getText()));
		dirChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
		dirChooser.setAcceptAllFileFilterUsed(false);
		int response = dirChooser.showSaveDialog(adapter.getCySwingApplication().getJFrame());
		String dirName = destFolderText.getText();
		if(response==JFileChooser.APPROVE_OPTION) 
		{ 
			try 
			{ 
				File f = dirChooser.getSelectedFile();
				dirName=f.getAbsolutePath();
			}
			catch(Exception e) 
			{
				System.out.println("Error choosing destination Folder");
			} 
		} 
		destFolderText.setText(dirName);
	}

	private void addOntButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int i=0;
		fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
		fileChooser.setMultiSelectionEnabled(true);
		int response = fileChooser.showOpenDialog(adapter.getCySwingApplication().getJFrame()); 
		String fname = null;
		String name=null;
		if(response==JFileChooser.APPROVE_OPTION) 
		{ 
			File[] list=fileChooser.getSelectedFiles();
			DefaultTableModel tm=(DefaultTableModel)tabOnt.getModel();
			for(i=0;i<list.length;i++)
			{
				//Controllo formato file
				FileFormatTask task = new FileFormatTask(list[i], null, "[^\t]+[\t][^\t]+[\t][^\t]+[\t][^\t]+[\t][^\t]+");
				CyServiceRegistrar csr=adapter.getCyServiceRegistrar();
				PanelTaskManager ptm=csr.getService(PanelTaskManager.class);
				TaskIterator taskIt=new TaskIterator(task);
				ptm.execute(taskIt);
				if(task.getError()!=null)
				{
					JOptionPane.showMessageDialog(adapter.getCySwingApplication().getJFrame(), task.getError());
					continue;
				}
					
				//Aggiunta del file delle ontologie, se non gia' presente
				if(!ontFiles.contains(list[i].getAbsolutePath()))
				{
					Vector row=new Vector();
					row.add(list[i].getName());
					tm.addRow(row);
					ontFiles.add(list[i].getAbsolutePath());
				}
			}
		}
	}
	
	private void removeOntButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int row=0;
		DefaultTableModel tm=(DefaultTableModel)tabOnt.getModel();
		while((row=tabOnt.getSelectedRow())!=-1)
		{
			tm.removeRow(row);
			ontFiles.remove(row);
		}
	}
	
	private void clearAllOntButtonActionPerformed(java.awt.event.ActionEvent evt) 
	{
		int i=0;
		DefaultTableModel tm=(DefaultTableModel)tabOnt.getModel();
		int numRows=tm.getRowCount();
		for(i=0;i<numRows;i++)
			tm.removeRow(0);
		ontFiles.removeAllElements();
	}
}