Example usage for javax.swing JTextArea setEditable

List of usage examples for javax.swing JTextArea setEditable

Introduction

In this page you can find the example usage for javax.swing JTextArea setEditable.

Prototype

@BeanProperty(description = "specifies if the text can be edited")
public void setEditable(boolean b) 

Source Link

Document

Sets the specified boolean to indicate whether or not this TextComponent should be editable.

Usage

From source file:display.ANNFileFilter.java

License:asdf

Yanng() {
    JPanel toolBars;//from w  ww  . j ava2  s.  c  o m
    JMenuBar menuBar;
    JToolBar utilBar, fileBar;
    JButton toJava, runner, trainer, modify, getTraininger, inputer, newwer, saver, saveAser, loader, helper;
    JMenu file;
    final JMenu util;
    JMenu help;

    ImageIcon IJava, IRun, ITrain, IModify, INew, ISave, ILoad, IGetTrainingSet, IGetInput, ISaveAs;

    //initialize main window
    mainWindow = new JFrame("YANNG - Yet Another Neural Network (simulator) Generator");
    mainWindow.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    mainWindow.setLayout(new BorderLayout());
    mainWindow.setSize(675, 525);
    mainWindow.setIconImage(new ImageIcon(ClassLoader.getSystemResource("display/icons/logo.png")).getImage());
    loadingImage = new ImageIcon(ClassLoader.getSystemResource("display/icons/loading.gif"));

    path = new Vector<String>();
    net = new Vector<NeuralNetwork>();
    oneNet = new Vector<JPanel>();
    tabPanel = new Vector<JPanel>();
    readOut = new Vector<JTextArea>();
    readOutLocale = new Vector<JScrollPane>();
    loadingBar = new Vector<JLabel>();
    title = new Vector<JLabel>();
    close = new Vector<JButton>();
    netName = new Vector<StringBuffer>();
    netKind = new Vector<StringBuffer>();

    resultsPane = new JTabbedPane();

    mainWindow.add(resultsPane);

    toolBars = new JPanel();
    toolBars.setLayout(new FlowLayout(FlowLayout.LEFT));

    //create utilities toolbar with 3 buttons
    utilBar = new JToolBar("Utilities");
    IRun = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/running.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    ITrain = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/training.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    IModify = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/modifyNet.png"))
            .getImage().getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    IGetTrainingSet = new ImageIcon(
            new ImageIcon(ClassLoader.getSystemResource("display/icons/trainingSet.png")).getImage()
                    .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    IGetInput = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/input.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    //set the icons/tooltips for the utilitiy bar    
    runner = new JButton(IRun);
    runner.setToolTipText(
            "<html>Run  the  Current  Neural   Network<br>Once Through with the Current Input</html>");

    trainer = new JButton(ITrain);
    trainer.setToolTipText(
            "<html>Train the Network with the Current<br>Configuration  and  Training  Set</html>");

    modify = new JButton(IModify);
    modify.setToolTipText("<html>Modify the Network<br>for Fun and Profit</html>");

    getTraininger = new JButton(IGetTrainingSet);
    getTraininger.setToolTipText("Get Training Set from File");

    inputer = new JButton(IGetInput);
    inputer.setToolTipText("Get Input Set from File");

    utilBar.add(inputer);
    utilBar.add(runner);
    utilBar.add(getTraininger);
    utilBar.add(trainer);
    utilBar.add(modify);

    //create file toolbar
    fileBar = new JToolBar("file");
    ISaveAs = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/saveAs.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    INew = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/new.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    ISave = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/save.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    ILoad = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/load.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));
    IJava = new ImageIcon(new ImageIcon(ClassLoader.getSystemResource("display/icons/toJava.png")).getImage()
            .getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH));

    newwer = new JButton(INew);
    newwer.setToolTipText("Create New Neural Network");

    saver = new JButton(ISave);
    saver.setToolTipText("Save Current Network Configuration");

    saveAser = new JButton(ISaveAs);
    saveAser.setToolTipText("Save Network As");

    loader = new JButton(ILoad);
    loader.setToolTipText("Load Network Configuration from File");

    toJava = new JButton(IJava);
    toJava.setToolTipText("Export Network to Java Project");

    fileBar.add(newwer);
    fileBar.add(loader);
    fileBar.add(saver);
    fileBar.add(saveAser);
    fileBar.add(toJava);
    toolBars.add(fileBar);
    toolBars.add(utilBar);
    mainWindow.add(toolBars, BorderLayout.NORTH);

    //create a menubar with three menus on it
    menuBar = new JMenuBar();
    file = new JMenu("File");
    util = new JMenu("Utilities");
    help = new JMenu("Help");

    //add menu items for file menu
    load = new JMenuItem("Load Network Configuration");
    newNet = new JMenuItem("New Network");
    saveAs = new JMenuItem("Save Network As");
    save = new JMenuItem("Save Current Configuration");
    exportNet = new JMenuItem("Export Network to Java Project");
    exportOutput = new JMenuItem("Export Output to Text File");
    file.add(load);
    file.add(newNet);
    file.addSeparator();
    file.add(saveAs);
    file.add(save);
    file.addSeparator();
    file.add(exportNet);
    file.add(exportOutput);
    menuBar.add(file);

    //add menu items for utilities menu
    changeConfig = new JMenuItem("Modify Network Settings");
    getInput = new JMenuItem("Get Input From File");
    getTraining = new JMenuItem("Get Training Set From File");
    run = new JMenuItem("Run");
    train = new JMenuItem("Train");
    getColorMap = new JMenuItem("View Color Map");
    getColorMap.setVisible(false);
    util.add(changeConfig);
    util.addSeparator();
    util.add(getInput);
    util.add(getTraining);
    util.addSeparator();
    util.add(run);
    util.add(train);
    menuBar.add(util);

    //add menu items for help menu
    quickStart = new JMenuItem("Quick Start Guide");
    searchHelp = new JMenuItem("Programming with Yanng");
    about = new JMenuItem("License");
    links = new JMenuItem("<html>Links to Resources<br>about Neural Networks</html>");
    help.add(quickStart);
    help.addSeparator();
    help.add(searchHelp);
    help.addSeparator();
    help.add(about);
    help.addSeparator();
    help.add(links);
    menuBar.add(help);

    mainWindow.setJMenuBar(menuBar);

    //opens the quickstart guide
    quickStart.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            try {
                File myFile = new File(URLDecoder
                        .decode(ClassLoader.getSystemResource("ann/quick-start.pdf").getFile(), "UTF-8"));
                Desktop.getDesktop().open(myFile);
            } catch (IOException ex) {
                try {
                    Runtime.getRuntime().exec("xdg-open ./yanng/src/ann/quick-start.pdf");
                } catch (Exception e) {
                    JOptionPane.showMessageDialog(mainWindow,
                            "Your desktop is not supported by java,\ngo to yanng/src/ann/quick-start.pdf to view the technical manual.",
                            "Desktop not Supported", JOptionPane.ERROR_MESSAGE);
                }
            }
        }
    });

    links.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            try {
                File myFile = new File(
                        URLDecoder.decode(ClassLoader.getSystemResource("ann/links.pdf").getFile(), "UTF-8"));
                Desktop.getDesktop().open(myFile);
            } catch (IOException ex) {
                try {
                    Runtime.getRuntime().exec("xdg-open ./yanng/src/ann/links.pdf");
                } catch (Exception e) {
                    JOptionPane.showMessageDialog(mainWindow,
                            "Your desktop is not supported by java,\ngo to yanng/src/ann/links.pdf to view the technical manual.",
                            "Desktop not Supported", JOptionPane.ERROR_MESSAGE);
                }
            }
        }
    });

    //Displays license information
    about.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            JTextArea x = new JTextArea("Copyright [2015] [Sam Findler and Michael Scott]\n" + "\n"
                    + "Licensed under the Apache License, Version 2.0 (the \"License\");\n"
                    + "you may not use this file except in compliance with the License.\n"
                    + "You may obtain a copy of the License at\n" + "\n"
                    + "http://www.apache.org/licenses/LICENSE-2.0\n" + "\n"
                    + "Unless required by applicable law or agreed to in writing, software\n"
                    + "distributed under the License is distributed on an \"AS IS\" BASIS,\n"
                    + "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"
                    + "See the License for the specific language governing permissions and\n"
                    + "limitations under the License.");
            JDialog aboutDialog = new JDialog(mainWindow, "License", true);
            aboutDialog.setSize(500, 250);
            aboutDialog.setLayout(new FlowLayout());
            aboutDialog.add(x);
            x.setEditable(false);
            aboutDialog.setVisible(true);
        }
    });

    //opens the more technical user guide
    searchHelp.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            try {
                File myFile = new File(URLDecoder
                        .decode(ClassLoader.getSystemResource("ann/technical-manual.pdf").getFile(), "UTF-8"));
                Desktop.getDesktop().open(myFile);
            } catch (IOException ex) {
                try {
                    Runtime.getRuntime().exec("xdg-open ./yanng/src/ann/technical-manual.pdf");
                } catch (Exception e) {
                    JOptionPane.showMessageDialog(mainWindow,
                            "Your desktop is not supported by java,\ngo to yanng/src/ann/technical-manual.pdf to view the technical manual.",
                            "Desktop not Supported", JOptionPane.ERROR_MESSAGE);
                }
            }
        }
    });
    //class trains the neural network in the background while the loading bar displays, then prints out the output/connections listings/average error to the readOut pane
    class Trainer extends SwingWorker<NeuralNetwork, Object> {
        protected NeuralNetwork doInBackground() {
            net.get(resultsPane.getSelectedIndex()).trainNet();
            setProgress(1);
            return net.get(resultsPane.getSelectedIndex());
        }

        public void done() {
            if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Feed Forward Network")) {
                if (Double.isNaN(net.get(resultsPane.getSelectedIndex()).getAverageError()))
                    JOptionPane.showMessageDialog(mainWindow, "Training Set Formatted Incorrectly",
                            "Formatting Error", JOptionPane.ERROR_MESSAGE);
                else {
                    printConnections();
                    readOut.get(resultsPane.getSelectedIndex()).append(
                            "Results of Training " + netName.get(resultsPane.getSelectedIndex()) + ":\n\n");
                    printOutput();
                    readOut.get(resultsPane.getSelectedIndex()).append("Average Error = "
                            + net.get(resultsPane.getSelectedIndex()).getAverageError() + "\n\n");
                    loadingBar.get(resultsPane.getSelectedIndex()).setVisible(false);
                    JOptionPane.showMessageDialog(mainWindow,
                            "<html>If the Input is not displaying as expected, chances are the input was inproperly formatted.<br>See help for more details<html>");
                }
            } else if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Self-Organizing Map")) {
                readOut.get(resultsPane.getSelectedIndex()).append("\nUpdated Untrained Map:\n");
                printInitMap();
                loadingBar.get(resultsPane.getSelectedIndex()).setVisible(false);
                JOptionPane.showMessageDialog(mainWindow,
                        "<html>If the Input is not displaying as expected, chances are the input was inproperly formatted.<br>See help for more details<html>");
            }
        }

    }
    //starts the training class when train is pressed in the utilities menu
    train.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {

            if (resultsPane.getTabCount() != 0) {
                if (net.get(resultsPane.getSelectedIndex()).getTrainingSet() != null) {
                    loadingBar.get(resultsPane.getSelectedIndex()).setText(
                            "<html><font color = rgb(160,0,0)>Training</font> <font color = rgb(0,0,248)>net...</font></html>");
                    loadingBar.get(resultsPane.getSelectedIndex()).setVisible(true);
                    (thisTrainer = new Trainer()).execute();
                } else
                    JOptionPane.showMessageDialog(mainWindow, "No Input Set Specified", "Empty Signifier Error",
                            JOptionPane.ERROR_MESSAGE);
            }

            else
                JOptionPane.showMessageDialog(mainWindow, "Can't Train Nonexistent Neural Network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
        }
    });
    //associates the toolbar button with the jump rope guy with the training button on the utilities menu
    trainer.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : train.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //runs through one set of inputs and prints the results to the readOut pane  
    run.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Feed Forward Network")) {
                if (net.get(resultsPane.getSelectedIndex()).getInputSet() != null) {
                    net.get(resultsPane.getSelectedIndex()).runNet();
                    if (Double.isNaN(net.get(resultsPane.getSelectedIndex()).getAverageError()))
                        JOptionPane.showMessageDialog(mainWindow, "Training Set Formatted Incorrectly",
                                "Formatting Error", JOptionPane.ERROR_MESSAGE);
                    else {
                        readOut.get(resultsPane.getSelectedIndex()).append("Results of Running through Network "
                                + netName.get(resultsPane.getSelectedIndex()) + ":\n\n");
                        printOutput();
                        System.out.println("Results:");
                        for (int i = 0; i < net.get(resultsPane.getSelectedIndex())
                                .getOutputSet().length; i++) {
                            System.out.println("\n   Output of Input Vector " + i + ":");
                            for (int j = 0; j < net.get(resultsPane.getSelectedIndex())
                                    .getOutputSet()[i].length; j++) {
                                System.out.println("      Output Node " + j + " = "
                                        + net.get(resultsPane.getSelectedIndex()).getOutputSet()[i][j]);
                            }
                        }
                        JOptionPane.showMessageDialog(mainWindow,
                                "<html>If the Input is not displaying as expected, chances are the input was inproperly formatted.<br>See help for more details<html>");
                    }
                } else
                    JOptionPane.showMessageDialog(mainWindow, "No Input Set Specified", "Empty Signifier Error",
                            JOptionPane.ERROR_MESSAGE);
            } else if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Self-Organizing Map")) {
                if (net.get(resultsPane.getSelectedIndex()).getInputValues() != null) {
                    loadingBar.get(resultsPane.getSelectedIndex()).setText(
                            "<html><font color = rgb(160,0,0)>Training</font> <font color = rgb(0,0,248)>net...</font></html>");
                    loadingBar.get(resultsPane.getSelectedIndex()).setVisible(true);
                    (thisTrainer = new Trainer()).execute();
                } else
                    JOptionPane.showMessageDialog(mainWindow, "No Input Set Specified", "Empty Signifier Error",
                            JOptionPane.ERROR_MESSAGE);
            } else
                JOptionPane.showMessageDialog(mainWindow, "Can't Run Nonexistent Neural Network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
        }
    });

    runner.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : run.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //the following code is for the getTraining button under utilities
    getTrainingSet = new JFileChooser();
    getTrainingSet.setFileFilter(new TrainingFileFilter());

    getTraining.addActionListener(new ActionListener() {
        //this method/class gets a training set (tsv/csv file) and parse it through the neural network.  Kind of test that the file is formatted correctly, but if the data is wrong, there isn't much it can do.
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Feed Forward Network")) {
                int result;
                result = getTrainingSet.showOpenDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION)
                    if (getTrainingSet.getSelectedFile().getName().endsWith(".csv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".tsv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".txt"))
                        if (net.get(resultsPane.getSelectedIndex())
                                .parseTrainingSet(getTrainingSet.getSelectedFile()))
                            JOptionPane.showMessageDialog(mainWindow,
                                    "<html>Method gives no Garuntee that this File is Formatted Correctly<br>(see help for more details)</html>",
                                    "Formatting Warning", JOptionPane.WARNING_MESSAGE);
                        else
                            JOptionPane.showMessageDialog(mainWindow,
                                    "File Mismatch with Network Configuration", "Correspondence Error",
                                    JOptionPane.ERROR_MESSAGE);
                    else {
                        JOptionPane.showMessageDialog(mainWindow, "Wrong File Type", "Category Error",
                                JOptionPane.ERROR_MESSAGE);
                    }
                else {
                    JOptionPane.showMessageDialog(mainWindow, "No File Selected", "Absence Warning",
                            JOptionPane.WARNING_MESSAGE);
                }
            } else if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Self-Organizing Map")) {
                int result;
                result = getTrainingSet.showOpenDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION)
                    if (getTrainingSet.getSelectedFile().getName().endsWith(".csv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".tsv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".txt"))
                        if (net.get(resultsPane.getSelectedIndex())
                                .parseTrainingSet(getTrainingSet.getSelectedFile())) {
                            JOptionPane.showMessageDialog(mainWindow,
                                    "<html>Method gives no Garuntee that this File is Formatted Correctly<br>(see help for more details)</html>",
                                    "Formatting Warning", JOptionPane.WARNING_MESSAGE);
                            readOut.get(resultsPane.getSelectedIndex()).append("\nUpdated Untrained Map:\n");
                            printInitMap();
                        } else
                            JOptionPane.showMessageDialog(mainWindow,
                                    "File Mismatch with Network Configuration", "Correspondence Error",
                                    JOptionPane.ERROR_MESSAGE);
                    else {
                        JOptionPane.showMessageDialog(mainWindow, "Wrong File Type", "Category Error",
                                JOptionPane.ERROR_MESSAGE);
                    }
                else {
                    JOptionPane.showMessageDialog(mainWindow, "No File Selected", "Absence Warning",
                            JOptionPane.WARNING_MESSAGE);
                }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Can't Train Nonexistent Neural Network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    getTraininger.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : getTraining.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //this ends the getTraining section of the code   

    getInput.addActionListener(new ActionListener() {
        //this method/class gets an input set (tsv/csv file) and parses it through the neural network.  Somewhat tests that the file is formatted correctly, but cannot give a garuntee.
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0) {
                int result;
                result = getTrainingSet.showOpenDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION)
                    if (getTrainingSet.getSelectedFile().getName().endsWith(".csv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".tsv")
                            || getTrainingSet.getSelectedFile().getName().endsWith(".txt"))
                        if (net.get(resultsPane.getSelectedIndex())
                                .parseInputSet(getTrainingSet.getSelectedFile())) {
                            JOptionPane.showMessageDialog(mainWindow,
                                    "<html>Method gives no Garuntee that this File is Formatted Correctly<br>(see help for more details)</html>",
                                    "Formatting Warning", JOptionPane.WARNING_MESSAGE);
                            if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                    .equals("Self-Organizing Map"))
                                printInitMap();
                        } else
                            JOptionPane.showMessageDialog(mainWindow,
                                    "File Mismatch with Network Configuration", "Correspondence Error",
                                    JOptionPane.ERROR_MESSAGE);
                    else
                        JOptionPane.showMessageDialog(mainWindow, "Wrong File Type", "Category Error",
                                JOptionPane.ERROR_MESSAGE);
                else
                    JOptionPane.showMessageDialog(mainWindow, "No File Selected", "Absence Warning",
                            JOptionPane.WARNING_MESSAGE);
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Can't train nonexistent network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    //opens and displays a color map of a SOM
    getColorMap.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0) {
                if (netKind.get(resultsPane.getSelectedIndex()).toString().equals("Self-Organizing Map")) {
                    MapNode[][] map;

                    map = net.get(resultsPane.getSelectedIndex()).getMapArray();

                    int lValue = net.get(resultsPane.getSelectedIndex()).getLatticeValue();

                    int inputDimensions = net.get(resultsPane.getSelectedIndex()).getInputDimensions();

                    int[][] colorValues = new int[(lValue * lValue)][3];

                    double dMax = net.get(resultsPane.getSelectedIndex()).getDataMax();
                    double dMin = net.get(resultsPane.getSelectedIndex()).getDataMin();

                    int count = 0;

                    for (int i = 0; i < lValue; i++) {
                        for (int j = 0; j < lValue; j++) {
                            for (int k = 0; k < 3; k++) {
                                Vector tempVec = map[i][j].getWeights();
                                if (inputDimensions % 3 == 0) {
                                    colorValues[count][k] = Integer.parseInt(String.valueOf((Math.round(255
                                            * (Double.parseDouble(String.valueOf(tempVec.elementAt(k))))))));
                                }
                                if (inputDimensions % 3 == 1) {
                                    if (k == 0)
                                        colorValues[count][k] = 0;
                                    if (k == 1) {
                                        colorValues[count][k] = Integer
                                                .parseInt(String.valueOf((Math.round(255 * (Double
                                                        .parseDouble(String.valueOf(tempVec.elementAt(0))))))));
                                    }
                                    if (k == 2)
                                        colorValues[count][k] = 0;
                                }
                                if (inputDimensions % 3 == 2) {
                                    if (k == 2) {
                                        colorValues[count][k] = 0;
                                    } else
                                        colorValues[count][k] = Integer
                                                .parseInt(String.valueOf((Math.round(255 * (Double
                                                        .parseDouble(String.valueOf(tempVec.elementAt(k))))))));
                                }
                            }
                            count++;
                        }
                    }

                    JFrame frame = new JFrame();

                    frame.setTitle("Color Map");
                    frame.setPreferredSize(new Dimension(525, 500));
                    frame.add(new DrawPanel(colorValues, lValue));
                    frame.pack();
                    frame.setVisible(true);
                }

                else {
                    JOptionPane.showMessageDialog(mainWindow,
                            "This Feauture is only available for Self-Organizing Maps", "Not a Som Error",
                            JOptionPane.ERROR_MESSAGE);
                }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Network does not exist", "Existential Error",
                        JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    inputer.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : getInput.getActionListeners())
                a.actionPerformed(ae);
        }
    });

    getNet = new JFileChooser();
    getNet.setFileFilter(new ANNFileFilter());

    //saves the net, or opens save as dialog if net is not saved yet
    save.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0) {
                if (!path.get(resultsPane.getSelectedIndex()).equals("")) {
                    net.get(resultsPane.getSelectedIndex())
                            .save(new File(path.get(resultsPane.getSelectedIndex())));
                }

                else {
                    for (ActionListener a : saveAs.getActionListeners()) {
                        a.actionPerformed(ae);
                    }
                }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Can't save NonExistent Neural Network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    saver.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : save.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //opens dialog for saving the net
    saveAs.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0) {
                int result, override;
                String tempName;
                result = getNet.showSaveDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION)
                    if ((new File(tempName = getNet.getSelectedFile().getName())).exists()
                            || (new File(tempName + ".ffn")).exists() || (new File(tempName + ".som")).exists()
                            || (new File(tempName + ".hfn")).exists()) {
                        override = JOptionPane.showConfirmDialog(mainWindow,
                                tempName + " already exists, do you want to override?", "File Exists",
                                JOptionPane.YES_NO_OPTION);
                        if (override == JOptionPane.YES_OPTION) {
                            if (net.get(resultsPane.getSelectedIndex()).save(getNet.getSelectedFile())) {
                                if (tempName.endsWith(".ffn") || tempName.endsWith(".som")) {
                                    netName.set(resultsPane.getSelectedIndex(), new StringBuffer(tempName));
                                    title.get(resultsPane.getSelectedIndex()).setText(tempName + " ");
                                } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                        .equals("Feed Forward Network")) {
                                    netName.set(resultsPane.getSelectedIndex(),
                                            new StringBuffer(tempName + ".ffn"));
                                    title.get(resultsPane.getSelectedIndex()).setText(tempName + ".ffn ");
                                } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                        .equals("Self-Organizing Map")) {
                                    netName.set(resultsPane.getSelectedIndex(),
                                            new StringBuffer(tempName + ".som"));
                                    title.get(resultsPane.getSelectedIndex()).setText(tempName + ".som ");
                                }
                                path.set(resultsPane.getSelectedIndex(), getNet.getSelectedFile().getPath());

                            } else
                                JOptionPane.showMessageDialog(mainWindow, "Could not save file", "File Error",
                                        JOptionPane.ERROR_MESSAGE);
                        }
                    } else {
                        if (net.get(resultsPane.getSelectedIndex()).save(getNet.getSelectedFile())) {
                            if (tempName.endsWith(".ffn") || tempName.endsWith(".som")
                                    || tempName.endsWith(".hfn")) {
                                netName.set(resultsPane.getSelectedIndex(), new StringBuffer(tempName));
                                title.get(resultsPane.getSelectedIndex()).setText(tempName + " ");
                            } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                    .equals("Feed Forward Network")) {
                                netName.set(resultsPane.getSelectedIndex(),
                                        new StringBuffer(tempName + ".ffn"));
                                title.get(resultsPane.getSelectedIndex()).setText(tempName + ".ffn ");
                            } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                    .equals("Self-Organizing Map")) {
                                netName.set(resultsPane.getSelectedIndex(),
                                        new StringBuffer(tempName + ".som"));
                                title.get(resultsPane.getSelectedIndex()).setText(tempName + ".som ");
                                path.set(resultsPane.getSelectedIndex(), getNet.getSelectedFile().getPath());
                            }
                        } else
                            JOptionPane.showMessageDialog(mainWindow, "Could not save file", "File Error",
                                    JOptionPane.ERROR_MESSAGE);
                    }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Nothing to Save", "Existetial Error",
                        JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    saveAser.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : saveAs.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //loads a net
    load.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            int result;
            boolean test = true;
            String tempName;
            result = getNet.showOpenDialog(mainWindow);
            if (result == JFileChooser.APPROVE_OPTION) {
                tempName = getNet.getSelectedFile().getName();
                for (StringBuffer names : netName) {
                    if (names.toString().equals(tempName))
                        test = false;
                }
                if (test != false) {
                    //creates and sets the network configuration
                    if (tempName.endsWith(".ffn")) {
                        net.add(new FullyConnectedFeedForwardNet());
                    }
                    if (tempName.endsWith(".som")) {
                        net.add(new SelfOrganizingMap());
                    }
                    if (net.get(openNets).load(getNet.getSelectedFile()))
                        try {
                            //adds a close button to the top corner of each tab
                            title.add(new JLabel(tempName + " "));
                            close.add(new JButton("X"));
                            close.get(openNets).setActionCommand(tempName);
                            close.get(openNets)
                                    .setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
                            close.get(openNets).setMargin(new Insets(0, 0, 0, 0));
                            tabPanel.add(new JPanel(new GridBagLayout()));
                            tabPanel.get(openNets).setOpaque(false);
                            GridBagConstraints grid = new GridBagConstraints();
                            grid.fill = GridBagConstraints.HORIZONTAL;
                            grid.gridx = 0;
                            grid.gridy = 0;
                            grid.weightx = 1;
                            tabPanel.get(openNets).add(title.get(openNets), grid);
                            grid.gridx = 1;
                            grid.gridy = 0;
                            grid.weightx = 0;
                            tabPanel.get(openNets).add(close.get(openNets), grid);

                            //adds a loading bar
                            loadingBar.add(new JLabel("", loadingImage, SwingConstants.CENTER));
                            loadingBar.get(openNets).setHorizontalTextPosition(SwingConstants.LEFT);
                            loadingBar.get(openNets).setVisible(false);

                            path.add(getNet.getSelectedFile().getPath());

                            netKind.add(new StringBuffer(netType.getSelectedItem().toString()));
                            netName.add(new StringBuffer(tempName));
                            oneNet.add(new JPanel());
                            oneNet.get(openNets).setLayout(new GridBagLayout());
                            GridBagConstraints constraints = new GridBagConstraints();
                            constraints.fill = GridBagConstraints.BOTH;

                            //creates the readOut space and formats it so that the scroll pane/text changes size with the window, reserves space for the loading bar
                            readOut.add(new JTextArea(""));
                            readOutLocale.add(new JScrollPane(readOut.get(openNets)));
                            readOut.get(openNets).setEditable(false);
                            constraints.gridx = 0;
                            constraints.gridy = 0;
                            constraints.weighty = 1.0;
                            constraints.weightx = 1.0;
                            constraints.gridwidth = 2;
                            constraints.ipady = 90;
                            oneNet.get(openNets).add(readOutLocale.get(openNets), constraints);
                            constraints.fill = GridBagConstraints.HORIZONTAL;
                            constraints.gridx = 0;
                            constraints.gridy = 1;
                            constraints.ipady = 0;
                            constraints.gridwidth = 2;
                            constraints.anchor = GridBagConstraints.PAGE_END;

                            //add everythign to the tabbed pane
                            oneNet.get(openNets).add(loadingBar.get(openNets), constraints);
                            resultsPane.addTab(netName.get(openNets).toString(), oneNet.get(openNets));
                            resultsPane.setTabComponentAt(openNets, tabPanel.get(openNets));

                            //display the starting configuration of the network
                            readOut.get(openNets).append("Network: " + netName.get(openNets) + "\n\n");
                            resultsPane.setSelectedIndex(openNets++);
                            if (tempName.endsWith(".ffn"))
                                printConnections();
                            if (tempName.endsWith(".som")) {
                                readOut.get(resultsPane.getSelectedIndex()).append("\nUpdated Map:\n");
                                printInitMap();
                            }

                            //unfortunately difficult way that I made to add the close button functionality to close a tab
                            //it works, but there has to be a better way to do this
                            close.get(resultsPane.getSelectedIndex()).addActionListener(new ActionListener() {
                                public void actionPerformed(final ActionEvent ae) {
                                    int result;
                                    result = 0;
                                    for (StringBuffer names : netName) {
                                        if (ae.getActionCommand().equals(names.toString())) {
                                            result = JOptionPane.showConfirmDialog(createFFN,
                                                    "<html>Exiting Without Saving can Cause you to Lose your Progress<br>Are you sure you want to Continue?</html>",
                                                    "Close Network", JOptionPane.OK_CANCEL_OPTION);
                                            resultsPane.setSelectedIndex(netName.indexOf(names));
                                        }
                                    }
                                    if (result == JOptionPane.OK_OPTION) {
                                        net.remove(resultsPane.getSelectedIndex());
                                        oneNet.remove(resultsPane.getSelectedIndex());
                                        readOutLocale.remove(resultsPane.getSelectedIndex());
                                        readOut.remove(resultsPane.getSelectedIndex());
                                        loadingBar.remove(resultsPane.getSelectedIndex());
                                        tabPanel.remove(resultsPane.getSelectedIndex());
                                        title.remove(resultsPane.getSelectedIndex());
                                        close.remove(resultsPane.getSelectedIndex());
                                        netName.remove(resultsPane.getSelectedIndex());
                                        resultsPane.remove(resultsPane.getSelectedIndex());
                                        openNets--;
                                    }
                                }
                            });
                        } catch (Error e) {
                            JOptionPane.showMessageDialog(mainWindow, "File Formatted Incorrectly",
                                    "Formatting Error", JOptionPane.ERROR_MESSAGE);
                        }
                    else {
                        //if file was unable to load, remove the newly created neural network and display an error message
                        net.remove(openNets);
                        JOptionPane.showMessageDialog(mainWindow, "File Formatted Incorrectly",
                                "Formatting Error", JOptionPane.ERROR_MESSAGE);
                    }
                }

                else {
                    JOptionPane.showMessageDialog(mainWindow, "File Already Open", "Duality Error",
                            JOptionPane.ERROR_MESSAGE);
                }
            }
        }
    });

    //associates the load toolbar button with load from the file menu
    loader.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : load.getActionListeners())
                a.actionPerformed(ae);
        }
    });

    textFileChooser = new JFileChooser();
    textFileChooser.setFileFilter(new TextFileFilter());

    //exports all text from readout to a text file
    exportOutput.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0) {
                int result;
                result = textFileChooser.showSaveDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION) {
                    if (textFileChooser.getSelectedFile().exists()
                            || (new File(textFileChooser.getSelectedFile().getPath() + ".txt")).exists()) {
                        result = JOptionPane.showConfirmDialog(mainWindow,
                                "The File you have selected already Exists, do you want to Overwrite it?",
                                "File Exits", JOptionPane.YES_NO_OPTION);
                        if (result == JOptionPane.YES_OPTION) {
                            try {
                                if (textFileChooser.getSelectedFile().getPath().endsWith(".txt"))
                                    FileUtils.writeStringToFile(textFileChooser.getSelectedFile(),
                                            readOut.get(resultsPane.getSelectedIndex()).getText());
                                else
                                    FileUtils.writeStringToFile(
                                            new File(textFileChooser.getSelectedFile().getPath() + ".txt"),
                                            readOut.get(resultsPane.getSelectedIndex()).getText());
                                JOptionPane.showMessageDialog(mainWindow, "Succesfully wrote readout to file");
                            } catch (Exception e) {
                                JOptionPane.showMessageDialog(mainWindow, "Could not write to file", "Error",
                                        JOptionPane.ERROR_MESSAGE);
                            }
                        }
                    } else {
                        try {
                            if (textFileChooser.getSelectedFile().getPath().endsWith(".txt"))
                                FileUtils.writeStringToFile(textFileChooser.getSelectedFile(),
                                        readOut.get(resultsPane.getSelectedIndex()).getText());
                            else
                                FileUtils.writeStringToFile(
                                        new File(textFileChooser.getSelectedFile().getPath() + ".txt"),
                                        readOut.get(resultsPane.getSelectedIndex()).getText());
                            JOptionPane.showMessageDialog(mainWindow, "Succesfully wrote readout to file");
                        } catch (Exception e) {
                            JOptionPane.showMessageDialog(mainWindow, "Could not write to file", "Error",
                                    JOptionPane.ERROR_MESSAGE);
                        }
                    }
                }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Nothing to Export", "Existential Error",
                        JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    projectFileChooser = new JFileChooser();
    projectFileChooser.setFileFilter(new ProjectFileFilter());

    //exports a neural network to a java/android project
    exportNet.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            int result, override, override2;
            String tempName;
            String templateFile;
            String directory;
            String path;
            if (resultsPane.getTabCount() != 0) {
                result = projectFileChooser.showSaveDialog(mainWindow);
                if (result == JFileChooser.APPROVE_OPTION) {
                    path = projectFileChooser.getSelectedFile().getPath();
                    directory = projectFileChooser.getSelectedFile().getPath().substring(0,
                            projectFileChooser.getSelectedFile().getPath().lastIndexOf(File.separator));
                    tempName = projectFileChooser.getSelectedFile().getName();
                    if (projectFileChooser.getSelectedFile().exists()
                            || (new File(directory, tempName + ".java")).exists()) {
                        override = JOptionPane.showConfirmDialog(mainWindow,
                                "Java Class File" + tempName + " already exists, do you want to overwrite it?",
                                "File Exists", JOptionPane.YES_NO_OPTION);
                        if (override == JOptionPane.YES_OPTION) {
                            try {
                                if (!(new File(directory, "ann")).exists())
                                    FileUtils.copyDirectoryToDirectory(
                                            FileUtils.toFile(ClassLoader.getSystemResource("ann/")),
                                            new File(directory));
                                if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                        .equals("Feed Forward Network")) {
                                    templateFile = FileUtils.readFileToString(FileUtils
                                            .toFile(ClassLoader.getSystemResource("ann/FFNTemplate.txt")));
                                    templateFile = templateFile.replaceAll("yourpackagename",
                                            (new File(directory)).getName());
                                    templateFile = templateFile.replaceAll("YourProjectName",
                                            projectFileChooser.getSelectedFile().getName());
                                    if (netName.get(resultsPane.getSelectedIndex()).toString().endsWith(".ffn"))
                                        templateFile = templateFile.replaceAll("networkName",
                                                (new File(directory)).getName() + File.separator + netName
                                                        .get(resultsPane.getSelectedIndex()).toString());
                                    else
                                        templateFile = templateFile.replaceAll("networkName",
                                                (new File(directory)).getName() + File.separator
                                                        + netName.get(resultsPane.getSelectedIndex()).toString()
                                                        + ".ffn");
                                    if (path.indexOf('.') > 0) {
                                        FileUtils.writeStringToFile(
                                                new File(path.substring(0, path.lastIndexOf('.')) + ".java"),
                                                templateFile);
                                    } else
                                        FileUtils.writeStringToFile(new File(path + ".java"), templateFile);
                                    if ((new File(directory,
                                            (tempName = netName.get(resultsPane.getSelectedIndex())
                                                    .toString()))).exists()
                                            || (new File(directory, tempName + ".ffn")).exists()) {
                                        override2 = JOptionPane.showConfirmDialog(mainWindow,
                                                "Neural Network " + tempName
                                                        + " already exists, do you want to overwrite it?",
                                                "File Exists", JOptionPane.YES_NO_OPTION);
                                        if (override2 == JOptionPane.YES_OPTION)
                                            if (net.get(resultsPane.getSelectedIndex())
                                                    .save(new File(directory + File.separator + tempName))) {
                                                JOptionPane.showMessageDialog(mainWindow, "Network Exported to "
                                                        + (new File(directory)).getName());
                                            } else {
                                                JOptionPane.showMessageDialog(mainWindow,
                                                        "Couldn't save neural network to file, the rest of the project is exported",
                                                        "Write Error", JOptionPane.ERROR_MESSAGE);
                                            }
                                    } else {
                                        if (net.get(resultsPane.getSelectedIndex())
                                                .save(new File(directory + File.separator + tempName))) {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Network Exported to " + (new File(directory)).getName());
                                        } else {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Couldn't save neural network to file, the rest of the project is exported",
                                                    "Write Error", JOptionPane.ERROR_MESSAGE);
                                        }
                                    }
                                } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                        .equals("Self-Organizing Map")) {
                                    templateFile = FileUtils.readFileToString(FileUtils
                                            .toFile(ClassLoader.getSystemResource("ann/SOMTemplate.txt")));
                                    templateFile = templateFile.replaceAll("yourpackagename",
                                            (new File(directory)).getName());
                                    templateFile = templateFile.replaceAll("YourProjectName",
                                            projectFileChooser.getSelectedFile().getName());
                                    if (netName.get(resultsPane.getSelectedIndex()).toString().endsWith(".som"))
                                        templateFile = templateFile.replaceAll("networkName",
                                                (new File(directory)).getName() + File.separator + netName
                                                        .get(resultsPane.getSelectedIndex()).toString());
                                    else
                                        templateFile = templateFile.replaceAll("networkName",
                                                (new File(directory)).getName() + File.separator
                                                        + netName.get(resultsPane.getSelectedIndex()).toString()
                                                        + ".som");
                                    if (path.indexOf('.') > 0) {
                                        FileUtils.writeStringToFile(
                                                new File(path.substring(0, path.lastIndexOf('.')) + ".java"),
                                                templateFile);
                                    } else
                                        FileUtils.writeStringToFile(new File(path + ".java"), templateFile);
                                    if ((new File(directory,
                                            (tempName = netName.get(resultsPane.getSelectedIndex())
                                                    .toString()))).exists()
                                            || (new File(directory, tempName + ".som")).exists()) {
                                        override2 = JOptionPane.showConfirmDialog(mainWindow,
                                                "Neural Network " + tempName
                                                        + " already exists, do you want to overwrite it?",
                                                "File Exists", JOptionPane.YES_NO_OPTION);
                                        if (override2 == JOptionPane.YES_OPTION)
                                            if (net.get(resultsPane.getSelectedIndex())
                                                    .save(new File(directory + File.separator + tempName))) {
                                                JOptionPane.showMessageDialog(mainWindow, "Network Exported to "
                                                        + (new File(directory)).getName());
                                            } else {
                                                JOptionPane.showMessageDialog(mainWindow,
                                                        "Couldn't save neural network to file, the rest of the project is exported",
                                                        "Write Error", JOptionPane.ERROR_MESSAGE);
                                            }
                                    } else {
                                        if (net.get(resultsPane.getSelectedIndex())
                                                .save(new File(directory + File.separator + tempName))) {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Network Exported to " + (new File(directory)).getName());
                                        } else {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Couldn't save neural network to file, the rest of the project is exported",
                                                    "Write Error", JOptionPane.ERROR_MESSAGE);
                                        }
                                    }
                                }
                            } catch (IOException io) {
                                System.out.println(io);
                            }

                        }
                    } else {
                        try {
                            if (!(new File(directory, "ann")).exists())
                                FileUtils.copyDirectoryToDirectory(
                                        FileUtils.toFile(ClassLoader.getSystemResource("ann/")),
                                        new File(directory));
                            if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                    .equals("Feed Forward Network")) {
                                templateFile = FileUtils.readFileToString(
                                        FileUtils.toFile(ClassLoader.getSystemResource("ann/FFNTemplate.txt")));
                                templateFile = templateFile.replaceAll("yourpackagename",
                                        (new File(directory)).getName());
                                templateFile = templateFile.replaceAll("YourProjectName",
                                        projectFileChooser.getSelectedFile().getName());
                                if (netName.get(resultsPane.getSelectedIndex()).toString().endsWith(".ffn"))
                                    templateFile = templateFile.replaceAll("networkName",
                                            (new File(directory)).getName() + File.separator
                                                    + netName.get(resultsPane.getSelectedIndex()).toString());
                                else
                                    templateFile = templateFile.replaceAll("networkName",
                                            (new File(directory)).getName() + File.separator
                                                    + netName.get(resultsPane.getSelectedIndex()).toString()
                                                    + ".ffn");
                                if (path.indexOf('.') > 0) {
                                    FileUtils.writeStringToFile(
                                            new File(path.substring(0, path.lastIndexOf('.')) + ".java"),
                                            templateFile);
                                } else
                                    FileUtils.writeStringToFile(new File(path + ".java"), templateFile);
                                if ((new File(directory + File.separator
                                        + (tempName = netName.get(resultsPane.getSelectedIndex()).toString())))
                                                .exists()
                                        || (new File(directory + File.separator + tempName + ".ffn"))
                                                .exists()) {
                                    override2 = JOptionPane.showConfirmDialog(mainWindow,
                                            "Neural Network " + tempName
                                                    + " already exists, do you want to overwrite it?",
                                            "File Exists", JOptionPane.YES_NO_OPTION);
                                    if (override2 == JOptionPane.YES_OPTION)
                                        if (net.get(resultsPane.getSelectedIndex())
                                                .save(new File(directory + File.separator + tempName))) {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Network Exported to " + (new File(directory)).getName());
                                        } else {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Couldn't save neural network to file, the rest of the project is exported",
                                                    "Write Error", JOptionPane.ERROR_MESSAGE);
                                        }
                                } else {
                                    if (net.get(resultsPane.getSelectedIndex())
                                            .save(new File(directory + File.separator + tempName))) {
                                        JOptionPane.showMessageDialog(mainWindow,
                                                "Network Exported to " + (new File(directory)).getName());
                                    } else {
                                        JOptionPane.showMessageDialog(mainWindow,
                                                "Couldn't save neural network to file, the rest of the project is exported",
                                                "Write Error", JOptionPane.ERROR_MESSAGE);
                                    }
                                }
                            } else if (netKind.get(resultsPane.getSelectedIndex()).toString()
                                    .equals("Self-Organizing Map")) {
                                templateFile = FileUtils.readFileToString(
                                        FileUtils.toFile(ClassLoader.getSystemResource("ann/SOMTemplate.txt")));
                                templateFile = templateFile.replaceAll("yourpackagename",
                                        (new File(directory)).getName());
                                templateFile = templateFile.replaceAll("YourProjectName",
                                        projectFileChooser.getSelectedFile().getName());
                                if (netName.get(resultsPane.getSelectedIndex()).toString().endsWith(".som"))
                                    templateFile = templateFile.replaceAll("networkName",
                                            (new File(directory)).getName() + File.separator
                                                    + netName.get(resultsPane.getSelectedIndex()).toString());
                                else
                                    templateFile = templateFile.replaceAll("networkName",
                                            (new File(directory)).getName() + File.separator
                                                    + netName.get(resultsPane.getSelectedIndex()).toString()
                                                    + ".som");
                                if (path.indexOf('.') > 0) {
                                    FileUtils.writeStringToFile(
                                            new File(path.substring(0, path.lastIndexOf('.')) + ".java"),
                                            templateFile);
                                } else
                                    FileUtils.writeStringToFile(new File(path + ".java"), templateFile);
                                if ((new File(directory,
                                        (tempName = netName.get(resultsPane.getSelectedIndex()).toString())))
                                                .exists()
                                        || (new File(directory, tempName + ".som")).exists()) {
                                    override2 = JOptionPane.showConfirmDialog(mainWindow,
                                            "Neural Network " + tempName
                                                    + " already exists, do you want to overwrite it?",
                                            "File Exists", JOptionPane.YES_NO_OPTION);
                                    if (override2 == JOptionPane.YES_OPTION)
                                        if (net.get(resultsPane.getSelectedIndex())
                                                .save(new File(directory + File.separator + tempName))) {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Network Exported to " + (new File(directory)).getName());
                                        } else {
                                            JOptionPane.showMessageDialog(mainWindow,
                                                    "Couldn't save neural network to file, the rest of the project is exported",
                                                    "Write Error", JOptionPane.ERROR_MESSAGE);
                                        }
                                } else {
                                    if (net.get(resultsPane.getSelectedIndex())
                                            .save(new File(directory + File.separator + tempName))) {
                                        JOptionPane.showMessageDialog(mainWindow,
                                                "Network Exported to " + (new File(directory)).getName());
                                    } else {
                                        JOptionPane.showMessageDialog(mainWindow,
                                                "Couldn't save neural network to file, the rest of the project is exported",
                                                "Write Error", JOptionPane.ERROR_MESSAGE);
                                    }
                                }
                            }
                        } catch (IOException io) {
                            System.out.println(io);
                        }
                    }
                }
            } else {
                JOptionPane.showMessageDialog(mainWindow, "Can't Export NonExistent Neural Network",
                        "Existential Error", JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    toJava.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : exportNet.getActionListeners())
                a.actionPerformed(ae);
        }
    });

    //settings menu
    changeConfig.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Feed Forward Network")) {

                modifyFFNDialog = new JDialog(mainWindow, "Network Settings", true);
                modifyFFNDialog.setSize(500, 500);
                modifyFFNDialog.setLayout(new GridBagLayout());
                GridBagConstraints asdf = new GridBagConstraints();
                asdf.gridwidth = 5;
                asdf.gridheight = 1;
                asdf.gridx = 0;
                asdf.gridy = 0;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.gridwidth = 5;
                asdf.gridheight = 15;
                asdf.weightx = 1.0;
                asdf.weighty = 1.0;
                asdf.gridx = 0;
                asdf.gridy = 1;
                asdf.fill = GridBagConstraints.BOTH;
                settings = new JTextArea();
                settings.setEditable(false);
                settings.setBorder(BorderFactory.createEtchedBorder());
                modifyFFNDialog.add(settings, asdf);
                asdf.fill = GridBagConstraints.HORIZONTAL;
                asdf.gridwidth = 5;
                asdf.gridheight = 1;
                asdf.gridx = 0;
                asdf.gridy = 16;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.gridwidth = 2;
                asdf.gridx = 7;
                asdf.gridy = 0;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 1;
                learningRateL = new JLabel("Set Learning Rate:");
                modifyFFNDialog.add(learningRateL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 2;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                learningRateTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getNumberInstance()));
                learningRateTF.setText("");
                modifyFFNDialog.add(learningRateTF, asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 3;
                momentumL = new JLabel("Set Momentum:");
                modifyFFNDialog.add(momentumL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 4;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                momentumTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getNumberInstance()));
                momentumTF.setText("");
                modifyFFNDialog.add(momentumTF, asdf);
                asdf.gridx = 7;
                asdf.gridy = 5;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                /*asdf.gridwidth = 2;
                asdf.gridheight = 1;
                asdf.gridx = 7;
                asdf.gridy = 6;
                setNoise = new JLabel("Use Noise: ");
                modifyFFNDialog.add(setNoise, asdf);
                asdf.gridx = 7;
                asdf.gridy = 7;
                asdf.gridwidth = 1;
                noiseOn = new JRadioButton("yes");
                noiseOff = new JRadioButton("no");
                noiseGroup = new ButtonGroup();
                noiseGroup.add(noiseOn);
                noiseGroup.add(noiseOff);
                modifyFFNDialog.add(noiseOn,asdf);
                asdf.gridx = 8;
                asdf.gridy = 7;
                modifyFFNDialog.add(noiseOff,asdf);
                asdf.gridx = 7;
                asdf.gridy = 8;
                asdf.gridwidth = 2;
                setNoiseRange = new JButton("Set Noise Range");
                modifyFFNDialog.add(setNoiseRange,asdf);
                asdf.gridx = 7;
                asdf.gridy = 9;
                setNoiseTiming = new JButton("Set Noise Timing");
                modifyFFNDialog.add(setNoiseTiming,asdf);*/
                asdf.gridx = 7;
                asdf.gridy = 10;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 11;
                setTrainingStyle = new JLabel("Set Training Style:");
                modifyFFNDialog.add(setTrainingStyle, asdf);
                asdf.gridx = 7;
                asdf.gridy = 12;
                asdf.gridwidth = 1;
                batchOn = new JRadioButton("batch");
                onlineOn = new JRadioButton("online");
                batchGroup = new ButtonGroup();
                batchGroup.add(batchOn);
                batchGroup.add(onlineOn);
                modifyFFNDialog.add(batchOn, asdf);
                asdf.gridx = 8;
                modifyFFNDialog.add(onlineOn, asdf);
                asdf.gridx = 7;
                asdf.gridy = 13;
                asdf.gridwidth = 2;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 14;
                modifyBiases = new JButton("Modify Biases");
                modifyFFNDialog.add(modifyBiases, asdf);
                asdf.gridx = 7;
                asdf.gridy = 15;
                trainingCompletionButton = new JButton("Modify End Condition");
                modifyFFNDialog.add(trainingCompletionButton, asdf);
                asdf.fill = GridBagConstraints.HORIZONTAL;
                asdf.gridy = 16;
                modifyFFNDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridwidth = 1;
                asdf.gridx = 3;
                asdf.gridy = 17;
                asdf.anchor = GridBagConstraints.PAGE_END;
                modifyFFN = new JButton("OK");
                modifyFFNDialog.add(modifyFFN, asdf);
                asdf.gridx = 7;
                cancelModifyFFN = new JButton("Cancel");
                modifyFFNDialog.add(cancelModifyFFN, asdf);
                settings.setText("");
                settings.append(
                        "\n\n\n\nLearning Rate: " + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                settings.append("\n\nMomentum: " + net.get(resultsPane.getSelectedIndex()).getMomentum());
                settings.append("\n\nTraining Style: ");
                if (net.get(resultsPane.getSelectedIndex()).getBatchvOnline()) {
                    settings.append("batch");
                    batchOn.setSelected(true);
                } else {
                    settings.append("online");
                    onlineOn.setSelected(true);
                }
                settings.append("\n\nTraining End Condition: ");
                if (net.get(resultsPane.getSelectedIndex()).getUseIteration()) {
                    settings.append("Iterative");
                    settings.append(
                            "\n\nIterations: " + net.get(resultsPane.getSelectedIndex()).getIterations());
                } else {
                    settings.append("Ideal Error");
                    settings.append(
                            "\n\nIdeal Error: " + net.get(resultsPane.getSelectedIndex()).getIdealError());
                }

                //expiremental feature, needs work on the back end to be properly implemented   
                modifyBiases.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        JButton addBiases, removeBiases;

                        biasesDialog = new JDialog(modifyFFNDialog, "Set Biases");
                        biasesDialog.setSize(200, 46);
                        biasesDialog.setLayout(new GridLayout(2, 1));
                        addBiases = new JButton("Add Bias");
                        removeBiases = new JButton("Remove Bias");

                        biasesDialog.add(addBiases);
                        biasesDialog.add(removeBiases);

                        addBiases.addActionListener(new ActionListener() {
                            public void actionPerformed(ActionEvent ae) {
                                JLabel howManyBiasLayersLabel, whatBiasNodeLabel, whatBiasValueLabel;
                                final JFormattedTextField howManyBiasLayers, whatBiasNode, whatBiasValue;
                                JButton addBiasOK, addBiasCancel;
                                biasesDialog.setVisible(false);
                                addBiasDialog = new JDialog(modifyFFNDialog, "Add Bias");
                                addBiasDialog.setSize(756, 90);
                                addBiasDialog.setLayout(new GridLayout(4, 2));
                                howManyBiasLayersLabel = new JLabel("What Layer will get the Bias?");
                                howManyBiasLayers = new JFormattedTextField(
                                        new NumberFormatter(NumberFormat.getIntegerInstance()));
                                whatBiasNodeLabel = new JLabel("Which Node will get the Bias?");
                                whatBiasNode = new JFormattedTextField(
                                        new NumberFormatter(NumberFormat.getIntegerInstance()));
                                whatBiasValueLabel = new JLabel("What Value will the Bias have?");
                                whatBiasValue = new JFormattedTextField(
                                        new NumberFormatter(NumberFormat.getInstance()));
                                addBiasOK = new JButton("OK");
                                addBiasCancel = new JButton("Cancel");
                                addBiasDialog.add(howManyBiasLayersLabel);
                                addBiasDialog.add(howManyBiasLayers);
                                addBiasDialog.add(whatBiasNodeLabel);
                                addBiasDialog.add(whatBiasNode);
                                addBiasDialog.add(whatBiasValueLabel);
                                addBiasDialog.add(whatBiasValue);
                                addBiasDialog.add(addBiasOK);
                                addBiasDialog.add(addBiasCancel);

                                addBiasOK.addActionListener(new ActionListener() {
                                    public void actionPerformed(ActionEvent ae) {
                                        if (!howManyBiasLayers.getText().equals("")
                                                && !whatBiasNode.getText().equals("")
                                                && !whatBiasValue.getText().equals("")) {
                                            addBiasDialog.setVisible(false);
                                            if (net.get(resultsPane.getSelectedIndex()).addBias(
                                                    Integer.parseInt(howManyBiasLayers.getText()) - 1,
                                                    Integer.parseInt(whatBiasNode.getText()) - 1,
                                                    Double.parseDouble(whatBiasValue.getText()))) {
                                            } else {
                                                JOptionPane.showMessageDialog(modifyFFNDialog,
                                                        "Existential Error", "Invalid Node for Bias",
                                                        JOptionPane.ERROR_MESSAGE);
                                            }
                                        } else {
                                            JOptionPane.showMessageDialog(modifyFFNDialog, "Form Error",
                                                    "Form not completed", JOptionPane.ERROR_MESSAGE);
                                        }
                                    }
                                });
                                addBiasCancel.addActionListener(new ActionListener() {
                                    public void actionPerformed(ActionEvent ae) {
                                        addBiasDialog.setVisible(false);
                                    }
                                });

                                addBiasDialog.setVisible(true);
                            }
                        });

                        removeBiases.addActionListener(new ActionListener() {
                            public void actionPerformed(ActionEvent ae) {
                                JLabel howManyBiasLayersLabel, whatBiasNodeLabel;
                                final JFormattedTextField howManyBiasLayers, whatBiasNode;
                                JButton addBiasOK, addBiasCancel;
                                biasesDialog.setVisible(false);
                                removeBiasDialog = new JDialog(modifyFFNDialog, "Remove Bias");
                                removeBiasDialog.setSize(756, 90);
                                removeBiasDialog.setLayout(new GridLayout(3, 2));
                                howManyBiasLayersLabel = new JLabel("What Layer will lose the Bias?");
                                howManyBiasLayers = new JFormattedTextField(
                                        new NumberFormatter(NumberFormat.getIntegerInstance()));
                                whatBiasNodeLabel = new JLabel("Which Node will get the Bias?");
                                whatBiasNode = new JFormattedTextField(
                                        new NumberFormatter(NumberFormat.getIntegerInstance()));
                                addBiasOK = new JButton("OK");
                                addBiasCancel = new JButton("Cancel");
                                removeBiasDialog.add(howManyBiasLayersLabel);
                                removeBiasDialog.add(howManyBiasLayers);
                                removeBiasDialog.add(whatBiasNodeLabel);
                                removeBiasDialog.add(whatBiasNode);
                                removeBiasDialog.add(addBiasOK);
                                removeBiasDialog.add(addBiasCancel);

                                addBiasOK.addActionListener(new ActionListener() {
                                    public void actionPerformed(ActionEvent ae) {
                                        if (!howManyBiasLayers.getText().equals("")
                                                && !whatBiasNode.getText().equals("")) {
                                            addBiasDialog.setVisible(false);
                                            if (net.get(resultsPane.getSelectedIndex()).removeBias(
                                                    Integer.parseInt(howManyBiasLayers.getText()) - 1,
                                                    Integer.parseInt(whatBiasNode.getText()) - 1)) {
                                            } else {
                                                JOptionPane.showMessageDialog(modifyFFNDialog,
                                                        "Existential Error", "Invalid Node for Bias",
                                                        JOptionPane.ERROR_MESSAGE);
                                            }
                                        } else {
                                            JOptionPane.showMessageDialog(modifyFFNDialog, "Form Error",
                                                    "Form not completed", JOptionPane.ERROR_MESSAGE);
                                        }
                                    }
                                });
                                addBiasCancel.addActionListener(new ActionListener() {
                                    public void actionPerformed(ActionEvent ae) {
                                        addBiasDialog.setVisible(false);
                                    }
                                });

                                removeBiasDialog.setVisible(true);
                            }
                        });

                        biasesDialog.setVisible(true);

                    }
                });

                trainingCompletionButton.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        final JDialog iterationsDialog;
                        JLabel numberOfIterationsLabel;
                        final JFormattedTextField numberOfIterations;
                        JButton iterationsOK, iterationsCancel;
                        iterationsDialog = new JDialog(modifyFFNDialog, "Set Iterations");
                        iterationsDialog.setSize(765, 75);
                        iterationsDialog.setLayout(new GridLayout(2, 2));
                        numberOfIterationsLabel = new JLabel("How Many Iterations do you want to Train?");
                        numberOfIterations = new JFormattedTextField(
                                new NumberFormatter(NumberFormat.getIntegerInstance()));
                        iterationsOK = new JButton("OK");
                        iterationsCancel = new JButton("Cancel");
                        iterationsDialog.add(numberOfIterationsLabel);
                        iterationsDialog.add(numberOfIterations);
                        iterationsDialog.add(iterationsOK);
                        iterationsDialog.add(iterationsCancel);
                        iterationsOK.addActionListener(new ActionListener() {
                            public void actionPerformed(ActionEvent ae) {
                                if (!numberOfIterations.getText().equals("")) {
                                    iterationsDialog.setVisible(false);
                                    if (net.get(resultsPane.getSelectedIndex())
                                            .setIterations(Integer.parseInt(numberOfIterations.getText()))) {
                                        settings.setText("");
                                        settings.append("\n\n\n\nLearning Rate: "
                                                + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                                        settings.append("\n\nMomentum: "
                                                + net.get(resultsPane.getSelectedIndex()).getMomentum());
                                        settings.append("\n\nTraining Style: ");
                                        if (net.get(resultsPane.getSelectedIndex()).getBatchvOnline()) {
                                            settings.append("batch");
                                            batchOn.setSelected(true);
                                        } else {
                                            settings.append("online");
                                            onlineOn.setSelected(true);
                                        }
                                        settings.append("\n\nTraining End Condition: ");
                                        if (net.get(resultsPane.getSelectedIndex()).getUseIteration()) {
                                            settings.append("Iterative");
                                            settings.append("\n\nIterations: "
                                                    + net.get(resultsPane.getSelectedIndex()).getIterations());
                                        } else {
                                            settings.append("Ideal Error");
                                            settings.append("\n\nIdeal Error: "
                                                    + net.get(resultsPane.getSelectedIndex()).getIdealError());
                                        }
                                        modifyFFNDialog.setVisible(true);
                                    } else {
                                        JOptionPane.showMessageDialog(modifyFFNDialog,
                                                "Invalid Number of Iterations", "Math Error",
                                                JOptionPane.ERROR_MESSAGE);
                                    }
                                } else {
                                    JOptionPane.showMessageDialog(iterationsDialog, "Field not filled out",
                                            "Form Error", JOptionPane.ERROR_MESSAGE);
                                }
                            }
                        });
                        iterationsCancel.addActionListener(new ActionListener() {
                            public void actionPerformed(ActionEvent ae) {
                                iterationsDialog.setVisible(false);
                            }
                        });
                        iterationsDialog.setVisible(true);
                    }
                });

                modifyFFN.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if (!learningRateTF.getText().equals("")) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setLearningRate(Double.parseDouble(learningRateTF.getText()));
                            learningRateTF.setText("");
                        }
                        if (!momentumTF.getText().equals("")) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setMomentum(Double.parseDouble(momentumTF.getText()));
                            momentumTF.setText("");
                        }
                        if (batchOn.isSelected()) {
                            net.get(resultsPane.getSelectedIndex()).setBatchvOnline(true);
                        } else {
                            net.get(resultsPane.getSelectedIndex()).setBatchvOnline(false);
                        }

                        modifyFFNDialog.setVisible(false);
                    }
                });

                learningRateTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if (learningRateTF.getText() != "") {
                            net.get(resultsPane.getSelectedIndex())
                                    .setLearningRate(Double.parseDouble(learningRateTF.getText()));
                        }
                        settings.setText("");
                        settings.append("\n\n\n\nLearning Rate: "
                                + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                        settings.append(
                                "\n\nMomentum: " + net.get(resultsPane.getSelectedIndex()).getMomentum());
                        settings.append("\n\nTraining Style: ");

                        if (net.get(resultsPane.getSelectedIndex()).getBatchvOnline()) {
                            settings.append("batch");
                            batchOn.setSelected(true);
                        } else {
                            settings.append("online");
                            onlineOn.setSelected(true);
                        }
                        settings.append("\n\nTraining End Condition: ");
                        if (net.get(resultsPane.getSelectedIndex()).getUseIteration()) {
                            settings.append("Iterative");
                            settings.append("\n\nIterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getIterations());
                        } else {
                            settings.append("Ideal Error");
                            settings.append("\n\nIdeal Error: "
                                    + net.get(resultsPane.getSelectedIndex()).getIdealError());
                        }
                        modifyFFNDialog.setVisible(true);
                    }
                });
                momentumTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if (momentumTF.getText() != "") {
                            net.get(resultsPane.getSelectedIndex())
                                    .setMomentum(Double.parseDouble(momentumTF.getText()));
                        }
                        settings.setText("");
                        settings.append("\n\n\n\nLearning Rate: "
                                + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                        settings.append(
                                "\n\nMomentum: " + net.get(resultsPane.getSelectedIndex()).getMomentum());
                        settings.append("\n\nTraining Style: ");
                        if (net.get(resultsPane.getSelectedIndex()).getBatchvOnline()) {
                            settings.append("batch");
                            batchOn.setSelected(true);
                        } else {
                            settings.append("online");
                            onlineOn.setSelected(true);
                        }
                        settings.append("\n\nTraining End Condition: ");
                        if (net.get(resultsPane.getSelectedIndex()).getUseIteration()) {
                            settings.append("Iterative");
                            settings.append("\n\nIterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getIterations());
                        } else {
                            settings.append("Ideal Error");
                            settings.append("\n\nIdeal Error: "
                                    + net.get(resultsPane.getSelectedIndex()).getIdealError());
                        }
                        modifyFFNDialog.setVisible(true);
                    }
                });
                cancelModifyFFN.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        modifyFFNDialog.setVisible(false);
                    }
                });
                modifyFFNDialog.setVisible(true);
            }
            if (resultsPane.getTabCount() != 0
                    && netKind.get(resultsPane.getSelectedIndex()).toString().equals("Self-Organizing Map")) {
                modifySOMDialog = new JDialog(mainWindow, "Network Settings", true);
                modifySOMDialog.setSize(500, 400);
                modifySOMDialog.setLayout(new GridBagLayout());
                GridBagConstraints asdf = new GridBagConstraints();
                asdf.gridwidth = 5;
                asdf.gridheight = 1;
                asdf.gridx = 0;
                asdf.gridy = 0;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                modifySOMDialog.add(new JSeparator(), asdf);
                asdf.gridwidth = 5;
                asdf.gridheight = 15;
                asdf.weightx = 1.0;
                asdf.weighty = 1.0;
                asdf.gridx = 0;
                asdf.gridy = 1;
                asdf.fill = GridBagConstraints.BOTH;
                settings = new JTextArea();
                settings.setEditable(false);
                settings.setBorder(BorderFactory.createEtchedBorder());
                modifySOMDialog.add(settings, asdf);
                asdf.fill = GridBagConstraints.HORIZONTAL;
                asdf.gridwidth = 5;
                asdf.gridheight = 1;
                asdf.gridx = 0;
                asdf.gridy = 16;
                modifySOMDialog.add(new JSeparator(), asdf);
                asdf.gridwidth = 2;
                asdf.gridx = 7;
                asdf.gridy = 0;
                modifySOMDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 1;
                mIterationL = new JLabel("Set Number of Iterations:");
                modifySOMDialog.add(mIterationL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 2;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                mIterationTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getIntegerInstance()));
                mIterationTF.setText("");
                modifySOMDialog.add(mIterationTF, asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 3;
                mLRL = new JLabel("Set Learning Rate (0-1):");
                modifySOMDialog.add(mLRL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 4;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                mLRTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getNumberInstance()));
                mLRTF.setText("");
                modifySOMDialog.add(mLRTF, asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 5;
                mMaxL = new JLabel("Set Data Maximum:");
                modifySOMDialog.add(mMaxL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 6;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                mMaxTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getNumberInstance()));
                mMaxTF.setText("");
                modifySOMDialog.add(mMaxTF, asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridx = 7;
                asdf.gridy = 7;
                mMinL = new JLabel("Set Data Minimum:");
                modifySOMDialog.add(mMinL, asdf);
                asdf.gridx = 7;
                asdf.gridy = 8;
                asdf.fill = GridBagConstraints.HORIZONTAL;
                mMinTF = new JFormattedTextField(new NumberFormatter(NumberFormat.getNumberInstance()));
                mMinTF.setText("");
                modifySOMDialog.add(mMinTF, asdf);
                asdf.fill = GridBagConstraints.HORIZONTAL;
                asdf.gridy = 16;
                modifySOMDialog.add(new JSeparator(), asdf);
                asdf.fill = GridBagConstraints.NONE;
                asdf.gridwidth = 1;
                asdf.gridx = 3;
                asdf.gridy = 17;
                asdf.anchor = GridBagConstraints.PAGE_END;
                modifySOM = new JButton("OK");
                modifySOMDialog.add(modifySOM, asdf);
                asdf.gridx = 7;
                cancelModifySOM = new JButton("Cancel");
                modifySOMDialog.add(cancelModifySOM, asdf);
                settings.setText("");
                settings.append("\n\nNumber of Iterations: "
                        + net.get(resultsPane.getSelectedIndex()).getNumIterations());
                settings.append(
                        "\n\nLearning Rate: " + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                settings.append("\n\nData Maximum: " + net.get(resultsPane.getSelectedIndex()).getDataMax());
                settings.append("\n\nData Minimum: " + net.get(resultsPane.getSelectedIndex()).getDataMin());

                mIterationTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if (mIterationTF.getText() != "") {
                            net.get(resultsPane.getSelectedIndex())
                                    .setNumIterations(Integer.parseInt(mIterationTF.getText()));

                            settings.setText("");
                            settings.append("\n\nNumber of Iterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getNumIterations());
                            settings.append("\n\nLearning Rate: "
                                    + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                            settings.append("\n\nData Maximum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMax());
                            settings.append("\n\nData Minimum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMin());
                        }
                    }
                });

                mLRTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if ((mLRTF.getText() != "") && ((Double.parseDouble(mLRTF.getText())) <= 1.0)) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setLearningRate(Double.parseDouble(mLRTF.getText()));

                            settings.setText("");
                            settings.append("\n\nNumber of Iterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getNumIterations());
                            settings.append("\n\nLearning Rate: "
                                    + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                            settings.append("\n\nData Maximum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMax());
                            settings.append("\n\nData Minimum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMin());
                        } else {
                            JOptionPane.showMessageDialog(mLRTF, "Pick a number from 0 - 1", "Incorrect Value",
                                    JOptionPane.ERROR_MESSAGE);
                            mLRTF.setText("");
                        }
                    }
                });

                mMaxTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if ((mMaxTF.getText() != "") && (((Double.parseDouble(mMaxTF.getText())) > net
                                .get(resultsPane.getSelectedIndex()).getDataMin()))) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setDataMax(Double.parseDouble(mMaxTF.getText()));

                            settings.setText("");
                            settings.append("\n\nNumber of Iterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getNumIterations());
                            settings.append("\n\nLearning Rate: "
                                    + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                            settings.append("\n\nData Maximum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMax());
                            settings.append("\n\nData Minimum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMin());
                        } else {
                            JOptionPane.showMessageDialog(mMaxTF, "Max value must be greater than Min value",
                                    "Incorrect Value", JOptionPane.ERROR_MESSAGE);
                            mMaxTF.setText("");
                        }
                    }
                });

                mMinTF.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        if ((mMinTF.getText() != "") && ((Double.parseDouble(mMinTF.getText())) < net
                                .get(resultsPane.getSelectedIndex()).getDataMax())) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setDataMin(Double.parseDouble(mMinTF.getText()));

                            settings.setText("");
                            settings.append("\n\nNumber of Iterations: "
                                    + net.get(resultsPane.getSelectedIndex()).getNumIterations());
                            settings.append("\n\nLearning Rate: "
                                    + net.get(resultsPane.getSelectedIndex()).getLearningRate());
                            settings.append("\n\nData Maximum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMax());
                            settings.append("\n\nData Minimum: "
                                    + net.get(resultsPane.getSelectedIndex()).getDataMin());
                        } else {
                            JOptionPane.showMessageDialog(mMinTF, "Min value must be less than Max value",
                                    "Incorrect Value", JOptionPane.ERROR_MESSAGE);
                            mMinTF.setText("");
                        }
                    }
                });

                modifySOM.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        boolean error = false;
                        if (!("".equals(mIterationTF.getText()))) {
                            net.get(resultsPane.getSelectedIndex())
                                    .setNumIterations(Integer.parseInt(mIterationTF.getText()));
                        }
                        if (!("".equals(mLRTF.getText()))) {
                            if ((Double.parseDouble(mLRTF.getText())) > 1.0) {
                                error = true;
                                mLRTF.setText("");
                            } else
                                net.get(resultsPane.getSelectedIndex())
                                        .setLearningRate(Double.parseDouble(mLRTF.getText()));
                        }
                        if (!("".equals(mMaxTF.getText()))) {
                            if (((Double.parseDouble(mMaxTF.getText())) < net
                                    .get(resultsPane.getSelectedIndex()).getDataMin())) {
                                error = true;
                                mMaxTF.setText("");
                            } else
                                net.get(resultsPane.getSelectedIndex())
                                        .setDataMax(Double.parseDouble(mMaxTF.getText()));
                        }
                        if (!("".equals(mMinTF.getText()))) {
                            if ((Double.parseDouble(mMinTF.getText())) > net.get(resultsPane.getSelectedIndex())
                                    .getDataMax()) {
                                error = true;
                                mMinTF.setText("");
                            } else
                                net.get(resultsPane.getSelectedIndex())
                                        .setDataMin(Double.parseDouble(mMinTF.getText()));
                        }

                        if (error == true) {
                            JOptionPane.showMessageDialog(modifySOMDialog,
                                    "One or more fields have incorrect values", "Incorrect Value",
                                    JOptionPane.ERROR_MESSAGE);
                        } else {
                            modifySOMDialog.setVisible(false);
                            readOut.get(resultsPane.getSelectedIndex()).append("\nUpdated Map:\n");
                            printInitMap();
                        }

                    }
                });

                cancelModifySOM.addActionListener(new ActionListener() {
                    public void actionPerformed(ActionEvent ae) {
                        modifySOMDialog.setVisible(false);
                    }
                });

                modifySOMDialog.setVisible(true);
            }
        }

    });

    modify.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : changeConfig.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //The following code is for the newNet button under file:

    //create a dialog to be activated when "New Network" is pressed in the file menu
    newDialog = new JDialog(mainWindow, "New Network", true);
    newDialog.setSize(375, 100);
    newDialog.setLayout(new GridLayout(3, 2)); //going to change the layout to GridBagLayout for better customization

    name = new JLabel("Network Name:");
    newName = new JTextField(10);
    type = new JLabel("Type of Network:");
    netTypes = new String[] { "Feed Forward Network", "Self-Organizing Map" };
    netType = new JComboBox<String>(netTypes);
    netType.setSelectedItem("Feed Forward Network");
    createNewNet = new JButton("create");
    cancelNew = new JButton("cancel");
    newDialog.add(name);
    newDialog.add(newName);
    newDialog.add(type);
    newDialog.add(netType);
    newDialog.add(createNewNet);
    newDialog.add(cancelNew);

    //utilities for a second dialog(Feed Forward Network) in the process of creating a new network   
    number = new JLabel("Enter the number of layers you want for your network:");
    howManyLayers = new JFormattedTextField(new NumberFormatter(NumberFormat.getIntegerInstance()));
    createFFNArchitecture = new JButton("OK");
    cancelFFN = new JButton("Cancel");

    howManyNodes = new JFormattedTextField(new NumberFormatter(NumberFormat.getIntegerInstance()));
    createFFN = new JButton("OK");
    cancelNodes = new JButton("Cancel");

    //Written by Michael Scott
    somLattice = new JLabel("   Lattice number for your Map:");
    somLatticeField = new JFormattedTextField(new NumberFormatter(NumberFormat.getIntegerInstance()));
    somLatticeField.setFocusLostBehavior(1);
    somMax = new JLabel("   Maximum value of your input (if known):");
    somMaxField = new JFormattedTextField(new NumberFormatter(NumberFormat.getInstance()));
    somMaxField.setFocusLostBehavior(1);
    somMin = new JLabel("   Minimum value of your input (if known):");
    somMinField = new JFormattedTextField(new NumberFormatter(NumberFormat.getInstance()));
    somMinField.setFocusLostBehavior(1);
    somDim = new JLabel("   Node Dimensions:");
    somDimField = new JFormattedTextField(new NumberFormatter(NumberFormat.getIntegerInstance()));
    somDimField.setFocusLostBehavior(1);
    createSOM = new JButton("OK");
    cancelSOM = new JButton("Cancel");

    //displays the newDialog window when newNet is pressed
    newNet.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {

            newDialog.setVisible(true);
        }
    });

    newwer.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            newDialog.setVisible(true);
        }
    });

    //makes hitting enter in the text box do the same thing as clicking "create"
    newName.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : createNewNet.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //when create net is pressed, this reads the selections from the newNet dialog and creates the approriate next dialog
    createNewNet.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            int test;
            test = 0;
            for (StringBuffer names : netName) {
                if (names.toString().equals(newName.getText()))
                    test = 1;
            }
            if (test == 0)
                if (!newName.getText().equals("")) {
                    if (netType.getSelectedIndex() == 0) { //if the net selected is Feed Forward, create and display the prompt for a feed forward network
                        newDialog.setVisible(false);
                        fFNDialog = new JDialog(mainWindow, newName.getText(), true);
                        fFNDialog.setSize(919, 65);
                        fFNDialog.setLayout(new GridLayout(2, 2));
                        fFNDialog.add(number);
                        fFNDialog.add(howManyLayers);
                        fFNDialog.add(createFFNArchitecture);
                        fFNDialog.add(cancelFFN);
                        fFNDialog.setVisible(true);
                    }
                    //Written by Michael Scott
                    if (netType.getSelectedIndex() == 1) {
                        newDialog.setVisible(false);
                        sOMDialog = new JDialog(mainWindow, newName.getText(), true);
                        sOMDialog.setSize(500, 180);
                        sOMDialog.setLayout(new GridLayout(5, 2));
                        sOMDialog.add(somLattice);
                        sOMDialog.add(somLatticeField);
                        sOMDialog.add(somDim);
                        sOMDialog.add(somDimField);
                        sOMDialog.add(somMax);
                        sOMDialog.add(somMaxField);
                        sOMDialog.add(somMin);
                        sOMDialog.add(somMinField);
                        sOMDialog.add(createSOM);
                        sOMDialog.add(cancelSOM);
                        sOMDialog.setVisible(true);

                    }
                } else
                    JOptionPane.showMessageDialog(createNewNet, "Network must have a Name",
                            "Namelessness Error", JOptionPane.ERROR_MESSAGE);
            else {
                JOptionPane.showMessageDialog(createNewNet, "Network " + newName.getText() + " already exists",
                        "Existential Naming Error", JOptionPane.ERROR_MESSAGE);
                newName.setText("");
            }
        }

    });
    //beginning of section about creating Feed Forward Networks   
    //cancel clears the name field and hides the newDialog dialog
    cancelNew.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            newDialog.setVisible(false);
            newName.setText("");
        }
    });

    //makes hitting enter the same as clicking "ok"
    howManyLayers.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : createFFNArchitecture.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //create a prompt for the first layer to determine how many nodes will go into the first layer
    createFFNArchitecture.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (!howManyLayers.getText().equals("")
                    && (layers = Integer.parseInt(howManyLayers.getText())) > 1) {
                nodeConfiguration = new int[layers]; //create an array to hold the node configuration that will be passed to the Net constructor
                layer = 1; //create a variable to hold the current layer the prompt series is on
                numberofNodes = new JLabel("How many nodes do you want in layer " + layer + "?");
                fFNDialog.setVisible(false);
                howManyNodesDialog = new JDialog(mainWindow, newName.getText(), true);
                howManyNodesDialog.setSize(919, 65);
                howManyNodesDialog.setLayout(new GridLayout(2, 2));
                howManyNodesDialog.add(numberofNodes);
                howManyNodesDialog.add(howManyNodes);
                howManyNodesDialog.add(createFFN);
                howManyNodesDialog.add(cancelNodes);
                howManyNodesDialog.setVisible(true);
            } else {
                //if the string is not valid, pop up an error message
                JOptionPane.showMessageDialog(fFNDialog,
                        "<html>Number Out of Bounds<br>Please Enter a Number Greater than 1</html>",
                        "Out of Bounds", JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    //runs each time ok is pressed, until all the layers have a vaule for the number of nodes in the layer
    createFFN.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (!howManyNodes.getText().equals("")
                    && (nodeConfiguration[layer - 1] = Integer.parseInt(howManyNodes.getText())) > 0) {
                if (layer == layers) {
                    try {
                        //adds a close button to the top corner of each tab
                        title.add(new JLabel(newName.getText() + " "));
                        close.add(new JButton("X"));
                        close.get(openNets).setActionCommand(newName.getText());
                        close.get(openNets).setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
                        close.get(openNets).setMargin(new Insets(0, 0, 0, 0));
                        tabPanel.add(new JPanel(new GridBagLayout()));
                        tabPanel.get(openNets).setOpaque(false);
                        GridBagConstraints grid = new GridBagConstraints();
                        grid.fill = GridBagConstraints.HORIZONTAL;
                        grid.gridx = 0;
                        grid.gridy = 0;
                        grid.weightx = 1;
                        tabPanel.get(openNets).add(title.get(openNets), grid);
                        grid.gridx = 1;
                        grid.gridy = 0;
                        grid.weightx = 0;
                        tabPanel.get(openNets).add(close.get(openNets), grid);

                        //adds a loading bar
                        loadingBar.add(new JLabel("", loadingImage, SwingConstants.CENTER));
                        loadingBar.get(openNets).setHorizontalTextPosition(SwingConstants.LEFT);
                        loadingBar.get(openNets).setVisible(false);
                        //creates and sets the network configuration
                        net.add(new FullyConnectedFeedForwardNet(nodeConfiguration));

                        netKind.add(new StringBuffer(netType.getSelectedItem().toString()));
                        netName.add(new StringBuffer(newName.getText()));
                        oneNet.add(new JPanel());
                        oneNet.get(openNets).setLayout(new GridBagLayout());
                        GridBagConstraints constraints = new GridBagConstraints();
                        constraints.fill = GridBagConstraints.BOTH;

                        //creates the readOut space and formats it so that the scroll pane/text changes size with the window, reserves space for the loading bar
                        readOut.add(new JTextArea(""));
                        readOutLocale.add(new JScrollPane(readOut.get(openNets)));
                        readOut.get(openNets).setEditable(false);
                        constraints.gridx = 0;
                        constraints.gridy = 0;
                        constraints.weighty = 1.0;
                        constraints.weightx = 1.0;
                        constraints.gridwidth = 2;
                        constraints.ipady = 90;
                        oneNet.get(openNets).add(readOutLocale.get(openNets), constraints);
                        constraints.fill = GridBagConstraints.HORIZONTAL;
                        constraints.gridx = 0;
                        constraints.gridy = 1;
                        constraints.ipady = 0;
                        constraints.gridwidth = 2;
                        constraints.anchor = GridBagConstraints.PAGE_END;

                        //add everythign to the tabbed pane
                        oneNet.get(openNets).add(loadingBar.get(openNets), constraints);
                        resultsPane.addTab(netName.get(openNets).toString(), oneNet.get(openNets));
                        resultsPane.setTabComponentAt(openNets, tabPanel.get(openNets));

                        path.add("");

                        //display the starting configuration of the network
                        readOut.get(openNets).append("Network: " + netName.get(openNets) + "\n\n");
                        resultsPane.setSelectedIndex(openNets++);
                        printConnections();

                        //erases all the text in the setup fields and closes the window
                        howManyNodes.setValue(null);
                        howManyLayers.setText("");
                        newName.setText("");
                        howManyNodesDialog.setVisible(false);

                        //unfortunately difficult way that I made to add the close button functionality to close a tab
                        //it works, but there has to be a better way to do this
                        close.get(resultsPane.getSelectedIndex()).addActionListener(new ActionListener() {
                            public void actionPerformed(final ActionEvent ae) {
                                int result;
                                result = 0;
                                for (StringBuffer names : netName) {
                                    if (ae.getActionCommand().equals(names.toString())) {
                                        result = JOptionPane.showConfirmDialog(createFFN,
                                                "<html>Exiting Without Saving can Cause you to Lose your Progress<br>Are you sure you want to Continue?</html>",
                                                "Close Network", JOptionPane.OK_CANCEL_OPTION);
                                        resultsPane.setSelectedIndex(netName.indexOf(names));
                                    }
                                }
                                if (result == JOptionPane.OK_OPTION) {
                                    net.remove(resultsPane.getSelectedIndex());
                                    oneNet.remove(resultsPane.getSelectedIndex());
                                    readOutLocale.remove(resultsPane.getSelectedIndex());
                                    readOut.remove(resultsPane.getSelectedIndex());
                                    loadingBar.remove(resultsPane.getSelectedIndex());
                                    tabPanel.remove(resultsPane.getSelectedIndex());
                                    title.remove(resultsPane.getSelectedIndex());
                                    close.remove(resultsPane.getSelectedIndex());
                                    netName.remove(resultsPane.getSelectedIndex());
                                    resultsPane.remove(resultsPane.getSelectedIndex());
                                    openNets--;
                                }
                            }
                        });
                    } catch (OutOfMemoryError e) {
                        JOptionPane.showMessageDialog(mainWindow,
                                "<html>Net too Large for Memory.<br>Try Closing some of the Nets.</html>",
                                "Memory Error", JOptionPane.ERROR_MESSAGE);
                    }
                } else {
                    layer++;
                    howManyNodes.setText("");
                    numberofNodes.setText("How many nodes do you want in layer " + layer + "?");
                }

            } else {
                JOptionPane.showMessageDialog(createFFN,
                        "<html>Number Out of Bounds<br>Please Enter a Number Greater than 0", "Out of Bounds",
                        JOptionPane.ERROR_MESSAGE);
            }
        }
    });

    //makes hitting enter in text box the same as clicking ok
    howManyNodes.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            for (ActionListener a : createFFN.getActionListeners()) {
                a.actionPerformed(ae);
            }
        }
    });

    //cancels the node prompt
    cancelNodes.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            newName.setText("");
            howManyLayers.setText("");
            howManyNodes.setText("");
            howManyNodesDialog.setVisible(false);
        }
    });

    //cancel clears both name fields so far filled in the series of dialogs and hides the dialog
    cancelFFN.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            newName.setText("");
            howManyLayers.setText("");
            fFNDialog.setVisible(false);
        }
    });
    //end of section about creating FFNs
    //end of section about newNet   

    //Method to create a SOM
    createSOM.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            if (somLatticeField.getText().equals("") || somDimField.getText().equals("")) {
                JOptionPane.showMessageDialog(createSOM, "<html>Empty Field<br>Please Fill All Fields",
                        "Empty Field", JOptionPane.ERROR_MESSAGE);
            } else {
                if (somMaxField.getText().equals(""))
                    somMaxField.setText("100");
                if (somMinField.getText().equals(""))
                    somMinField.setText("0");
                if (Double.parseDouble(somMaxField.getText().replace(",", "")) < Double
                        .parseDouble(somMinField.getText().replace(",", ""))) {
                    JOptionPane.showMessageDialog(createSOM, "MIN GREATER THAN MAX!!!!", "Stupidity Error",
                            JOptionPane.ERROR_MESSAGE);
                }

                try {
                    //adds a close button to the top corner of each tab
                    title.add(new JLabel(newName.getText() + " "));
                    close.add(new JButton("X"));
                    close.get(openNets).setActionCommand(newName.getText());
                    close.get(openNets).setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
                    close.get(openNets).setMargin(new Insets(0, 0, 0, 0));
                    tabPanel.add(new JPanel(new GridBagLayout()));
                    tabPanel.get(openNets).setOpaque(false);
                    GridBagConstraints grid = new GridBagConstraints();
                    grid.fill = GridBagConstraints.HORIZONTAL;
                    grid.gridx = 0;
                    grid.gridy = 0;
                    grid.weightx = 1;
                    tabPanel.get(openNets).add(title.get(openNets), grid);
                    grid.gridx = 1;
                    grid.gridy = 0;
                    grid.weightx = 0;
                    tabPanel.get(openNets).add(close.get(openNets), grid);

                    //adds a loading bar
                    loadingBar.add(new JLabel("", loadingImage, SwingConstants.CENTER));
                    loadingBar.get(openNets).setHorizontalTextPosition(SwingConstants.LEFT);
                    loadingBar.get(openNets).setVisible(false);
                    //creates and sets the network configuration
                    net.add(new SelfOrganizingMap());

                    netKind.add(new StringBuffer(netType.getSelectedItem().toString()));
                    netName.add(new StringBuffer(newName.getText()));
                    oneNet.add(new JPanel());
                    oneNet.get(openNets).setLayout(new GridBagLayout());
                    GridBagConstraints constraints = new GridBagConstraints();
                    constraints.fill = GridBagConstraints.BOTH;

                    //creates the readOut space and formats it so that the scroll pane/text changes size with the window, reserves space for the loading bar
                    readOut.add(new JTextArea(""));
                    readOutLocale.add(new JScrollPane(readOut.get(openNets)));
                    readOut.get(openNets).setEditable(false);
                    constraints.gridx = 0;
                    constraints.gridy = 0;
                    constraints.weighty = 1.0;
                    constraints.weightx = 1.0;
                    constraints.gridwidth = 2;
                    constraints.ipady = 90;
                    oneNet.get(openNets).add(readOutLocale.get(openNets), constraints);
                    constraints.fill = GridBagConstraints.HORIZONTAL;
                    constraints.gridx = 0;
                    constraints.gridy = 1;
                    constraints.ipady = 0;
                    constraints.gridwidth = 2;
                    constraints.anchor = GridBagConstraints.PAGE_END;

                    //add everythign to the tabbed pane
                    oneNet.get(openNets).add(loadingBar.get(openNets), constraints);
                    resultsPane.addTab(netName.get(openNets).toString(), oneNet.get(openNets));
                    resultsPane.setTabComponentAt(openNets, tabPanel.get(openNets));

                    path.add("");

                    //display the starting configuration of the network
                    readOut.get(openNets).append("Network: " + netName.get(openNets) + "\n\n");
                    resultsPane.setSelectedIndex(openNets++);
                    try {
                        net.get(resultsPane.getSelectedIndex())
                                .setLatticeValue(Integer.parseInt(somLatticeField.getText().replace(",", "")));
                        net.get(resultsPane.getSelectedIndex())
                                .setDataMax(Double.parseDouble(somMaxField.getText().replace(",", "")));
                        net.get(resultsPane.getSelectedIndex())
                                .setDataMin(Double.parseDouble(somMinField.getText().replace(",", "")));
                        net.get(resultsPane.getSelectedIndex())
                                .setInputDimensions(Integer.parseInt(somDimField.getText().replace(",", "")));
                        net.get(resultsPane.getSelectedIndex()).runNet();
                        readOut.get(resultsPane.getSelectedIndex()).append("Initial Untrained Map:\n");
                        printInitMap();

                        if (!getColorMap.isVisible()) {
                            util.addSeparator();
                            util.add(getColorMap);
                            getColorMap.setVisible(true);
                        }

                        //erases all the text in the setup fields and closes the window
                        newName.setText("");
                        somLatticeField.setText("");
                        somDimField.setText("");
                        somMaxField.setText("");
                        somMinField.setText("");
                        sOMDialog.setVisible(false);

                        //unfortunately difficult way that I made to add the close button functionality to close a tab
                        //it works, but there has to be a better way to do this
                        close.get(resultsPane.getSelectedIndex()).addActionListener(new ActionListener() {
                            public void actionPerformed(final ActionEvent ae) {
                                int result;
                                result = 0;
                                for (StringBuffer names : netName) {
                                    if (ae.getActionCommand().equals(names.toString())) {
                                        result = JOptionPane.showConfirmDialog(createSOM,
                                                "<html>Exiting Without Saving can Cause you to Lose your Progress<br>Are you sure you want to Continue?</html>",
                                                "Close Network", JOptionPane.OK_CANCEL_OPTION);
                                        resultsPane.setSelectedIndex(netName.indexOf(names));
                                    }
                                }
                                if (result == JOptionPane.OK_OPTION) {
                                    net.remove(resultsPane.getSelectedIndex());
                                    oneNet.remove(resultsPane.getSelectedIndex());
                                    readOutLocale.remove(resultsPane.getSelectedIndex());
                                    readOut.remove(resultsPane.getSelectedIndex());
                                    loadingBar.remove(resultsPane.getSelectedIndex());
                                    tabPanel.remove(resultsPane.getSelectedIndex());
                                    title.remove(resultsPane.getSelectedIndex());
                                    close.remove(resultsPane.getSelectedIndex());
                                    netName.remove(resultsPane.getSelectedIndex());
                                    resultsPane.remove(resultsPane.getSelectedIndex());
                                    openNets--;
                                }
                            }
                        });
                    } catch (Exception e) {
                        net.remove(resultsPane.getSelectedIndex());
                        oneNet.remove(resultsPane.getSelectedIndex());
                        readOutLocale.remove(resultsPane.getSelectedIndex());
                        readOut.remove(resultsPane.getSelectedIndex());
                        loadingBar.remove(resultsPane.getSelectedIndex());
                        tabPanel.remove(resultsPane.getSelectedIndex());
                        title.remove(resultsPane.getSelectedIndex());
                        close.remove(resultsPane.getSelectedIndex());
                        netName.remove(resultsPane.getSelectedIndex());
                        resultsPane.remove(resultsPane.getSelectedIndex());
                        openNets--;
                        JOptionPane.showMessageDialog(sOMDialog, "Numbers too large to parse", "Parse error",
                                JOptionPane.ERROR_MESSAGE);
                    }
                } catch (OutOfMemoryError e) {
                    JOptionPane.showMessageDialog(mainWindow,
                            "<html>Net too Large for Memory.<br>Try Closing some of the Nets.</html>",
                            "Memory Error", JOptionPane.ERROR_MESSAGE);
                }
            }
        }
    });

    cancelSOM.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent ae) {
            newName.setText("");
            somLatticeField.setText("");
            somMaxField.setText("");
            somMinField.setText("");
            sOMDialog.setVisible(false);
        }
    });

    //end of SOM creation
    mainWindow.setVisible(true);
}

From source file:mobi.omegacentauri.brainflex.LicenseDialog.java

public LicenseDialog() {
    super();//from www.j a  v a 2 s.co  m
    setSize(640, 480);
    setTitle("Licenses");
    Container pane = getContentPane();
    pane.setLayout(new BoxLayout(pane, BoxLayout.Y_AXIS));
    JTextArea licenseArea = new JTextArea();
    licenseArea.setText("Copyright (c) 2014 Omega Centauri Software\n" + "includes:\n"
            + "* jSSC (Java Simple Serial Connector) - serial port communication library.\n"
            + "  Copyright (c) 2010-13 Alexey Sokolov (scream3r)\n" + "* Apache Commons Math\n"
            + "  Copyright 2001-2014 The Apache Software Foundation\n" + "\n"
            + "Overall licensing: GPL, version 3 or later\n" + "Apache Commons Math: Apache 2.0 license\n"
            + "\n" + "----------- OVERALL LICENSE -----------\n" + "\n"
            + "                    GNU GENERAL PUBLIC LICENSE\n"
            + "                       Version 3, 29 June 2007\n" + "\n"
            + " Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>\n"
            + " Everyone is permitted to copy and distribute verbatim copies\n"
            + " of this license document, but changing it is not allowed.\n" + "\n"
            + "                            Preamble\n" + "\n"
            + "  The GNU General Public License is a free, copyleft license for\n"
            + "software and other kinds of works.\n" + "\n"
            + "  The licenses for most software and other practical works are designed\n"
            + "to take away your freedom to share and change the works.  By contrast,\n"
            + "the GNU General Public License is intended to guarantee your freedom to\n"
            + "share and change all versions of a program--to make sure it remains free\n"
            + "software for all its users.  We, the Free Software Foundation, use the\n"
            + "GNU General Public License for most of our software; it applies also to\n"
            + "any other work released this way by its authors.  You can apply it to\n"
            + "your programs, too.\n" + "\n"
            + "  When we speak of free software, we are referring to freedom, not\n"
            + "price.  Our General Public Licenses are designed to make sure that you\n"
            + "have the freedom to distribute copies of free software (and charge for\n"
            + "them if you wish), that you receive source code or can get it if you\n"
            + "want it, that you can change the software or use pieces of it in new\n"
            + "free programs, and that you know you can do these things.\n" + "\n"
            + "  To protect your rights, we need to prevent others from denying you\n"
            + "these rights or asking you to surrender the rights.  Therefore, you have\n"
            + "certain responsibilities if you distribute copies of the software, or if\n"
            + "you modify it: responsibilities to respect the freedom of others.\n" + "\n"
            + "  For example, if you distribute copies of such a program, whether\n"
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            + "know their rights.\n" + "\n"
            + "  Developers that use the GNU GPL protect your rights with two steps:\n"
            + "(1) assert copyright on the software, and (2) offer you this License\n"
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            + "  For the developers\' and authors\' protection, the GPL clearly explains\n"
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            + "  Some devices are designed to deny users access to install or run\n"
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            + "\n" + "                       TERMS AND CONDITIONS\n" + "\n" + "  0. Definitions.\n" + "\n"
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            + "  The Corresponding Source for a work in source code form is that\n" + "same work.\n" + "\n"
            + "  2. Basic Permissions.\n" + "\n"
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            + "  When you convey a covered work, you waive any legal power to forbid\n"
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            + "used to limit the access or legal rights of the compilation\'s users\n"
            + "beyond what the individual works permit.  Inclusion of a covered work\n"
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            + "  You may convey a covered work in object code form under the terms\n"
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            + "  A \"User Product\" is either (1) a \"consumer product\", which means any\n"
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            + "  \"Additional permissions\" are terms that supplement the terms of this\n"
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            + "Additional permissions that are applicable to the entire Program shall\n"
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            + "  When you convey a copy of a covered work, you may at your option\n"
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            + "  You may not propagate or modify a covered work except as expressly\n"
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            + "  You are not required to accept this License in order to receive or\n"
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            + "  10. Automatic Licensing of Downstream Recipients.\n" + "\n"
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            + "  A \"contributor\" is a copyright holder who authorizes use under this\n"
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            + "  A patent license is \"discriminatory\" if it does not include within\n"
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            + "or that patent license was granted, prior to 28 March 2007.\n" + "\n"
            + "  Nothing in this License shall be construed as excluding or limiting\n"
            + "any implied license or other defenses to infringement that may\n"
            + "otherwise be available to you under applicable patent law.\n" + "\n"
            + "  12. No Surrender of Others\' Freedom.\n" + "\n"
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            + "combination as such.\n" + "\n" + "  14. Revised Versions of this License.\n" + "\n"
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            + "Foundation.  If the Program does not specify a version number of the\n"
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            + "IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\n"
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            + "EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF\n" + "SUCH DAMAGES.\n"
            + "\n" + "  17. Interpretation of Sections 15 and 16.\n" + "\n"
            + "  If the disclaimer of warranty and limitation of liability provided\n"
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            + "reviewing courts shall apply local law that most closely approximates\n"
            + "an absolute waiver of all civil liability in connection with the\n"
            + "Program, unless a warranty or assumption of liability accompanies a\n"
            + "copy of the Program in return for a fee.\n" + "\n"
            + "                     END OF TERMS AND CONDITIONS\n" + "\n"
            + "            How to Apply These Terms to Your New Programs\n" + "\n"
            + "  If you develop a new program, and you want it to be of the greatest\n"
            + "possible use to the public, the best way to achieve this is to make it\n"
            + "free software which everyone can redistribute and change under these terms.\n" + "\n"
            + "  To do so, attach the following notices to the program.  It is safest\n"
            + "to attach them to the start of each source file to most effectively\n"
            + "state the exclusion of warranty; and each file should have at least\n"
            + "the \"copyright\" line and a pointer to where the full notice is found.\n" + "\n"
            + "    <one line to give the program\'s name and a brief idea of what it does.>\n"
            + "    Copyright (C) <year>  <name of author>\n" + "\n"
            + "    This program is free software: you can redistribute it and/or modify\n"
            + "    it under the terms of the GNU General Public License as published by\n"
            + "    the Free Software Foundation, either version 3 of the License, or\n"
            + "    (at your option) any later version.\n" + "\n"
            + "    This program is distributed in the hope that it will be useful,\n"
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            + "    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n"
            + "    GNU General Public License for more details.\n" + "\n"
            + "    You should have received a copy of the GNU General Public License\n"
            + "    along with this program.  If not, see <http://www.gnu.org/licenses/>.\n" + "\n"
            + "Also add information on how to contact you by electronic and paper mail.\n" + "\n"
            + "  If the program does terminal interaction, make it output a short\n"
            + "notice like this when it starts in an interactive mode:\n" + "\n"
            + "    <program>  Copyright (C) <year>  <name of author>\n"
            + "    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n"
            + "    This is free software, and you are welcome to redistribute it\n"
            + "    under certain conditions; type `show c\' for details.\n" + "\n"
            + "The hypothetical commands `show w\' and `show c\' should show the appropriate\n"
            + "parts of the General Public License.  Of course, your program\'s commands\n"
            + "might be different; for a GUI interface, you would use an \"about box\".\n" + "\n"
            + "  You should also get your employer (if you work as a programmer) or school,\n"
            + "if any, to sign a \"copyright disclaimer\" for the program, if necessary.\n"
            + "For more information on this, and how to apply and follow the GNU GPL, see\n"
            + "<http://www.gnu.org/licenses/>.\n" + "\n"
            + "  The GNU General Public License does not permit incorporating your program\n"
            + "into proprietary programs.  If your program is a subroutine library, you\n"
            + "may consider it more useful to permit linking proprietary applications with\n"
            + "the library.  If this is what you want to do, use the GNU Lesser General\n"
            + "Public License instead of this License.  But first, please read\n"
            + "<http://www.gnu.org/philosophy/why-not-lgpl.html>.\n" + "\n"
            + "----------- MATH COMMONS LICENSE -----------\n" + "\n" + "\n"
            + "                                 Apache License\n"
            + "                           Version 2.0, January 2004\n"
            + "                        http://www.apache.org/licenses/\n" + "\n"
            + "   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n" + "\n"
            + "   1. Definitions.\n" + "\n"
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            + "      outstanding shares, or (iii) beneficial ownership of such entity.\n" + "\n"
            + "      \"You\" (or \"Your\") shall mean an individual or Legal Entity\n"
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            + "   8. Limitation of Liability. In no event and under no legal theory,\n"
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            + "   END OF TERMS AND CONDITIONS\n" + "\n"
            + "   APPENDIX: How to apply the Apache License to your work.\n" + "\n"
            + "      To apply the Apache License to your work, attach the following\n"
            + "      boilerplate notice, with the fields enclosed by brackets \"[]\"\n"
            + "      replaced with your own identifying information. (Don\'t include\n"
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            + "      same \"printed page\" as the copyright notice for easier\n"
            + "      identification within third-party archives.\n" + "\n"
            + "   Copyright [yyyy] [name of copyright owner]\n" + "\n"
            + "   Licensed under the Apache License, Version 2.0 (the \"License\");\n"
            + "   you may not use this file except in compliance with the License.\n"
            + "   You may obtain a copy of the License at\n" + "\n"
            + "       http://www.apache.org/licenses/LICENSE-2.0\n" + "\n"
            + "   Unless required by applicable law or agreed to in writing, software\n"
            + "   distributed under the License is distributed on an \"AS IS\" BASIS,\n"
            + "   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"
            + "   See the License for the specific language governing permissions and\n"
            + "   limitations under the License.\n" + "\n" + "\n" + "APACHE COMMONS MATH DERIVATIVE WORKS: \n"
            + "\n" + "The Apache commons-math library includes a number of subcomponents\n"
            + "whose implementation is derived from original sources written\n"
            + "in C or Fortran.  License terms of the original sources\n" + "are reproduced below.\n" + "\n"
            + "===============================================================================\n"
            + "For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in\n"
            + "the LevenbergMarquardtOptimizer class in package\n"
            + "org.apache.commons.math3.optimization.general \n"
            + "Original source copyright and license statement:\n" + "\n"
            + "Minpack Copyright Notice (1999) University of Chicago.  All rights reserved\n" + "\n"
            + "Redistribution and use in source and binary forms, with or\n"
            + "without modification, are permitted provided that the\n" + "following conditions are met:\n"
            + "\n" + "1. Redistributions of source code must retain the above\n"
            + "copyright notice, this list of conditions and the following\n" + "disclaimer.\n" + "\n"
            + "2. Redistributions in binary form must reproduce the above\n"
            + "copyright notice, this list of conditions and the following\n"
            + "disclaimer in the documentation and/or other materials\n" + "provided with the distribution.\n"
            + "\n" + "3. The end-user documentation included with the\n"
            + "redistribution, if any, must include the following\n" + "acknowledgment:\n" + "\n"
            + "   \"This product includes software developed by the\n"
            + "   University of Chicago, as Operator of Argonne National\n" + "   Laboratory.\n" + "\n"
            + "Alternately, this acknowledgment may appear in the software\n"
            + "itself, if and wherever such third-party acknowledgments\n" + "normally appear.\n" + "\n"
            + "4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED \"AS IS\"\n"
            + "WITHOUT WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE\n"
            + "UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND\n"
            + "THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR\n"
            + "IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES\n"
            + "OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE\n"
            + "OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY\n"
            + "OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR\n"
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            + "DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION\n"
            + "UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL\n" + "BE CORRECTED.\n" + "\n"
            + "5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT\n"
            + "HOLDER, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF\n"
            + "ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,\n"
            + "INCIDENTAL, CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF\n"
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            + "PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, WHETHER\n"
            + "SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT\n"
            + "(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,\n"
            + "EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE\n" + "POSSIBILITY OF SUCH LOSS OR DAMAGES.\n"
            + "===============================================================================\n" + "\n"
            + "Copyright and license statement for the odex Fortran routine developed by\n"
            + "E. Hairer and G. Wanner and translated in GraggBulirschStoerIntegrator class\n"
            + "in package org.apache.commons.math3.ode.nonstiff:\n" + "\n" + "\n"
            + "Copyright (c) 2004, Ernst Hairer\n" + "\n"
            + "Redistribution and use in source and binary forms, with or without \n"
            + "modification, are permitted provided that the following conditions are \n" + "met:\n" + "\n"
            + "- Redistributions of source code must retain the above copyright \n"
            + "notice, this list of conditions and the following disclaimer.\n" + "\n"
            + "- Redistributions in binary form must reproduce the above copyright \n"
            + "notice, this list of conditions and the following disclaimer in the \n"
            + "documentation and/or other materials provided with the distribution.\n" + "\n"
            + "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS \n"
            + "IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED \n"
            + "TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A \n"
            + "PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR \n"
            + "CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, \n"
            + "EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, \n"
            + "PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR \n"
            + "PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF \n"
            + "LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING \n"
            + "NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS \n"
            + "SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n"
            + "===============================================================================\n" + "\n"
            + "Copyright and license statement for the original lapack fortran routines\n"
            + "translated in EigenDecompositionImpl class in package\n" + "org.apache.commons.math3.linear:\n"
            + "\n" + "Copyright (c) 1992-2008 The University of Tennessee.  All rights reserved.\n" + "\n"
            + "$COPYRIGHT$\n" + "\n" + "Additional copyrights may follow\n" + "\n" + "$HEADER$\n" + "\n"
            + "Redistribution and use in source and binary forms, with or without\n"
            + "modification, are permitted provided that the following conditions are\n" + "met:\n" + "\n"
            + "- Redistributions of source code must retain the above copyright\n"
            + "  notice, this list of conditions and the following disclaimer. \n" + "  \n"
            + "- Redistributions in binary form must reproduce the above copyright\n"
            + "  notice, this list of conditions and the following disclaimer listed\n"
            + "  in this license in the documentation and/or other materials\n"
            + "  provided with the distribution.\n" + "  \n"
            + "- Neither the name of the copyright holders nor the names of its\n"
            + "  contributors may be used to endorse or promote products derived from\n"
            + "  this software without specific prior written permission.\n" + "  \n"
            + "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS\n"
            + "\"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT  \n"
            + "LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR\n"
            + "A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT \n"
            + "OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n"
            + "SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n"
            + "LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,\n"
            + "DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY\n"
            + "THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT  \n"
            + "(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\n"
            + "OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \n"
            + "===============================================================================\n" + "\n"
            + "Copyright and license statement for the original Mersenne twister C\n"
            + "routines translated in MersenneTwister class in package \n"
            + "org.apache.commons.math3.random:\n" + "\n"
            + "   Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,\n"
            + "   All rights reserved.                          \n" + "\n"
            + "   Redistribution and use in source and binary forms, with or without\n"
            + "   modification, are permitted provided that the following conditions\n" + "   are met:\n" + "\n"
            + "     1. Redistributions of source code must retain the above copyright\n"
            + "        notice, this list of conditions and the following disclaimer.\n" + "\n"
            + "     2. Redistributions in binary form must reproduce the above copyright\n"
            + "        notice, this list of conditions and the following disclaimer in the\n"
            + "        documentation and/or other materials provided with the distribution.\n" + "\n"
            + "     3. The names of its contributors may not be used to endorse or promote \n"
            + "        products derived from this software without specific prior written \n"
            + "        permission.\n" + "\n"
            + "   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS\n"
            + "   \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT\n"
            + "   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR\n"
            + "   A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR\n"
            + "   CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,\n"
            + "   EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,\n"
            + "   PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR\n"
            + "   PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF\n"
            + "   LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING\n"
            + "   NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\n"
            + "   SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n" + "\n"
            + "===============================================================================\n" + "\n"
            + "The class \"org.apache.commons.math3.exception.util.LocalizedFormatsTest\" is\n"
            + "an adapted version of \"OrekitMessagesTest\" test class for the Orekit library\n"
            + "The \"org.apache.commons.math3.analysis.interpolation.HermiteInterpolator\"\n"
            + "has been imported from the Orekit space flight dynamics library.\n" + "\n"
            + "Th Orekit library is described at:\n" + "  https://www.orekit.org/forge/projects/orekit\n"
            + "The original files are distributed under the terms of the Apache 2 license\n"
            + "which is: Copyright 2010 CS Communication & Systmes\n" + "\n"
            + "===============================================================================\n" + "\n"
            + "The initial code for shuffling an array (originally in class\n"
            + "\"org.apache.commons.math3.random.RandomDataGenerator\", now replaced by\n"
            + "a method in class \"org.apache.commons.math3.util.MathArrays\") was\n"
            + "inspired from the algorithm description provided in\n"
            + "\"Algorithms\", by Ian Craw and John Pulham (University of Aberdeen 1999).\n"
            + "The textbook (containing a proof that the shuffle is uniformly random) is\n"
            + "available here:\n"
            + "  http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf\n" + "\n"
            + "===============================================================================\n"
            + "License statement for the direction numbers in the resource files for Sobol sequences.\n" + "\n"
            + "-----------------------------------------------------------------------------\n"
            + "Licence pertaining to sobol.cc and the accompanying sets of direction numbers\n" + "\n"
            + "-----------------------------------------------------------------------------\n"
            + "Copyright (c) 2008, Frances Y. Kuo and Stephen Joe\n" + "All rights reserved.\n" + "\n"
            + "Redistribution and use in source and binary forms, with or without\n"
            + "modification, are permitted provided that the following conditions are met:\n" + "\n"
            + "    * Redistributions of source code must retain the above copyright\n"
            + "      notice, this list of conditions and the following disclaimer.\n" + "\n"
            + "    * Redistributions in binary form must reproduce the above copyright\n"
            + "      notice, this list of conditions and the following disclaimer in the\n"
            + "      documentation and/or other materials provided with the distribution.\n" + "\n"
            + "    * Neither the names of the copyright holders nor the names of the\n"
            + "      University of New South Wales and the University of Waikato\n"
            + "      and its contributors may be used to endorse or promote products derived\n"
            + "      from this software without specific prior written permission.\n" + "\n"
            + "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS\'\' AND ANY\n"
            + "EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\n"
            + "WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n"
            + "DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY\n"
            + "DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\n"
            + "(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;\n"
            + "LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n"
            + "ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n"
            + "(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\n"
            + "SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n"
            + "===============================================================================\n" + "\n"
            + "The initial commit of package \"org.apache.commons.math3.ml.neuralnet\" is\n"
            + "an adapted version of code developed in the context of the Data Processing\n"
            + "and Analysis Consortium (DPAC) of the \"Gaia\" project of the European Space\n"
            + "Agency (ESA).\n"
            + "===============================================================================\n");
    licenseArea.setEditable(false);
    licenseArea.setCaretPosition(0);
    JScrollPane license = new JScrollPane(licenseArea);
    pane.add(license);
    JButton ok = new JButton("OK");
    ok.setAlignmentX(Component.CENTER_ALIGNMENT);
    ok.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent arg0) {
            dispose();
        }
    });
    pane.add(ok);
}

From source file:nz.co.fortytwo.freeboard.installer.InstalManager.java

private void addWidgets() {

    JTabbedPane tabPane = new JTabbedPane();
    this.add(tabPane, BorderLayout.CENTER);
    // upload to arduinos
    JPanel uploadPanel = new JPanel();
    uploadPanel.setLayout(new BorderLayout());
    uploadPanel.add(uploadingPanel, BorderLayout.CENTER);
    final JPanel westUploadPanel = new JPanel(new MigLayout());

    String info = "\nUse this panel to upload compiled code to the arduino devices.\n\n"
            + "NOTE: directories with spaces will probably not work!\n\n"
            + "First select the base directory of your Arduino IDE installation, eg C:/devtools/arduino-1.5.2\n\n"
            + "Then select target files to upload, these are ended in '.hex'\n"
            + "\nand can be downloaded from github (https://github.com/rob42),\n"
            + " see the 'Release*' sub-directories\n\n"
            + "Output of the process will display in the right-side window\n\n";
    JTextArea jTextInfo = new JTextArea(info);
    jTextInfo.setEditable(false);
    westUploadPanel.add(jTextInfo, "span,wrap");

    westUploadPanel.add(new JLabel("Select Arduino IDE directory:"), "wrap");
    arduinoDirTextField.setEditable(false);
    westUploadPanel.add(arduinoDirTextField, "span 2");
    arduinoIdeChooser.setApproveButtonText("Select");
    arduinoIdeChooser.setAcceptAllFileFilterUsed(false);
    arduinoIdeChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
    arduinoIdeChooser.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent evt) {
            if (JFileChooser.APPROVE_SELECTION.equals(evt.getActionCommand())) {

                toolsDir = new File(arduinoIdeChooser.getSelectedFile(),
                        File.separator + "hardware" + File.separator + "tools" + File.separator);
                if (!toolsDir.exists()) {
                    toolsDir = null;/*w w  w.  ja  v a 2s. c  o m*/
                    JOptionPane.showMessageDialog(westUploadPanel, "Not a valid Arduino IDE directory");
                    return;
                }
                arduinoDirTextField.setText(arduinoIdeChooser.getSelectedFile().getAbsolutePath());
            }
        }
    });
    JButton arduinoDirButton = new JButton("Select");
    arduinoDirButton.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            arduinoIdeChooser.showDialog(westUploadPanel, "Select");

        }
    });
    westUploadPanel.add(arduinoDirButton, "wrap");

    westUploadPanel.add(new JLabel("Select comm port:"));
    westUploadPanel.add(portComboBox, "wrap");

    westUploadPanel.add(new JLabel("Select device:"), "gap unrelated");
    westUploadPanel.add(deviceComboBox, "wrap");

    hexFileChooser.setApproveButtonText("Upload");
    hexFileChooser.setAcceptAllFileFilterUsed(false);
    hexFileChooser.addChoosableFileFilter(new FileFilter() {
        @Override
        public String getDescription() {
            return "*.hex - Hex file";
        }

        @Override
        public boolean accept(File f) {
            if (f.isDirectory()) {
                return true;
            }
            if (f.getName().toUpperCase().endsWith(".HEX")) {
                return true;
            }
            return false;
        }
    });
    westUploadPanel.add(hexFileChooser, "span, wrap");

    uploadPanel.add(westUploadPanel, BorderLayout.WEST);
    tabPane.addTab("Upload", uploadPanel);

    // charts
    JPanel chartPanel = new JPanel();
    chartPanel.setLayout(new BorderLayout());
    FileNameExtensionFilter filter = new FileNameExtensionFilter("Charts", "tiff", "kap", "KAP", "TIFF", "tif",
            "TIF");
    chartFileChooser.setFileFilter(filter);
    chartFileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
    chartFileChooser.setMultiSelectionEnabled(true);
    final JPanel chartWestPanel = new JPanel(new MigLayout());
    String info2 = "\nUse this panel to convert charts into the correct format for FreeBoard.\n"
            + "\nYou need to select the charts or directories containing charts, then click 'Process'.\n "
            + "\nThe results will be in a directory with the same name as the chart, and the chart "
            + "\ndirectory will also be compressed into a zip file ready to transfer to your FreeBoard "
            + "\nserver\n" + "\nOutput of the process will display in the right-side window\n\n";
    JTextArea jTextInfo2 = new JTextArea(info2);
    jTextInfo2.setEditable(false);
    chartWestPanel.add(jTextInfo2, "wrap");

    chartFileChooser.setApproveButtonText("Process");
    chartWestPanel.add(chartFileChooser, "span,wrap");

    final JPanel loggingPanel = new JPanel(new MigLayout());
    loggingGroup.add(infoButton);
    loggingGroup.add(debugButton);
    debugButton.setSelected(logger.isDebugEnabled());
    infoButton.setSelected(!logger.isDebugEnabled());
    infoButton.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            if (infoButton.isSelected()) {
                LogManager.getRootLogger().setLevel(Level.INFO);
            }
        }
    });
    debugButton.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            if (debugButton.isSelected()) {
                LogManager.getRootLogger().setLevel(Level.DEBUG);
            }
        }
    });

    loggingPanel.add(new JLabel("Logging Level"));
    loggingPanel.add(infoButton);
    loggingPanel.add(debugButton);
    chartWestPanel.add(loggingPanel, "span,wrap");

    final JPanel transparentPanel = new JPanel(new MigLayout());
    charsetGroup.add(utf8Button);
    charsetGroup.add(iso8859Button);
    iso8859Button.setSelected(logger.isDebugEnabled());
    utf8Button.setSelected(!logger.isDebugEnabled());
    utf8Button.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            if (utf8Button.isSelected()) {
                charset = "UTF-8";
            }
        }
    });
    iso8859Button.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            if (iso8859Button.isSelected()) {
                charset = "ISO-8859-1";
            }
        }
    });

    transparentPanel.add(new JLabel("KAP Character set:"));
    transparentPanel.add(utf8Button);
    transparentPanel.add(iso8859Button);
    chartWestPanel.add(transparentPanel);

    chartPanel.add(chartWestPanel, BorderLayout.WEST);
    chartPanel.add(processingPanel, BorderLayout.CENTER);
    tabPane.addTab("Charts", chartPanel);

    // IMU calibration
    JPanel calPanel = new JPanel();
    calPanel.setLayout(new BorderLayout());
    JPanel westCalPanel = new JPanel(new MigLayout());
    String info3 = "\nUse this panel to calibrate your ArduIMU.\n"
            + "\nYou should do this as near to the final location as possible,\n"
            + "and like all compasses, as far from wires and magnetic materials \n" + "as possible.\n"
            + "\nSelect your comm port, then click 'Start'.\n "
            + "\nSmoothly and steadily rotate the ArduIMU around all 3 axes (x,y,z)\n"
            + "several times. Then press stop and the calibration will be performed and\n"
            + "uploaded to the ArduIMU\n\n" + "Output of the process will display in the right-side window\n\n";
    JTextArea jTextInfo3 = new JTextArea(info3);
    jTextInfo3.setEditable(false);
    westCalPanel.add(jTextInfo3, "span, wrap");
    westCalPanel.add(new JLabel("Select comm port:"));

    westCalPanel.add(portComboBox1, "wrap");
    JButton startCal = new JButton("Start");
    startCal.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            calibrationPanel.process((String) portComboBox.getSelectedItem());
        }
    });
    westCalPanel.add(startCal);
    JButton stopCal = new JButton("Stop");
    stopCal.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
            calibrationPanel.stopProcess();
        }
    });
    westCalPanel.add(stopCal);

    calPanel.add(westCalPanel, BorderLayout.WEST);
    calPanel.add(calibrationPanel, BorderLayout.CENTER);

    tabPane.addTab("Calibration", calPanel);

}

From source file:org.apache.jackrabbit.oak.explorer.Explorer.java

private void createAndShowGUI(final File path, boolean skipSizeCheck) throws IOException {
    JTextArea log = new JTextArea(5, 20);
    log.setMargin(new Insets(5, 5, 5, 5));
    log.setLineWrap(true);/*from w w  w.jav a 2  s .  c  o  m*/
    log.setEditable(false);

    final NodeStoreTree treePanel = new NodeStoreTree(backend, log, skipSizeCheck);

    final JFrame frame = new JFrame("Explore " + path + " @head");
    frame.addWindowListener(new java.awt.event.WindowAdapter() {
        @Override
        public void windowClosing(java.awt.event.WindowEvent windowEvent) {
            IOUtils.closeQuietly(treePanel);
            System.exit(0);
        }
    });

    JPanel content = new JPanel(new GridBagLayout());

    GridBagConstraints c = new GridBagConstraints();
    c.fill = GridBagConstraints.BOTH;
    c.weightx = 1;
    c.weighty = 1;

    JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, new JScrollPane(treePanel),
            new JScrollPane(log));
    splitPane.setDividerLocation(0.3);
    content.add(new JScrollPane(splitPane), c);
    frame.getContentPane().add(content);

    JMenuBar menuBar = new JMenuBar();
    menuBar.setMargin(new Insets(2, 2, 2, 2));

    JMenuItem menuReopen = new JMenuItem("Reopen");
    menuReopen.setMnemonic(KeyEvent.VK_R);
    menuReopen.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            try {
                treePanel.reopen();
            } catch (IOException e) {
                throw new RuntimeException(e);
            }
        }
    });

    JMenuItem menuCompaction = new JMenuItem("Time Machine");
    menuCompaction.setMnemonic(KeyEvent.VK_T);
    menuCompaction.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            List<String> revs = backend.readRevisions();
            String s = (String) JOptionPane.showInputDialog(frame, "Revert to a specified revision",
                    "Time Machine", JOptionPane.PLAIN_MESSAGE, null, revs.toArray(), revs.get(0));
            if (s != null && treePanel.revert(s)) {
                frame.setTitle("Explore " + path + " @" + s);
            }
        }
    });

    JMenuItem menuRefs = new JMenuItem("Tar File Info");
    menuRefs.setMnemonic(KeyEvent.VK_I);
    menuRefs.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            List<String> tarFiles = new ArrayList<String>();
            for (File f : path.listFiles()) {
                if (f.getName().endsWith(".tar")) {
                    tarFiles.add(f.getName());
                }
            }

            String s = (String) JOptionPane.showInputDialog(frame, "Choose a tar file", "Tar File Info",
                    JOptionPane.PLAIN_MESSAGE, null, tarFiles.toArray(), tarFiles.get(0));
            if (s != null) {
                treePanel.printTarInfo(s);
            }
        }
    });

    JMenuItem menuSCR = new JMenuItem("Segment Refs");
    menuSCR.setMnemonic(KeyEvent.VK_R);
    menuSCR.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            String s = JOptionPane.showInputDialog(frame, "Segment References\nUsage: <segmentId>",
                    "Segment References", JOptionPane.PLAIN_MESSAGE);
            if (s != null) {
                treePanel.printSegmentReferences(s);
            }
        }
    });

    JMenuItem menuDiff = new JMenuItem("SegmentNodeState diff");
    menuDiff.setMnemonic(KeyEvent.VK_D);
    menuDiff.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            String s = JOptionPane.showInputDialog(frame,
                    "SegmentNodeState diff\nUsage: <recordId> <recordId> [<path>]", "SegmentNodeState diff",
                    JOptionPane.PLAIN_MESSAGE);
            if (s != null) {
                treePanel.printDiff(s);
            }
        }
    });

    JMenuItem menuPCM = new JMenuItem("Persisted Compaction Maps");
    menuPCM.setMnemonic(KeyEvent.VK_P);
    menuPCM.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ev) {
            treePanel.printPCMInfo();
        }
    });

    menuBar.add(menuReopen);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));
    menuBar.add(menuCompaction);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));
    menuBar.add(menuRefs);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));
    menuBar.add(menuSCR);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));
    menuBar.add(menuDiff);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));
    menuBar.add(menuPCM);
    menuBar.add(new JSeparator(JSeparator.VERTICAL));

    frame.setJMenuBar(menuBar);
    frame.pack();
    frame.setSize(960, 720);
    frame.setLocationRelativeTo(null);
    frame.setVisible(true);

}

From source file:org.broad.igv.hic.MainWindow.java

private void getEigenvectorActionPerformed(ActionEvent e) {
    double[] rv;/*www  . j a v  a  2 s  .  c o m*/
    try {
        String number = JOptionPane.showInputDialog("Which eigenvector do you want to see?");
        int num = Integer.parseInt(number) - 1;

        rv = hic.getEigenvector(num);

        if (rv != null) {
            String str = "";
            for (int i = 0; i < rv.length; i++) {
                str += rv[i] + "\n";

            }
            JTextArea textArea = new JTextArea(str, 20, 20);
            textArea.setEditable(false);
            textArea.selectAll();
            JScrollPane pane = new JScrollPane(textArea);
            JFrame frame = new JFrame("Principal Eigenvector");
            frame.getContentPane().add(pane);
            frame.pack();
            frame.setVisible(true);

        } else {
            System.err.println("No densities available for this file.");
        }

    } catch (InvalidMatrixException error) {
        JOptionPane.showMessageDialog(this, "Unable to calculate eigenvectors after 30 iterations",
                "Eigenvector error", JOptionPane.ERROR_MESSAGE);
    } catch (NumberFormatException error) {
        JOptionPane.showMessageDialog(this, "You must enter a valid number.\n" + error.getMessage(),
                "Eigenvector error", JOptionPane.ERROR_MESSAGE);
    }

}

From source file:org.broad.igv.track.TrackMenuUtils.java

public static JMenuItem getRemoveMenuItem(final Collection<Track> selectedTracks) {

    boolean multiple = selectedTracks.size() > 1;

    JMenuItem item = new JMenuItem("Remove Track" + (multiple ? "s" : ""));
    item.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent evt) {
            if (selectedTracks.isEmpty()) {
                return;
            }//from www . jav  a 2  s  . c om

            StringBuffer buffer = new StringBuffer();
            for (Track track : selectedTracks) {
                buffer.append("\n\t");
                buffer.append(track.getName());
            }
            String deleteItems = buffer.toString();

            JTextArea textArea = new JTextArea();
            textArea.setEditable(false);
            JScrollPane scrollPane = new JScrollPane(textArea);
            textArea.setText(deleteItems);

            JOptionPane optionPane = new JOptionPane(scrollPane, JOptionPane.PLAIN_MESSAGE,
                    JOptionPane.YES_NO_OPTION);
            optionPane.setPreferredSize(new Dimension(550, 500));
            JDialog dialog = optionPane.createDialog(IGV.getMainFrame(), "Remove The Following Tracks");
            dialog.setVisible(true);

            Object choice = optionPane.getValue();
            if ((choice == null) || (JOptionPane.YES_OPTION != ((Integer) choice).intValue())) {
                return;
            }

            IGV.getInstance().removeTracks(selectedTracks);
            IGV.getInstance().doRefresh();
        }
    });
    return item;
}

From source file:org.colombbus.tangara.update.SoftwareUpdateDialog.java

private void addCenterPane() {
    JPanel centerPane = new JPanel();
    BoxLayout layout = new BoxLayout(centerPane, BoxLayout.Y_AXIS);
    centerPane.setLayout(layout);// w  ww.  ja  v  a 2 s  .co m

    JTextArea descPane = new JTextArea(info.getDescription());
    descPane.setFont(font);
    descPane.setEditable(false);
    centerPane.add(descPane);

    JPanel linkPanel = new JPanel();
    linkPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
    String linkTitle = bundle.getString("SoftwareUpdateDialog.linkTitle"); //$NON-NLS-1$
    JLabel linkTitleLabel = new JLabel(linkTitle);
    linkTitleLabel.setFont(font);
    linkPanel.add(linkTitleLabel);
    HyperLinkLabel linkLabel = new HyperLinkLabel(info.getLink(), info.getLink());
    linkLabel.setFont(font);
    linkPanel.add(linkLabel);
    linkPanel.setBackground(Color.white);
    linkPanel.setOpaque(true);
    centerPane.add(linkPanel);
    add(centerPane, BorderLayout.CENTER);
}

From source file:org.executequery.gui.editor.LobDataItemViewerPanel.java

private JTextArea createTextArea() {

    JTextArea textArea = new JTextArea();
    textArea.setEditable(false);
    textArea.setLineWrap(true);/*from   www  . j a va  2s  . c o  m*/
    textArea.setWrapStyleWord(true);
    textArea.setFont(new Font("monospaced", Font.PLAIN, 11));

    return textArea;
}

From source file:org.formic.wizard.step.gui.TemplateStep.java

/**
 * {@inheritDoc}/*  ww w . j  av a 2s . c om*/
 * @see org.formic.wizard.step.GuiStep#init()
 */
public Component init() {
    JPanel panel = new JPanel();
    panel.setLayout(new BorderLayout());

    if (html != null) {
        JEditorPane editor = new JEditorPane("text/html", StringUtils.EMPTY);
        editor.setEditable(false);
        editor.setOpaque(false);
        editor.addHyperlinkListener(new HyperlinkListener());
        editor.setBorder(null);
        editor.setFocusable(false);
        content = editor;
    } else {
        JTextArea area = new JTextArea();
        area.setEditable(false);
        content = area;
    }
    JScrollPane scroll = new JScrollPane(content);
    scroll.setBorder(null);
    panel.add(scroll, BorderLayout.CENTER);

    return panel;
}

From source file:org.genedb.jogra.plugins.TermRationaliser.java

private Box createRationaliserPanel(final String name, final RationaliserJList rjlist) {

    int preferredHeight = 500; //change accordingly
    int preferredWidth = 500;

    Toolkit tk = Toolkit.getDefaultToolkit();
    Dimension size = tk.getScreenSize();
    int textboxHeight = 10; //change accordingly
    int textboxWidth = size.width;

    Box box = Box.createVerticalBox();
    box.add(new JLabel(name));

    JTextField searchField = new JTextField(20); //Search field on top
    /* We don't want this textfield's height to expand when
     * the Rationaliser is dragged to exapnd. So we set it's
     * height to what we want and the width to the width of
     * the screen  /*from  ww w.j  av a 2s  .  c  om*/
     */
    searchField.setMaximumSize(new Dimension(textboxWidth, textboxHeight));
    rjlist.installJTextField(searchField);
    box.add(searchField);

    JScrollPane scrollPane = new JScrollPane(); //scroll pane
    scrollPane.setViewportView(rjlist);
    scrollPane.setPreferredSize(new Dimension(preferredWidth, preferredHeight));
    box.add(scrollPane);

    TitledBorder sysidBorder = BorderFactory.createTitledBorder("Systematic IDs"); //systematic ID box
    sysidBorder.setTitleColor(Color.DARK_GRAY);

    final JTextArea idField = new JTextArea(1, 1);
    idField.setMaximumSize(new Dimension(textboxWidth, textboxHeight));
    idField.setEditable(false);
    idField.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
    idField.setForeground(Color.DARK_GRAY);
    JScrollPane scroll = new JScrollPane(idField);
    scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);

    Box sysidBox = Box.createVerticalBox();
    sysidBox.add(scroll /*idField*/);
    sysidBox.setBorder(sysidBorder);
    box.add(sysidBox);

    rjlist.addListSelectionListener(new ListSelectionListener() {
        @Override
        public void valueChanged(ListSelectionEvent e) {
            Term highlightedTerm = (Term) rjlist.getSelectedValue();
            if (highlightedTerm != null) {
                /* For each list, call the relevant methods
                 * to get the systematic IDs. Then for the
                 * right list, add the term name in the
                 * text box below
                 */
                if (name.equals(FROM_LIST_NAME)) {
                    idField.setText(StringUtils.collectionToCommaDelimitedString(
                            termService.getSystematicIDs(highlightedTerm, selectedTaxons)));
                } else if (name.equals(TO_LIST_NAME)) {
                    idField.setText(StringUtils.collectionToCommaDelimitedString(
                            termService.getSystematicIDs(highlightedTerm, null)));
                    /* We allow the user to edit the term name */
                    textField.setText(highlightedTerm.getName());
                }

            }
        }
    });

    return box;

}