Example usage for java.io File listRoots

List of usage examples for java.io File listRoots

Introduction

In this page you can find the example usage for java.io File listRoots.

Prototype

public static File[] listRoots() 

Source Link

Document

List the available filesystem roots.

Usage

From source file:org.pentaho.vfs.ui.VfsFileChooserDialog.java

public void updateParentFileCombo(FileObject selectedItem) {
    try {//  w ww .j  a  v  a  2 s.  c o  m
        List<FileObject> parentChain = new ArrayList<FileObject>();
        // are we a directory?
        try {
            if (selectedItem.getType() == FileType.FOLDER && selectedItem.getType().hasChildren()) {
                // we have real children....
                parentChain.add(selectedItem);
            }
        } catch (Exception e) {
            // we are not a folder
        }
        FileObject parentFileObject;
        parentFileObject = selectedItem.getParent();
        while (parentFileObject != null) {
            parentChain.add(parentFileObject);
            parentFileObject = parentFileObject.getParent();
        }

        File roots[] = File.listRoots();
        if (currentPanel != null) {
            for (int i = 0; i < roots.length; i++) {
                parentChain.add(currentPanel.resolveFile(roots[i].getAbsolutePath()));
            }
        }

        String items[] = new String[parentChain.size()];
        int idx = 0;
        for (int i = parentChain.size() - 1; i >= 0; i--) {
            items[idx++] = ((FileObject) parentChain.get(i)).getName().getURI();
        }

        openFileCombo.setItems(items);
        openFileCombo.select(items.length - 1);
    } catch (Exception e) {
        e.printStackTrace();
        // then let's not update the GUI
    }
}

From source file:gtu._work.etc._3DSMovieRenamer.java

static void reload3DSDir() {
    File tmp = null;/*from www . j  a  v  a  2s  .com*/
    for (File f : File.listRoots()) {
        if ((tmp = new File(f, "DCIM")).exists()) {
            load3DSDir = tmp;
            break;
        }
    }
}

From source file:org.dbgl.util.FileUtils.java

public static boolean isStoredOnFloppyDrive(File file) {
    if (PlatformUtils.IS_OSX)
        return false; // FileSystemView doesn't work on OSX and leads to freeze on application exit

    FileSystemView fsv = FileSystemView.getFileSystemView();
    for (File f : File.listRoots()) {
        if (areRelated(f, file)) {
            return fsv.isFloppyDrive(f);
        }/*from   w w w  . j  a v a  2  s  .  c  om*/
    }
    return false;
}

From source file:org.dbgl.util.FileUtils.java

public static boolean isStoredOnCDRomDrive(File file) {
    if (PlatformUtils.IS_OSX)
        return false; // FileSystemView doesn't work on OSX and leads to freeze on application exit

    FileSystemView fsv = FileSystemView.getFileSystemView();
    for (File f : File.listRoots()) {
        if (areRelated(f, file)) {
            return fsv.isDrive(f) && fsv.getSystemTypeDescription(f).toUpperCase().contains("CD");
        }//  w ww .j  a  v a  2s .  c om
    }
    return false;
}

From source file:au.org.ala.delta.util.Utils.java

/**
 * Return a file object for the file at the supplied path (may be a relative
 * path)//from   w w w  . ja  v  a2  s  .co m
 * 
 * @param filePath
 *            the path of the file - may be a relative path
 * @param defaultDirectory
 *            the default parent directory - this directory will be used as
 *            the parent directory if the filePath is not absolute
 * @return
 */
public static File createFileFromPath(String filePath, File defaultDirectory) {
    File file = null;
    // If the supplied file path starts with one of the file system
    // roots, then it is absolute. Otherwise, assume that
    // it is relative to the directory in which the dataset is located.
    filePath = FilenameUtils.separatorsToSystem(filePath);
    boolean fileAbsolute = false;
    for (File root : File.listRoots()) {
        if (filePath.toLowerCase().startsWith(root.getAbsolutePath().toLowerCase())) {
            fileAbsolute = true;
            break;
        }
    }

    if (fileAbsolute) {
        file = new File(filePath);
    } else {
        file = new File(defaultDirectory, filePath);
    }

    return file;
}

From source file:base.BasePlayer.Main.java

public Main() {

    super(new GridBagLayout());
    try {//ww  w .  ja v  a2  s . c o  m

        //UIManager.put("PopupMenu.border", BorderFactory.createMatteBorder(0, 20, 0, 0, new Color(230,230,230)));
        //URL fontUrl = new URL("http://www.webpagepublicity.com/" +
        //       "free-fonts/a/Airacobra%20Condensed.ttf");
        //      URL fontUrl = new URL("C:/HY-Data/RKATAINE/WinPython-64bit-3.5.3.1Qt5/python-3.5.3.amd64/share/numdifftools/docs/_build/html/_static/fonts/Inconsolata-Regular.ttf");
        //   URL fonturl = this.getClass().getResource("OpenSans-Regular.ttf");
        //   menuFont = Font.createFont(Font.TRUETYPE_FONT, new File(fonturl.getFile()));
        //   C:\HY-Data\RKATAINE\WinPython-64bit-3.5.3.1Qt5\python-3.5.3.amd64\Lib\site-packages\reportlab\fonts
        Launcher.fromMain = true;
        Launcher.main(args);
        VariantHandler.main(argsit);
        glass = Toolkit.getDefaultToolkit().getImage(getClass().getResource("icons/glass.jpg"));
        ToolTipManager.sharedInstance().setInitialDelay(100);
        // ToolTipManager.sharedInstance().setDismissDelay(2000);
        UIManager.put("ToolTip.background", new Color(255, 255, 214));
        UIManager.put("ToolTip.border", BorderFactory.createCompoundBorder(
                UIManager.getBorder("ToolTip.border"), BorderFactory.createEmptyBorder(4, 4, 4, 4)));
        lineseparator = System.getProperty("line.separator");

        proxysettings = new ProxySettings();
        panel = new JPanel(new GridBagLayout());
        //menuFont = menuFont.deriveFont(Font.PLAIN,12);
        Draw.defaultFont = menuFont;

        gd = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice();
        width = gd.getDisplayMode().getWidth();
        height = gd.getDisplayMode().getHeight();
        if (Launcher.fontSize.equals("")) {
            if (width < 1500) {
                defaultFontSize = 11;

                buttonHeight = Main.defaultFontSize * 2;
                buttonWidth = Main.defaultFontSize * 6;

            } else if (width < 2000) {
                defaultFontSize = 12;

                buttonHeight = Main.defaultFontSize * 2 + 4;
                buttonWidth = Main.defaultFontSize * 6 + 4;

            } else if (width < 3000) {
                defaultFontSize = 15;
                buttonHeight = Main.defaultFontSize * 2 + 4;
                buttonWidth = Main.defaultFontSize * 6 + 4;
            } else {
                defaultFontSize = 19;
                buttonHeight = Main.defaultFontSize * 2 + 4;
                buttonWidth = Main.defaultFontSize * 6 + 4;
            }
        } else {
            try {
                defaultFontSize = Integer.parseInt(Launcher.fontSize);
            } catch (Exception e) {
                defaultFontSize = 12;
            }
        }

        menuFont = new Font("SansSerif", Font.PLAIN, Main.defaultFontSize);
        menuFontBold = new Font("SansSerif", Font.BOLD, Main.defaultFontSize);
        //   menuFont = new Font("SansSerif", Font.BOLD, Main.defaultFontSize);
    } catch (Exception e) {
        e.printStackTrace();
    }
    FileSystemView fsv = FileSystemView.getFileSystemView();
    File[] paths = File.listRoots();

    for (File path : paths) {
        if (fsv.getSystemDisplayName(path).contains("merit")) {
            pleiades = true;
        }
    }

    screenSize = new Dimension(width, height);

    drawHeight = (int) (screenSize.getHeight() * 0.6);
    sidebarWidth = (int) (screenSize.getWidth() * 0.1);
    drawWidth = (int) (screenSize.getWidth() - sidebarWidth);
    thisMainListener = this;
    try {
        htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.ERROR);
        /*   for(int i=0;i<snow.length; i++) {
              snow[i][0] = (height*Math.random());
              snow[i][1] = (4*Math.random() +1);
              snow[i][2] = (12*Math.random() -6);
              snow[i][3] = (2*Math.random() +1);
           }*/
        frame.addWindowListener(new java.awt.event.WindowAdapter() {
            @Override
            public void windowClosing(java.awt.event.WindowEvent windowEvent) {
                /*if (JOptionPane.showConfirmDialog(frame, "Are you sure to close this window?", "Really Closing?", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION){
                    System.exit(0);
                }*/
                if (configChanged) {

                    try {
                        BufferedWriter fileWriter = new BufferedWriter(new FileWriter(Launcher.configfile));
                        for (int i = 0; i < Launcher.config.size(); i++) {
                            fileWriter.write(Launcher.config.get(i) + lineseparator);
                        }
                        fileWriter.close();

                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }

            }
        });
        baseMap.put((byte) 'A', 1);
        baseMap.put((byte) 'C', 2);
        baseMap.put((byte) 'G', 3);
        baseMap.put((byte) 'T', 4);
        baseMap.put((byte) 'N', 5);
        baseMap.put((byte) 'I', 6);
        baseMap.put((byte) 'D', 7);
        mutTypes.put("TA", 0);
        mutTypes.put("AT", 0);
        mutTypes.put("TC", 1);
        mutTypes.put("AG", 1);
        mutTypes.put("TG", 2);
        mutTypes.put("AC", 2);
        mutTypes.put("CA", 3);
        mutTypes.put("GT", 3);
        mutTypes.put("CG", 4);
        mutTypes.put("GC", 4);
        mutTypes.put("CT", 5);
        mutTypes.put("GA", 5);

        getBase.put((byte) 'A', "A");
        getBase.put((byte) 'C', "C");
        getBase.put((byte) 'G', "G");
        getBase.put((byte) 'T', "T");
        getBase.put((byte) 'N', "N");
        getBase.put((byte) 'a', "A");
        getBase.put((byte) 'c', "C");
        getBase.put((byte) 'g', "G");
        getBase.put((byte) 't', "T");
        getBase.put((byte) 'n', "N");
        java.net.URL imgUrl = getClass().getResource("icons/save.gif");
        save = new ImageIcon(imgUrl);
        imgUrl = getClass().getResource("icons/open.gif");
        open = new ImageIcon(imgUrl);
        imgUrl = getClass().getResource("icons/settings.png");
        settingsIcon = new ImageIcon(imgUrl);
        userDir = new File(Main.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getParent()
                .replace("%20", " ");
        settings = new JMenuItem("Settings", settingsIcon);

        //   Average.frame.setVisible(false);

        try {

            savedir = Launcher.defaultSaveDir;
            path = Launcher.defaultDir;
            gerp = Launcher.gerpfile;
            defaultGenome = Launcher.defaultGenome;
            defaultAnnotation = Launcher.defaultAnnotation;
            isProxy = Launcher.isProxy;
            proxyHost = Launcher.proxyHost;
            proxyPort = Launcher.proxyPort;
            proxyType = Launcher.proxyType;
            if (isProxy) {
                ProxySettings.useProxy.setSelected(true);
            }
            if (!proxyHost.equals("")) {
                ProxySettings.hostField.setText(proxyHost);
            }
            if (!proxyPort.equals("")) {
                ProxySettings.portField.setText(proxyPort);
            }
            if (!Launcher.proxyType.equals("")) {
                ProxySettings.proxytypes.setSelectedItem(proxyType);
            }
            if (Launcher.backColor.equals("")) {
                Draw.backColor = new Color(90, 90, 90);
            }

            else {

                Draw.backColor = new Color(Integer.parseInt(Launcher.backColor),
                        Integer.parseInt(Launcher.backColor), Integer.parseInt(Launcher.backColor));
                Settings.graySlider.setValue(Integer.parseInt(Launcher.backColor));
            }

            if (Launcher.genomeDir.equals("")) {

                genomeDir = new File(userDir + "/genomes/");
            } else {
                if (new File(Launcher.genomeDir).exists()) {

                    genomeDir = new File(Launcher.genomeDir);
                } else {
                    genomeDir = new File(userDir + "/genomes/");
                }
            }

            annotationfile = defaultAnnotation;
            controlDir = Launcher.ctrldir;
            trackDir = Launcher.trackDir;
            projectDir = Launcher.projectDir;
            downloadDir = Launcher.downloadDir;
        } catch (Exception e) {
            e.printStackTrace();
        }
        File[] genomes = genomeDir.listFiles(new FilenameFilter() {
            public boolean accept(File dir, String name) {
                return !name.contains(".txt") && !name.startsWith(".");
            }
        });
        chromHeight = (int) (drawHeight * 0.1);
        drawDimensions = new Dimension(drawWidth, drawHeight - chromHeight);
        bedDimensions = new Dimension(drawWidth, bedHeight);
        chromDimensions = new Dimension(drawWidth - Main.sidebarWidth - 1, drawHeight);
        drawCanvas = new Draw((int) drawDimensions.getWidth(), (int) drawDimensions.getHeight());
        controlDraw = new ControlCanvas((int) bedDimensions.getWidth(), (int) bedDimensions.getHeight());
        iconImage = Toolkit.getDefaultToolkit().getImage(getClass().getResource("icons/icon.png"));
        frame.setIconImage(iconImage);
        /*   if(args.length > 0) {
               for(int i = 0; i<args.length; i++) {
                  if(args[i].startsWith("-opendir")) {
                     path = args[i].substring(9).replace(" ", "");
                  }
                  else if(args[i].startsWith("-ctrldir")) {
                     Control.path = args[i].substring(9).replace(" ", "");
                  }             
               }       
            }*/

        //   BGZIPInputStream in = this.getClass().getResourceAsStream("SELEX_1505_representative_matrices.bedhead.gz");
        searchField.getDocument().addDocumentListener(new DocumentListener() {
            private String searchstring;

            public void changedUpdate(DocumentEvent e) {
                if (searchField.getText().contains(";")) {
                    searchList = searchField.getText().split(";");
                    for (int i = 0; i < searchList.length; i++) {
                        warn(searchList[i].replace(" ", ""));
                    }
                } else {
                    warn(searchField.getText().replace(" ", ""));
                }

            }

            public void removeUpdate(DocumentEvent e) {
                if (searchField.getText().contains(";")) {
                    searchList = searchField.getText().split(";");
                    for (int i = 0; i < searchList.length; i++) {
                        warn(searchList[i].replace(" ", ""));
                    }
                } else {
                    warn(searchField.getText().replace(" ", ""));
                }
            }

            public void insertUpdate(DocumentEvent e) {
                if (searchField.getText().contains(";")) {
                    searchList = searchField.getText().split(";");
                    for (int i = 0; i < searchList.length; i++) {
                        warn(searchList[i].replace(" ", ""));
                    }
                } else {
                    warn(searchField.getText().replace(" ", ""));
                }
            }

            public void warn(String searchtext) {

                if (searchTable.containsKey(searchtext.toUpperCase())) {
                    if (searchTable.get(searchtext.toUpperCase())[0]
                            .equals(Main.chromosomeDropdown.getSelectedItem())) {
                        searchChrom = searchTable.get(searchtext.toUpperCase())[0];
                        searchStart = Integer.parseInt(searchTable.get(searchtext.toUpperCase())[1]);
                        searchEnd = Integer.parseInt(searchTable.get(searchtext.toUpperCase())[2]);
                    } else {
                        chromDraw.repaint();
                        searchStart = -1;
                        searchEnd = -1;
                    }
                    chromDraw.repaint();
                    searchField.setForeground(Color.black);
                } else if (searchField.getText().toUpperCase().matches("CHR.{1,2}(?!:)")) {

                    if (Main.chromnamevector.contains(searchtext.toUpperCase().substring(3))) {
                        searchField.setForeground(Color.black);

                    } else {
                        chromDraw.repaint();
                        searchField.setForeground(Color.red);
                    }
                } else if (searchtext.toUpperCase().replace(",", "").matches("(CHR)?(.+:)?\\d+(-\\d+)?")) {

                    searchField.setForeground(Color.black);
                    if (searchtext.contains(":")) {
                        searchstring = searchtext.substring(searchtext.indexOf(":") + 1).replace(",", "");
                    } else {
                        chromDraw.repaint();
                        searchstring = searchtext.replace(",", "");
                    }

                    if (!searchstring.contains("-")) {
                        try {
                            searchStart = Integer.parseInt(searchstring);
                        } catch (Exception ex) {

                        }
                        searchEnd = -1;
                    } else {
                        try {
                            searchStart = Integer
                                    .parseInt(searchstring.substring(0, searchstring.indexOf("-")));
                            searchEnd = Integer.parseInt(searchstring.substring(searchstring.indexOf("-") + 1));
                        } catch (Exception ex) {

                        }
                    }
                    chromDraw.repaint();

                } else {
                    chromDraw.repaint();
                    searchField.setForeground(Color.red);
                    searchStart = -1;
                    searchEnd = -1;
                }
            }
        });

        try {

            A = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/A.png"));
            C = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/C.png"));
            G = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/G.png"));
            T = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/T.png"));

        } catch (Exception e) {
            e.printStackTrace();
        }
        ErrorLog.main(args);

        this.setBackground(Color.black);
        UIManager.put("FileChooser.readOnly", Boolean.TRUE);

        panel.setBackground(Draw.sidecolor);
        panel.setBorder(BorderFactory.createLineBorder(Color.white));
        searchField.addKeyListener(this);

        frame.addKeyListener(this);
        frame.getContentPane().setBackground(Color.black);

        glassPane.addMouseListener(this);
        glassPane.addMouseMotionListener(new MouseMotionListener() {

            @Override
            public void mouseDragged(MouseEvent arg0) {

            }

            @Override
            public void mouseMoved(MouseEvent event) {

                // g.drawRect(drawScroll.getWidth()/2-Main.canceltextwidth/2-Main.defaultFontSize/2, Main.drawScroll.getViewport().getHeight()*2/3+Draw.loadingFont.getSize()*3-Main.defaultFontSize/4, Main.canceltextwidth+Main.defaultFontSize, Draw.loadingFont.getSize()+Main.defaultFontSize/2);                

                if (drawCanvas.loading
                        && event.getX() > drawScroll.getWidth() / 2 - Main.canceltextwidth / 2
                                - Main.defaultFontSize / 2
                        && event.getX() < drawScroll.getWidth() / 2 + Main.canceltextwidth / 2
                                + Main.defaultFontSize / 2
                        && event.getY() > frame.getHeight() * 1 / 3 + Draw.loadingFont.getSize() * 3
                                - Main.defaultFontSize / 4
                        && event.getY() < frame.getHeight() * 1 / 3 + Draw.loadingFont.getSize() * 4
                                + Main.defaultFontSize / 2) {
                    if (!Main.cancelhover) {
                        Main.cancelhover = true;
                        Main.glassPane.requestFocus();
                    }
                } else {
                    if (Main.cancelhover) {
                        Main.cancelhover = false;
                        Main.glassPane.requestFocus(false);
                    }
                }
            }
        });

        background.put((byte) 'A', 0.3);
        background.put((byte) 'C', 0.2);
        background.put((byte) 'G', 0.2);
        background.put((byte) 'T', 0.3);

        bases = new Hashtable<String, String>();
        bases.put("A", "A");
        bases.put("C", "C");
        bases.put("G", "G");
        bases.put("T", "T");
        bases.put("N", "N");
        bases.put("delA", "delA");
        bases.put("delC", "delC");
        bases.put("delG", "delG");
        bases.put("delT", "delT");
        bases.put("insA", "insA");
        bases.put("insC", "insC");
        bases.put("insG", "insG");
        bases.put("insT", "insT");

        chromDraw = new ChromDraw(drawWidth, chromHeight);

        VariantCaller.main(argsit);
        PeakCaller.main(argsit);
        tablebrowser = new TableBrowser();
        bedconverter = new BEDconvert();

        try {

            File annodir;

            File[] annotations;
            addGenome.addMouseListener(this);
            genome = new JMenu("Genomes");
            genome.setName("genomeMenu");
            genome.add(addGenome);
            genome.addComponentListener(this);
            File[] fastadir;
            String[] empty = {};

            refModel = new DefaultComboBoxModel<String>(empty);

            refDropdown = new SteppedComboBox(refModel);
            refDropdown.addMouseListener(this);
            String[] emptygenes = {};
            refDropdown.addActionListener(refDropActionListener);

            geneModel = new DefaultComboBoxModel<String>(emptygenes);
            geneDropdown = new SteppedComboBox(geneModel);
            geneDropdown.addMouseListener(this);
            if (genomes != null) {
                for (int i = 0; i < genomes.length; i++) {
                    if (!genomes[i].isDirectory()) {
                        continue;
                    }
                    annodir = new File(genomes[i].getAbsolutePath() + "/annotation/");
                    if (genomes[i].isDirectory()) {
                        fastadir = genomes[i].listFiles();
                        for (int f = 0; f < fastadir.length; f++) {
                            if (fastadir[f].isDirectory()) {
                                continue;
                            }
                            if (fastadir[f].getName().contains(".fai")) {
                                continue;
                            } else if (fastadir[f].getName().contains(".fa")) {
                                fastahash.put(genomes[i].getName(), fastadir[f]);
                            }
                        }
                    }

                    annotations = annodir.listFiles();
                    genomehash.put(genomes[i].getName(), new ArrayList<File>());

                    refModel.addElement(genomes[i].getName());
                    if (genomes[i].getName().length() > reflength) {
                        reflength = genomes[i].getName().length();
                    }
                    JMenu addMenu = new JMenu(genomes[i].getName());
                    addMenu.addMouseListener(this);
                    addMenu.setName(genomes[i].getName());
                    JMenuItem addAnnotation = new JMenuItem("Add new annotation file...");
                    addAnnotation.addMouseListener(this);
                    addAnnotation.setName("add_annotation");
                    addMenu.add(addAnnotation);
                    JLabel addLabel = new JLabel("  Select annotation: ");
                    labels.add(addLabel);
                    addMenu.add(addLabel);
                    addMenu.add(new JSeparator());

                    genome.add(addMenu);
                    addMenu.addComponentListener(this);
                    if (annotations != null) {
                        for (int j = 0; j < annotations.length; j++) {
                            annofiles = annotations[j].listFiles();
                            for (int f = 0; f < annofiles.length; f++) {
                                if (annofiles[f].getName().endsWith(".bed.gz")) {
                                    if (annofiles[f].getName()
                                            .substring(0, annofiles[f].getName().indexOf(".bed.gz"))
                                            .length() > annolength) {
                                        annolength = annofiles[f].getName().length();
                                    }

                                    genomehash.get(genomes[i].getName()).add(annofiles[f].getAbsoluteFile());
                                    JMenuItem additem = new JMenuItem(annofiles[f].getName().substring(0,
                                            annofiles[f].getName().indexOf(".bed.gz")));
                                    additem.setName(annofiles[f].getName().substring(0,
                                            annofiles[f].getName().indexOf(".bed.gz")));
                                    additem.addMouseListener(this);
                                    addMenu.add(additem);
                                    additem.addComponentListener(this);
                                    break;
                                }
                            }
                        }
                    }
                }
                refModel.addElement("Add new reference...");

            }

            if (genomes.length == 0) {
                /*if(Launcher.firstStart) {
                   Main.writeToConfig("FirstStart=false");
                }*/
                AddGenome.createAndShowGUI();
                AddGenome.frame.setTitle("Add new genome");

                AddGenome.remove.setEnabled(false);
                AddGenome.download.setEnabled(false);

                AddGenome.frame.setLocation((int) (screenSize.getWidth() / 2 - AddGenome.frame.getWidth() / 2),
                        (int) (screenSize.getHeight() / 6));

                AddGenome.frame.setState(JFrame.NORMAL);
                AddGenome.frame.setVisible(true);
                AddGenome.frame.setAlwaysOnTop(true);
                /*
                WelcomeScreen.main(args);
                WelcomeScreen.frame.setVisible(true);
                WelcomeScreen.frame.setLocation(frame.getLocationOnScreen().x+frame.getWidth()/2 - WelcomeScreen.frame.getWidth()/2, frame.getLocationOnScreen().y+frame.getHeight()/6);
                */
                if (genomes.length != 0) {
                    if (!genomehash.containsKey(defaultGenome)) {

                        setChromDrop(genomes[0].getName());
                        defaultGenome = genomes[0].getName();
                    } else {

                        setChromDrop(defaultGenome);
                    }
                    getBands();
                    getExons();
                } else {
                    setChromDrop(null);
                }
            } else {
                if (!genomehash.containsKey(defaultGenome)) {

                    setChromDrop(genomes[0].getName());
                    defaultGenome = genomes[0].getName();

                } else {

                    setChromDrop(defaultGenome);
                }
                getBands();
                getExons();
            }

            if (Launcher.firstStart) {

                WelcomeScreen.createAndShowGUI();
                WelcomeScreen.frame.setLocation(
                        (int) (screenSize.getWidth() / 2 - WelcomeScreen.frame.getWidth() / 2),
                        (int) (screenSize.getHeight() / 6));
                WelcomeScreen.frame.setVisible(true);
            }
            setMenuBar();
            setButtons();
            Settings.main(args);

            // Settings.main(args);
            frame.requestFocus();

            drawCanvas.addKeyListener(this);
            bedCanvas.addKeyListener(this);
            setFonts();
            chromLabel.setText("Chromosome " + chromosomeDropdown.getSelectedItem().toString());
            CheckUpdates check = new CheckUpdates();
            check.execute();
            //   Main.drawCanvas.loading("test");
            Main.drawCanvas.splits.get(0)
                    .setCytoImage(Main.chromDraw.createBands(Main.drawCanvas.splits.get(0)));
        } catch (Exception e) {
            e.printStackTrace();
        }

    } catch (Exception ex) {
        ex.printStackTrace();
        Main.showError(ex.getMessage(), "Error");

    }

}

From source file:com.epam.catgenome.manager.FileManager.java

/**
 * Returns contents of a directory, specified by path, to browse NGS files
 *
 * @param path a path to directory to browse
 * @return {@link List} of {@link FsDirectory}s, and {@link FsFile}, representing subdirectories and files
 * @throws IOException/*from   w  w w. j a v a 2s  .c  om*/
 */
public List<AbstractFsItem> loadDirectoryContents(String path) throws IOException {
    if (!filesBrowsingAllowed) {
        throw new AccessDeniedException("Server file system browsing is not allowed");
    }

    List<File> parentDirs = new ArrayList<>();
    if (path == null) {
        if ("/".equals(ngsDataRootPath)) {
            parentDirs = Arrays.asList(File.listRoots());
        } else {
            parentDirs.add(new File(ngsDataRootPath));
        }
    } else {
        parentDirs.add(new File(path));
    }

    Assert.isTrue(parentDirs.stream().allMatch(File::exists), "Specified path does not exist: " + path);
    Assert.isTrue(parentDirs.stream().allMatch(File::isDirectory),
            "Specified path is not a directory: " + path);

    List<AbstractFsItem> items = new ArrayList<>();

    boolean accessDenied = false;
    String fileName = "";
    String otherFileName = "";

    for (File parentDir : parentDirs) {
        if (parentDir.listFiles() == null) {
            continue;
        }

        try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(parentDir.toPath())) {
            for (Path child : dirStream) {
                try {
                    File childFile = child.toFile();
                    if (childFile.isDirectory()) {
                        FsDirectory directory = new FsDirectory();
                        directory.setPath(childFile.getAbsolutePath());
                        if (childFile.canRead()) {
                            directory.setFileCount(countChildrenFiles(child));
                        }

                        items.add(directory);
                    } else {
                        addFsFile(items, childFile);
                    }
                } catch (AccessDeniedException e) {
                    LOGGER.error("Access denied:", e);
                    accessDenied = true;
                    fileName = e.getFile();
                    otherFileName = e.getOtherFile();
                }
            }

            if (items.isEmpty() && accessDenied) {
                throw new AccessDeniedException(fileName, otherFileName, "Access denied");
            }
        }
    }

    return items;
}

From source file:base.BasePlayer.Main.java

public void actionPerformed(ActionEvent e) {
    //Logo.frame.setVisible(false);
    if (e.getSource() == pleiadesButton) {
        gotoURL("http://kaptah.local.lab.helsinki.fi/pleiades/");

    } else if (e.getSource() == manage) {

        if (VariantHandler.frame == null) {
            VariantHandler.main(argsit);
        }/*from  ww w . ja v  a 2 s.c o m*/
        VariantHandler.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantHandler.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);

        VariantHandler.frame.setState(JFrame.NORMAL);
        VariantHandler.frame.setVisible(true);
        Draw.calculateVars = true;
        Draw.updatevars = true;
        drawCanvas.repaint();

    } else if (e.getSource() == tbrowser) {
        tablebrowser.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);
        tablebrowser.frame.setState(JFrame.NORMAL);

        tablebrowser.frame.setVisible(true);
    } else if (e.getSource() == bconvert) {
        bedconverter.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);
        bedconverter.frame.setState(JFrame.NORMAL);

        bedconverter.frame.setVisible(true);
    } else if (e.getSource() == peakCaller) {
        if (PeakCaller.frame == null) {

            PeakCaller.main(argsit);

        }
        PeakCaller.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);
        PeakCaller.frame.setState(JFrame.NORMAL);
        PeakCaller.frame.setVisible(true);
    } else if (e.getSource() == variantCaller) {

        //FileRead.checkSamples();

        if (VariantCaller.frame == null) {

            VariantCaller.main(argsit);

        }
        VariantCaller.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);
        VariantCaller.frame.setState(JFrame.NORMAL);
        VariantCaller.frame.setVisible(true);
    } else if (e.getSource() == average) {
        if (Average.frame == null) {
            Average.createAndShowGUI();
        }
        Average.setSamples();

        Average.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - Average.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);

        Average.frame.setState(JFrame.NORMAL);
        Average.frame.setVisible(true);
    } else if (e.getSource() == errorlog) {

        ErrorLog.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - ErrorLog.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);

        //      VariantHandler.frame.setAlwaysOnTop(true);   
        ErrorLog.frame.setState(JFrame.NORMAL);
        ErrorLog.frame.setVisible(true);

    }
    /*   else if(e.getSource() == help) {
          JOptionPane.showMessageDialog(Main.chromDraw, "This is pre-release version of BasePlayer\nContact: help@baseplayer.fi\nUniversity of Helsinki", "Help", JOptionPane.INFORMATION_MESSAGE);
       }*/
    else if (e.getSource() == settings) {

        Settings.frame.setLocation(
                frame.getLocationOnScreen().x + frame.getWidth() / 2 - Settings.frame.getWidth() / 2,
                frame.getLocationOnScreen().y + frame.getHeight() / 6);

        Settings.frame.setState(JFrame.NORMAL);
        Settings.frame.setVisible(true);
    } else if (e.getSource() == update) {
        try {
            Updater update = new Updater();
            update.execute();

        } catch (Exception ex) {
            ex.printStackTrace();
        }

    } else if (e.getSource() == clearMemory) {
        FileRead.nullifyVarNodes();

        //FileRead.removeNonListVariants();f
        System.gc();
        chromDraw.repaint();
    } else if (e.getSource() == zoomout) {

        zoomout();
    } else if (e.getSource() == dosomething) {

        BedNode currentbed = bedCanvas.bedTrack.get(0).getHead().getNext();
        VarNode currentvar = FileRead.head.getNext();

        while (currentbed != null) {

            while (currentvar != null && currentvar.getPosition() < currentbed.getPosition()) {
                currentvar = currentvar.getNext();
            }
            while (currentbed != null
                    && currentvar.getPosition() > currentbed.getPosition() + currentbed.getLength()) {
                currentbed = currentbed.getNext();
            }

            if (currentvar != null && currentvar.getPosition() >= currentbed.getPosition()
                    && currentvar.getPosition() < currentbed.getPosition() + currentbed.getLength()) {
                currentvar.setBedhit(true);
                currentvar = currentvar.getNext();
            }
            if (currentvar == null) {
                break;
            }
            currentbed = currentbed.getNext();
        }

    } else if (e.getSource() == clear) {
        clearData();
    } else if (e.getSource() == exit) {

        System.exit(0);
    } else if (e.getSource() == openbams) {
        try {
            if (!checkGenome())
                return;
            if (VariantHandler.frame != null) {
                VariantHandler.frame.setState(Frame.ICONIFIED);
            }

            FileDialog fc = new FileDialog(frame, "Choose BAM file(s)", FileDialog.LOAD);
            fc.setDirectory(path);
            fc.setFile("*.bam;*.cram;*.link");
            fc.setFilenameFilter(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    return name.toLowerCase().endsWith(".bam") || name.toLowerCase().endsWith(".cram")
                            || name.toLowerCase().endsWith(".link");
                }
            });
            fc.setMultipleMode(true);
            fc.setVisible(true);
            File[] openfiles = fc.getFiles();

            if (openfiles != null && openfiles.length > 0) {

                path = openfiles[0].getParent();
                writeToConfig("DefaultDir=" + path);
                FileRead filereader = new FileRead(openfiles);

                filereader.start = (int) drawCanvas.selectedSplit.start;
                filereader.end = (int) drawCanvas.selectedSplit.end;
                filereader.readBAM = true;
                filereader.execute();

            } else {
                //Main.showError("File(s) does not exist.", "Error");
            }

        } catch (Exception ex) {
            Main.showError(ex.getMessage(), "Error");
        }
    } else if (e.getSource() == openvcfs) {
        try {
            if (!checkGenome())
                return;
            if (VariantHandler.frame != null) {
                VariantHandler.frame.setState(Frame.ICONIFIED);
            }

            FileDialog fc = new FileDialog(frame, "Choose VCF file(s)", FileDialog.LOAD);
            fc.setDirectory(path);
            fc.setFile("*.vcf");
            fc.setFilenameFilter(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    return name.toLowerCase().endsWith(".vcf") || name.toLowerCase().endsWith(".vcf.gz");
                }
            });

            fc.setMultipleMode(true);
            fc.setVisible(true);
            File[] openfiles = fc.getFiles();

            if (openfiles != null && openfiles.length > 0) {

                path = openfiles[0].getParent();
                writeToConfig("DefaultDir=" + path);
                FileRead filereader = new FileRead(openfiles);

                filereader.start = (int) drawCanvas.selectedSplit.start;
                filereader.end = (int) drawCanvas.selectedSplit.end;
                filereader.readVCF = true;
                filereader.execute();

            } else {
                //Main.showError("File(s) does not exist.", "Error");
            }

            if (1 == 1) {
                return;
            }

            JFileChooser chooser = new JFileChooser(path);
            getText(chooser.getComponents());
            chooser.setMultiSelectionEnabled(true);
            //chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
            chooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
            chooser.setAcceptAllFileFilterUsed(false);
            chooser.addChoosableFileFilter(vcfFilter);
            chooser.addChoosableFileFilter(bamFilter);
            chooser.addChoosableFileFilter(linkFilter);
            if (defaultSelectType == "vcf") {
                chooser.setFileFilter(vcfFilter);
            } else if (defaultSelectType == "bam") {
                chooser.setFileFilter(bamFilter);
            } else {
                chooser.setFileFilter(linkFilter);
            }
            chooser.setDialogTitle("Add samples");
            chooser.setPreferredSize(
                    new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3));
            int returnVal = chooser.showOpenDialog((Component) this.getParent());

            if (returnVal == JFileChooser.APPROVE_OPTION) {

                File vcffiles[] = chooser.getSelectedFiles();
                if (vcffiles.length == 1 && !vcffiles[0].exists() && pleiades) {

                    if (Main.chooserText.contains("`")) {
                        Main.chooserText.replace("`", "?");
                    }
                    if (Main.chooserText.contains(" ")) {
                        Main.chooserText.replace(" ", "%20");
                    }
                    if (Main.chooserText.contains("pleiades")) {
                        try {
                            URL url = new URL(Main.chooserText);
                            //System.out.println(Main.chooserText);
                            HttpURLConnection httpConn = (HttpURLConnection) url.openConnection();
                            httpConn.connect();

                            int responseCode = httpConn.getResponseCode();

                            if (responseCode == HttpsURLConnection.HTTP_OK) {

                                String loading = drawCanvas.loadingtext;
                                InputStream inputStream = httpConn.getInputStream();
                                BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
                                Main.drawCanvas.loadingtext = loading + " 0MB";
                                String line;
                                StringBuffer buffer = new StringBuffer("");
                                while ((line = reader.readLine()) != null) {

                                    buffer.append(line);

                                }
                                inputStream.close();
                                reader.close();
                                String split2;
                                String[] split = buffer.toString().split("dataUnit");
                                String location;
                                ArrayList<File> array = new ArrayList<File>();
                                File[] paths;
                                FileSystemView fsv = FileSystemView.getFileSystemView();
                                paths = File.listRoots();
                                String loc = "/mnt";
                                boolean missingfiles = false;
                                for (File path : paths) {
                                    if (fsv.getSystemDisplayName(path).contains("merit")) {
                                        loc = path.getCanonicalPath();
                                    }
                                }

                                for (int i = 0; i < split.length; i++) {

                                    if (!split[i].contains("lastLocation")) {

                                        continue;
                                    }

                                    split2 = split[i].split("\"lastLocation\":\"")[1];
                                    location = split2.substring(0, split2.indexOf("\"}"));
                                    String filename = "";
                                    String testloc = location.replace("/mnt", loc) + "/wgspipeline/";
                                    File testDir = new File(testloc);
                                    if (testDir.exists() && testDir.isDirectory()) {
                                        if (chooser.getFileFilter()
                                                .equals(chooser.getChoosableFileFilters()[1])) {
                                            File[] addDir = testDir.listFiles(new FilenameFilter() {
                                                public boolean accept(File dir, String name) {
                                                    return name.toLowerCase().endsWith(".bam")
                                                            || name.toLowerCase().endsWith(".cram");
                                                }
                                            });
                                            if (addDir.length > 0) {
                                                filename = addDir[0].getName();
                                            }
                                        } else {
                                            File[] addDir = testDir.listFiles(new FilenameFilter() {
                                                public boolean accept(File dir, String name) {
                                                    return name.toLowerCase().endsWith(".vcf.gz");
                                                }
                                            });
                                            if (addDir.length > 0) {
                                                filename = addDir[0].getName();
                                            }
                                        }
                                    }

                                    location = testloc + "/" + filename;

                                    if (!new File(location).exists()) {

                                        if (!new File(location).exists()) {
                                            missingfiles = true;
                                            ErrorLog.addError("No sample files found in " + testloc);

                                        } else {
                                            array.add(new File(location));
                                        }
                                    } else {

                                        array.add(new File(location));
                                    }
                                }

                                File[] files = new File[array.size()];
                                for (int i = 0; i < files.length; i++) {

                                    files[i] = array.get(i);
                                }
                                FileRead filereader = new FileRead(files);
                                filereader.start = (int) drawCanvas.selectedSplit.start;
                                filereader.end = (int) drawCanvas.selectedSplit.end;
                                if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[1])) {
                                    filereader.readBAM = true;
                                } else {
                                    filereader.readVCF = true;
                                }
                                filereader.execute();
                                if (missingfiles) {
                                    JOptionPane.showMessageDialog(Main.drawScroll,
                                            "Missing files. Check Tools->View log", "Note",
                                            JOptionPane.INFORMATION_MESSAGE);
                                }

                            }
                        } catch (Exception ex) {
                            ex.printStackTrace();
                        }
                    }

                    return;
                }

                if (vcffiles.length > 0) {
                    path = vcffiles[0].getParent();
                    writeToConfig("DefaultDir=" + path);
                    FileRead filereader = new FileRead(vcffiles);

                    if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[0])) {
                        defaultSelectType = "vcf";
                        filereader.start = (int) drawCanvas.selectedSplit.start;
                        filereader.end = (int) drawCanvas.selectedSplit.end;
                        filereader.readVCF = true;
                        filereader.execute();
                    } else if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[1])) {
                        defaultSelectType = "bam";
                        filereader.readBAM = true;
                        filereader.execute();
                    } else if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[2])) {

                        defaultSelectType = "link";
                        filereader.readBAM = true;
                        filereader.execute();
                    }
                } else {

                    JOptionPane.showMessageDialog(Main.drawScroll,
                            "The file does not exist. The file link may be broken.\nThe problem may also be the Java run time version in Linux.",
                            "Note", JOptionPane.INFORMATION_MESSAGE);
                }
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }

    } else if (e.getSource() == addcontrols) {
        if (!checkGenome())
            return;
        if (VariantHandler.frame != null) {
            VariantHandler.frame.setState(Frame.ICONIFIED);
        }
        FileDialog fc = new FileDialog(frame, "Choose control file(s)", FileDialog.LOAD);
        fc.setDirectory(Main.controlDir);
        fc.setFile("*.vcf.gz");
        fc.setFilenameFilter(new FilenameFilter() {
            public boolean accept(File dir, String name) {
                return name.toLowerCase().endsWith(".vcf.gz");
            }
        });
        fc.setMultipleMode(true);
        fc.setVisible(true);
        File[] openfiles = fc.getFiles();

        if (openfiles != null && openfiles.length > 0) {

            controlDir = openfiles[0].getParent();
            writeToConfig("DefaultControlDir=" + controlDir);

            Control.addFiles(openfiles);
        }
        if (1 == 1) {
            return;
        }
        JFileChooser chooser = new JFileChooser(controlDir);
        //        JFileChooser chooser = new JFileChooser(path);            
        chooser.setMultiSelectionEnabled(true);
        chooser.setAcceptAllFileFilterUsed(false);
        Control.MyFilter vcfFilter = new Control.MyFilter();
        chooser.addChoosableFileFilter(vcfFilter);

        chooser.setDialogTitle("Add controls");
        chooser.setPreferredSize(
                new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3));
        int returnVal = chooser.showOpenDialog((Component) this.getParent());

        if (returnVal == JFileChooser.APPROVE_OPTION) {

            File vcffiles[] = chooser.getSelectedFiles();
            controlDir = vcffiles[0].getParent();
            writeToConfig("DefaultControlDir=" + controlDir);

            if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[0])) {
                Control.addFiles(vcffiles);
            }
        }
    } else if (e.getSource() == addtracks) {
        if (!checkGenome())
            return;
        try {
            if (!checkGenome())
                return;
            if (VariantHandler.frame != null) {
                VariantHandler.frame.setState(Frame.ICONIFIED);
            }

            FileDialog fc = new FileDialog(frame, "Choose track file(s)", FileDialog.LOAD);
            fc.setDirectory(Main.trackDir);
            fc.setFile(
                    "*.bed;*.bedgraph.gz;*.gff.gz;*.gff3.gz;*.bigwig;*.bw;*.bigbed;*.bb;*.tsv.gz;*.tsv.bgz;*.txt");
            fc.setFilenameFilter(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    return name.toLowerCase().endsWith(".bed") || name.toLowerCase().endsWith(".bed.gz")
                            || name.toLowerCase().endsWith(".bedgraph.gz")
                            || name.toLowerCase().endsWith(".bedgraph.gz")
                            || name.toLowerCase().endsWith(".bedgraph.gz")
                            || name.toLowerCase().endsWith(".gff.gz") || name.toLowerCase().endsWith(".gff3.gz")
                            || name.toLowerCase().endsWith(".bigwig") || name.toLowerCase().endsWith(".bw")
                            || name.toLowerCase().endsWith(".bigbed") || name.toLowerCase().endsWith(".bb")
                            || name.toLowerCase().endsWith(".tsv.gz") || name.toLowerCase().endsWith(".tsv.bgz")
                            || name.toLowerCase().endsWith(".txt");
                }
            });
            fc.setMultipleMode(true);
            fc.setVisible(true);
            File[] openfiles = fc.getFiles();

            if (openfiles != null && openfiles.length > 0) {

                trackDir = openfiles[0].getParent();
                writeToConfig("DefaultTrackDir=" + trackDir);
                FileRead filereader = new FileRead(openfiles);
                filereader.readBED = true;
                filereader.execute();

            } else {
                //Main.showError("File(s) does not exist.", "Error");
            }

        } catch (Exception ex) {
            Main.showError(ex.getMessage(), "Error");
        }
        if (1 == 1) {
            return;
        }
        if (VariantHandler.frame != null) {
            VariantHandler.frame.setState(Frame.ICONIFIED);
        }
        JFileChooser chooser = new JFileChooser(Main.trackDir);
        getText(chooser.getComponents());
        chooser.setMultiSelectionEnabled(true);
        chooser.setAcceptAllFileFilterUsed(false);
        MyFilterBED bedFilter = new MyFilterBED();
        MyFilterTXT txtFilter = new MyFilterTXT();
        chooser.addChoosableFileFilter(bedFilter);
        chooser.addChoosableFileFilter(txtFilter);
        chooser.setDialogTitle("Add tracks");
        chooser.setPreferredSize(
                new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3));
        int returnVal = chooser.showOpenDialog((Component) this.getParent());

        try {

            if (returnVal == JFileChooser.APPROVE_OPTION) {

                File bedfiles[] = chooser.getSelectedFiles();
                if (bedfiles[0].exists()) {

                    trackDir = bedfiles[0].getParent();
                    writeToConfig("DefaultTrackDir=" + trackDir);
                    FileRead filereader = new FileRead(bedfiles);
                    filereader.readBED(bedfiles);

                } else {

                    if (Main.chooserText.length() > 5 && Main.chooserText.endsWith(".bed.gz")
                            || Main.chooserText.endsWith(".gff.gz") || Main.chooserText.endsWith(".gff3.gz")
                            || Main.chooserText.endsWith(".bedgraph.gz")) {

                        if (Main.chooserText.startsWith("http://") || Main.chooserText.startsWith("ftp://")) {

                            URL url = new URL(Main.chooserText);
                            SeekableStream stream = SeekableStreamFactory.getInstance().getStreamFor(url);
                            TabixReader tabixReader = null;
                            String index = null;

                            try {
                                tabixReader = new TabixReader(Main.chooserText, Main.chooserText + ".tbi",
                                        stream);
                                index = Main.chooserText + ".tbi";
                            } catch (Exception ex) {
                                try {
                                    tabixReader = new TabixReader(Main.chooserText,
                                            Main.chooserText.substring(0, Main.chooserText.indexOf(".gz"))
                                                    + ".tbi",
                                            stream);
                                    index = Main.chooserText.substring(0, Main.chooserText.indexOf(".gz"))
                                            + ".tbi";
                                } catch (Exception exc) {
                                    exc.printStackTrace();
                                }
                            }
                            if (tabixReader != null && index != null) {

                                FileRead filereader = new FileRead(bedfiles);
                                filereader.readBED(Main.chooserText, index, false);

                                tabixReader.close();
                            }
                        }
                    } else {
                        if (Main.chooserText.contains("://")) {

                            try {
                                //        bbreader = new BBFileReader(Main.chooserText, stream);

                            } catch (Exception ex) {
                                ex.printStackTrace();
                            }

                            //  if(bbreader != null) {

                            FileRead filereader = new FileRead(bedfiles);
                            filereader.readBED(Main.chooserText, "nan", false);

                            //     }
                            //     stream.close();
                        }
                    }
                }
            }

        } catch (Exception ex) {
            ex.printStackTrace();
        }
    } else if (e.getSource() == openProject) {
        if (!checkGenome())
            return;
        if (VariantHandler.frame != null) {
            VariantHandler.frame.setState(Frame.ICONIFIED);
        }
        openProject();
    } else if (e.getSource() == saveProjectAs) {
        if (VariantHandler.frame != null) {
            VariantHandler.frame.setState(Frame.ICONIFIED);
        }
        try {
            File savefile = null;
            FileDialog fs = new FileDialog(frame, "Save project as...", FileDialog.SAVE);
            fs.setDirectory(projectDir);
            fs.setFile("*.ses");
            fs.setFilenameFilter(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    return name.toLowerCase().endsWith(".ses");
                }
            });
            fs.setVisible(true);

            while (true) {
                String filename = fs.getFile();

                if (filename != null) {
                    savefile = new File(fs.getDirectory() + "/" + filename);
                    projectDir = fs.getDirectory();
                    writeToConfig("DefaultProjectDir=" + projectDir);

                    /* if(!Files.isWritable(Paths.get(savefile.getParent()))) {
                       Main.showError("No permission to write.", "Error");
                       continue;
                     }*/

                    if (!savefile.getAbsolutePath().endsWith(".ses")) {
                        savefile = new File(savefile.getAbsolutePath() + ".ses");
                    }

                    Serializer ser = new Serializer();
                    ser.serialize(savefile);
                    break;
                } else {
                    break;
                }
            }
            if (1 == 1) {
                return;
            }
            JFileChooser chooser = new JFileChooser();
            chooser.setAcceptAllFileFilterUsed(false);
            MyFilterSES sesFilter = new MyFilterSES();
            chooser.addChoosableFileFilter(sesFilter);
            chooser.setDialogTitle("Save project as...");
            int returnVal = chooser.showSaveDialog((Component) this.getParent());

            if (returnVal == JFileChooser.APPROVE_OPTION) {
                File outfile = chooser.getSelectedFile();
                if (!outfile.getAbsolutePath().endsWith(".ses")) {
                    outfile = new File(outfile.getAbsolutePath() + ".ses");
                }

                Serializer ser = new Serializer();
                ser.serialize(outfile);
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }

    } else if (e.getSource() == saveProject) {
        if (drawCanvas.drawVariables.projectName.equals("Untitled")) {
            saveProjectAs.doClick();
        } else {

            Serializer ser = new Serializer();
            ser.serialize(drawCanvas.drawVariables.projectFile);
        }
    }
    /*      else if(e.getSource() == welcome) {
             WelcomeScreen.main(args);
             WelcomeScreen.frame.setVisible(true);
             WelcomeScreen.frame.setLocation(frame.getLocationOnScreen().x+frame.getWidth()/2 - WelcomeScreen.frame.getWidth()/2, frame.getLocationOnScreen().y+frame.getHeight()/6);
                     
          }*/
}