X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=6a6ba2fd12f54bedb1845a2a2d2a220b1105b8aa;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=2a1979e518621c7f53e675901da0019c8df86f37;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 2a1979e..6a6ba2f 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -18,453 +18,573 @@ */ package jalview.gui; +import jalview.datamodel.*; + +import jalview.io.*; + import java.awt.*; import java.awt.datatransfer.*; import java.awt.dnd.*; import java.awt.event.*; + import javax.swing.*; -import jalview.datamodel.*; -import jalview.io.*; -public class Desktop - extends jalview.jbgui.GDesktop implements DropTargetListener +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Desktop extends jalview.jbgui.GDesktop + implements DropTargetListener { - public static JDesktopPane desktop; - static int openFrameCount = 0; - static final int xOffset = 30; - static final int yOffset = 30; - - public Desktop() - { - Image image = null; - - try + /** DOCUMENT ME!! */ + public static JDesktopPane desktop; + static int openFrameCount = 0; + static final int xOffset = 30; + static final int yOffset = 30; + + /** + * Creates a new Desktop object. + */ + public Desktop() { - java.net.URL url = getClass().getResource("/images/logo.gif"); + Image image = null; + + try + { + java.net.URL url = getClass().getResource("/images/logo.gif"); - if (url != null) - { - image = java.awt.Toolkit.getDefaultToolkit().createImage(url); + if (url != null) + { + image = java.awt.Toolkit.getDefaultToolkit().createImage(url); - MediaTracker mt = new MediaTracker(this); - mt.addImage(image, 0); - mt.waitForID(0); - setIconImage(image); - } - } - catch (Exception ex) - { - } + MediaTracker mt = new MediaTracker(this); + mt.addImage(image, 0); + mt.waitForID(0); + // setIconImage(image); + } + } + catch (Exception ex) + { + } - setTitle("Jalview 2005"); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - desktop = new JDesktopPane(); - desktop.setBackground(Color.white); - setContentPane(desktop); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + setTitle("Jalview 2005"); + setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + desktop = new JDesktopPane(); + desktop.setBackground(Color.white); + setContentPane(desktop); + desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - // This line prevents Windows Look&Feel resizing all new windows to maximum - // if previous window was maximised - desktop.setDesktopManager(new DefaultDesktopManager()); + // This line prevents Windows Look&Feel resizing all new windows to maximum + // if previous window was maximised + desktop.setDesktopManager(new DefaultDesktopManager()); - Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - String x = jalview.bin.Cache.getProperty("SCREEN_X"); - String y = jalview.bin.Cache.getProperty("SCREEN_Y"); - String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH"); - String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT"); + Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); + String x = jalview.bin.Cache.getProperty("SCREEN_X"); + String y = jalview.bin.Cache.getProperty("SCREEN_Y"); + String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH"); + String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT"); - if ( (x != null) && (y != null) && (width != null) && (height != null)) - { - setBounds(Integer.parseInt(x), Integer.parseInt(y), + if ((x != null) && (y != null) && (width != null) && (height != null)) + { + setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer.parseInt(width), Integer.parseInt(height)); - } - else - { - setBounds( (int) (screenSize.width - 900) / 2, + } + else + { + setBounds((int) (screenSize.width - 900) / 2, (int) (screenSize.height - 650) / 2, 900, 650); - } + } - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - quit(); - } - }); - setVisible(true); - - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - - /////////Add a splashscreen on startup - /////////Add a splashscreen on startup - JInternalFrame frame = new JInternalFrame(); - - SplashScreen splash = new SplashScreen(frame, image); - frame.setContentPane(splash); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - addInternalFrame(frame, "", 750, 160, false); - frame.setLocation( (int) ( (getWidth() - 750) / 2), - (int) ( (getHeight() - 160) / 2)); - } - - public static void addInternalFrame(final JInternalFrame frame, - String title, int w, int h) - { - addInternalFrame(frame, title, w, h, true); - } - - public static void addInternalFrame(final JInternalFrame frame, - String title, int w, int h, - boolean resizable) - { - desktop.add(frame); - openFrameCount++; - - try - { - frame.setSelected(true); + this.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + quit(); + } + }); + + this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); + + /////////Add a splashscreen on startup + /////////Add a splashscreen on startup + JInternalFrame frame = new JInternalFrame(); + + SplashScreen splash = new SplashScreen(frame, image); + frame.setContentPane(splash); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + addInternalFrame(frame, "", 750, 160, false); + frame.setLocation((int) ((getWidth() - 750) / 2), + (int) ((getHeight() - 160) / 2)); } - catch (java.beans.PropertyVetoException e) + + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + */ + public static void addInternalFrame(final JInternalFrame frame, + String title, int w, int h) { + addInternalFrame(frame, title, w, h, true); } - frame.setTitle(title); - frame.setSize(w, h); - frame.setClosable(true); - frame.setResizable(resizable); - frame.setMaximizable(resizable); - frame.setIconifiable(resizable); - frame.setFrameIcon(null); - frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount); - frame.toFront(); - - final JMenuItem menuItem = new JMenuItem(title); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + * @param resizable DOCUMENT ME! + */ + public static void addInternalFrame(final JInternalFrame frame, + String title, int w, int h, boolean resizable) { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - openFrameCount--; - windowMenu.remove(menuItem); - } - ; - }); - - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { + desktop.add(frame); + openFrameCount++; + try { - frame.setSelected(true); - frame.setIcon(false); + frame.setSelected(true); } - catch (java.beans.PropertyVetoException ex) + catch (java.beans.PropertyVetoException e) { } - ; - } - }); - - frame.setVisible(true); - windowMenu.add(menuItem); - } - - public void dragEnter(DropTargetDragEvent evt) - { - } - - public void dragExit(DropTargetEvent evt) - { - } - - public void dragOver(DropTargetDragEvent evt) - { - } + frame.setTitle(title); + frame.setSize(w, h); + frame.setClosable(true); + frame.setResizable(resizable); + frame.setMaximizable(resizable); + frame.setIconifiable(resizable); + frame.setFrameIcon(null); + frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount); + frame.toFront(); + + final JMenuItem menuItem = new JMenuItem(title); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + openFrameCount--; + windowMenu.remove(menuItem); + } + ; + }); + + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + try + { + frame.setSelected(true); + frame.setIcon(false); + } + catch (java.beans.PropertyVetoException ex) + { + } + + ; + } + }); + + frame.setVisible(true); + windowMenu.add(menuItem); + } - public void dropActionChanged(DropTargetDragEvent evt) - { - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void dragEnter(DropTargetDragEvent evt) + { + } - public void drop(DropTargetDropEvent evt) - { - Transferable t = evt.getTransferable(); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void dragExit(DropTargetEvent evt) + { + } - if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void dragOver(DropTargetDragEvent evt) { - return; } - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void dropActionChanged(DropTargetDragEvent evt) + { + } - try + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void drop(DropTargetDropEvent evt) { - java.util.List files = (java.util.List) t.getTransferData(DataFlavor. - javaFileListFlavor); + Transferable t = evt.getTransferable(); - for (int i = 0; i < files.size(); i++) - { - String file = files.get(i).toString(); - String protocol = "File"; + if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + return; + } + + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - if (file.endsWith(".jar")) + try { - Jalview2XML.LoadJalviewAlign(file); + java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor); + + for (int i = 0; i < files.size(); i++) + { + String file = files.get(i).toString(); + String protocol = "File"; + String format = null; + + if (file.endsWith(".jar")) + { + format = "Jalview"; + + } + else + { + format = jalview.io.IdentifyFile.Identify(file, + protocol); + } + LoadFile(file, protocol, format); + } } - else + catch (Exception ex) { - String format = jalview.io.IdentifyFile.Identify(file, - protocol); - LoadFile(file, protocol, format); + ex.printStackTrace(); } - } } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) { - ex.printStackTrace(); - } - } - - public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), - new String[] + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), + new String[] + { + "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", + "jar" + }, + new String[] + { + "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" + }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Open local file"); + chooser.setToolTipText("Open"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) { - "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", - "jar" - }, - new String[] - { - "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" - }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Open local file"); - chooser.setToolTipText("Open"); - - int value = chooser.showOpenDialog(this); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + + String format = null; + if (chooser.getSelectedFormat().equals("Jalview")) + { + format = "Jalview"; + } + else + { + format = IdentifyFile.Identify(choice, "File"); + } + + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + LoadFile(choice, "File", format); + } + } - if (value == JalviewFileChooser.APPROVE_OPTION) + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + * @param protocol DOCUMENT ME! + * @param format DOCUMENT ME! + */ + public void LoadFile(String file, String protocol, String format) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - if (chooser.getSelectedFormat().equals("Jalview")) - { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew"); - Jalview2XML.LoadJalviewAlign(choice); - } - else - { - String format = IdentifyFile.Identify(choice, "File"); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); - LoadFile(choice, "File", format); - } + LoadingThread loader = new LoadingThread(file, protocol, format); + loader.start(); } - } - - public void LoadFile(String file, String protocol, String format) - { - LoadingThread loader = new LoadingThread(file, protocol, format); - loader.start(); - } - - public void inputURLMenuItem_actionPerformed(ActionEvent e) - { - String url = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Enter url of input file", "Input alignment from URL", - JOptionPane.QUESTION_MESSAGE, null, null, "http://www.") - .toString(); - - if (url == null) + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + * @param protocol DOCUMENT ME! + * @param format DOCUMENT ME! + */ + public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format) { - return; - } + LoadingThread loader = new LoadingThread(file, protocol, format); + loader.start(); + + while (loader.isAlive()) + { + try + { + Thread.sleep(50); + } + catch (Exception ex) + {} + } - String format = IdentifyFile.Identify(url, "URL"); + return loader.af; + } - if (format.equals("URL NOT FOUND")) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputURLMenuItem_actionPerformed(ActionEvent e) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't locate " + url, - "URL not found", - JOptionPane.WARNING_MESSAGE); + String url = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter url of input file", "Input alignment from URL", + JOptionPane.QUESTION_MESSAGE, null, null, "http://www.") + .toString(); + + if (url == null) + { + return; + } + + if (url.trim().toLowerCase().endsWith(".jar")) + { + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview"); + Jalview2XML.LoadJalviewAlign(url); + } + else + { - return; + String format = IdentifyFile.Identify(url, "URL"); + + if (format.equals("URL NOT FOUND")) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't locate " + url, + "URL not found", + JOptionPane.WARNING_MESSAGE); + + return; + } + + LoadFile(url, "URL", format); + } } - LoadFile(url, "URL", format); - } - - public void inputTextboxMenuItem_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(); - Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); - } - - /* - * Exit the program - */ - public void quit() - { - if (jalview.bin.Jalview.applet != null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputTextboxMenuItem_actionPerformed(ActionEvent e) { - jalview.bin.Jalview.applet.destroy(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(); + Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); } - else + + /* + * Exit the program + */ + public void quit() { - jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + - ""); - jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + - ""); - jalview.bin.Cache.setProperty("SCREEN_WIDTH", - getWidth() + ""); - jalview.bin.Cache.setProperty("SCREEN_HEIGHT", - getHeight() + ""); - System.exit(0); + jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + ""); + jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + ""); + jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + ""); + jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + ""); + System.exit(0); } - } - - public void aboutMenuItem_actionPerformed(ActionEvent e) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "JalView 2005 version " + - jalview.bin.Cache.VERSION + - "; last updated: " + - jalview.bin.Cache.BUILD_DATE + - "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." + - "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." + - "\nFor all issues relating to Jalview, email help@jalview.org" + - "\n\nIf you use JalView, please cite:" + - "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" + - "\nBioinformatics, 2004 12;426-7.", - "About Jalview", - JOptionPane.INFORMATION_MESSAGE); - } - - public void documentationMenuItem_actionPerformed(ActionEvent e) - { - try + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void aboutMenuItem_actionPerformed(ActionEvent e) { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setLocation(new Point(200, 50)); - hb.setSize(new Dimension(800, 700)); - hb.setCurrentID("home"); - hb.setDisplayed(true); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "JalView 2005 version " + jalview.bin.Cache.VERSION + + "; last updated: " + jalview.bin.Cache.BUILD_DATE + + "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." + + "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." + + "\nFor all issues relating to Jalview, email help@jalview.org" + + "\n\nIf you use JalView, please cite:" + + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" + + "\nBioinformatics, 2004 12;426-7.", "About Jalview", + JOptionPane.INFORMATION_MESSAGE); } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void documentationMenuItem_actionPerformed(ActionEvent e) { - ex.printStackTrace(); + try + { + ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); + java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); + javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + + javax.help.HelpBroker hb = hs.createHelpBroker(); + hb.setLocation(new Point(200, 50)); + hb.setSize(new Dimension(800, 700)); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - } - protected void preferences_actionPerformed(ActionEvent e) - { - Preferences pref = new Preferences(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void preferences_actionPerformed(ActionEvent e) + { + new Preferences(); + } - public void saveState_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), new String[] - {"jar"}, - new String[] - {"Jalview Project"}, "Jalview Project"); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void saveState_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] { "jar" }, + new String[] { "Jalview Project" }, "Jalview Project"); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save State"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save State"); - int value = chooser.showSaveDialog(this); + int value = chooser.showSaveDialog(this); - if (value == JalviewFileChooser.APPROVE_OPTION) - { - java.io.File choice = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - Jalview2XML.SaveState(choice); + if (value == JalviewFileChooser.APPROVE_OPTION) + { + java.io.File choice = chooser.getSelectedFile(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + Jalview2XML.SaveState(choice); + } } - } - - public void loadState_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), new String[] - {"jar"}, - new String[] - {"Jalview Project"}, "Jalview Project"); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Restore state"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void loadState_actionPerformed(ActionEvent e) { - String choice = chooser.getSelectedFile().getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - Jalview2XML.LoadJalviewAlign(choice); - } - } + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] { "jar" }, + new String[] { "Jalview Project" }, "Jalview Project"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Restore state"); - class LoadingThread - extends Thread - { - String file; - String protocol; - String format; + int value = chooser.showOpenDialog(this); - public LoadingThread(String file, String protocol, String format) - { - this.file = file; - this.protocol = protocol; - this.format = format; + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getAbsolutePath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + Jalview2XML.LoadJalviewAlign(choice); + } } - public void run() + class LoadingThread extends Thread { - SequenceI[] sequences = null; + String file; + String protocol; + String format; + AlignFrame af; - if (FormatAdapter.formats.contains(format)) - { - sequences = FormatAdapter.readFile(file, protocol, format); - } - - if ( (sequences != null) && (sequences.length > 0)) - { - AlignFrame af = new AlignFrame(new Alignment(sequences)); - addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); - af.currentFileFormat = format; - af.statusBar.setText("Successfully loaded file " + file); - - try + public LoadingThread(String file, String protocol, String format) { - af.setMaximum(Preferences.showFullscreen); + this.file = file; + this.protocol = protocol; + this.format = format; } - catch (Exception ex) + + public void run() { + SequenceI[] sequences = null; + + if(format.equalsIgnoreCase("Jalview")) + { + Jalview2XML.LoadJalviewAlign(file); + } + else + { + if (FormatAdapter.formats.contains(format)) + { + sequences = FormatAdapter.readFile(file, protocol, format); + } + + if ( (sequences != null) && (sequences.length > 0)) + { + af = new AlignFrame(new Alignment(sequences)); + addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, + AlignFrame.NEW_WINDOW_HEIGHT); + af.currentFileFormat = format; + af.statusBar.setText("Successfully loaded file " + file); + + try + { + af.setMaximum(Preferences.showFullscreen); + } + catch (Exception ex) + { + } + } + else + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't open file.\n" + + "Formats currently supported are\n" + + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter! + , "Error loading file", JOptionPane.WARNING_MESSAGE); + } + } } - } - else - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't open file.\n" + - "Formats currently supported are\n" + - "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter! - , "Error loading file", - JOptionPane.WARNING_MESSAGE); - } } - } }