X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=cdb18e751c541c9c3cbb3234ddcb04073b9a2ce5;hb=4f90c01f2b85f6c042ddba89e4dacb8cc2f86881;hp=b6fd73ee09357fbcc609ecc7f059c255886321a4;hpb=852d4fcf2280f3595f9b77e78c7f8c92fcff9a1c;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index b6fd73e..cdb18e7 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,372 +1,1385 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - - -package jalview.gui; - -import jalview.gui.*; -import jalview.io.*; -import jalview.datamodel.*; -import javax.swing.*; -import java.awt.*; -import java.awt.event.*; -import java.awt.dnd.*; -import javax.swing.*; -import java.awt.datatransfer.*; -import jalview.bin.Cache; - - -public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener -{ - public static JDesktopPane desktop; - static int openFrameCount = 0; - static final int xOffset = 30, yOffset = 30; - - public Desktop() - { - Image image =null; - try{ - java.net.URL url = getClass().getResource("/images/logo.gif"); - 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){} - - 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() ); - - - 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), - Integer.parseInt(width), Integer.parseInt(height)); - } - else - setBounds( (int)(screenSize.width-900)/2, - (int)(screenSize.height-650)/2, - 900 , - 650); - -this.addWindowListener(new WindowAdapter() -{ -public void windowClosing(WindowEvent evt) -{ - 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() + ""); -} -}); -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); - } catch (java.beans.PropertyVetoException e) {} - 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 dragEnter(DropTargetDragEvent evt){} - public void dragExit(DropTargetEvent evt){} - public void dragOver(DropTargetDragEvent evt){} - public void dropActionChanged(DropTargetDragEvent evt){} - public void drop(DropTargetDropEvent evt) -{ - Transferable t = evt.getTransferable(); - if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - return; - - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - try{ - 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"; - if(file.endsWith(".jar")) - Jalview2XML.LoadJalviewAlign(file); - else - { - String format = jalview.io.IdentifyFile.Identify(file, protocol); - LoadFile(file, protocol, format); - } - } - - }catch(Exception ex){ex.printStackTrace();} - } - - - public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) - { - 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) - { - 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); - } - } - } - - public void LoadFile(String file, String protocol, String format) - { - LoadingThread loader = new LoadingThread(file, protocol, format); - loader.start(); - } - - class LoadingThread extends Thread - { - String file, protocol, format; - - public LoadingThread(String file, String protocol, String format) - { - this.file = file; - this.protocol = protocol; - this.format = format; - } - public void run() - { - SequenceI [] sequences = null; - - 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{ - 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); - - } - } - - - 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) - 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); - } - - 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_actionPerformed(ActionEvent e) - { - if(jalview.bin.Jalview.applet!=null) - jalview.bin.Jalview.applet.destroy(); - else - 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 - { - 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(); - } - - 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"); - 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); - } - - } - - - 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) - { - String choice = chooser.getSelectedFile().getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent()); - Jalview2XML.LoadJalviewAlign(choice); - } - } -} - - +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +import jalview.io.*; +import java.awt.*; +import java.awt.datatransfer.*; +import java.awt.dnd.*; +import java.awt.event.*; +import java.lang.reflect.Constructor; +import java.util.*; + +import javax.swing.*; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Desktop + extends jalview.jbgui.GDesktop implements DropTargetListener, + ClipboardOwner +{ + /** DOCUMENT ME!! */ + public static Desktop instance; + + //Need to decide if the Memory Usage is to be included in + //Next release or not. + public static MyDesktopPane desktop; + // public static JDesktopPane desktop; + + + static int openFrameCount = 0; + static final int xOffset = 30; + static final int yOffset = 30; + public static jalview.ws.Discoverer discoverer; + + public static Object[] jalviewClipboard; + public static boolean internalCopy = false; + + static int fileLoadingCount = 0; + + /** + * Creates a new Desktop object. + */ + public Desktop() + { + instance = this; + doVamsasClientCheck(); + doGroovyCheck(); + + + setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); + setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",false); + desktop = new MyDesktopPane(selmemusage); + showMemusage.setSelected(selmemusage); + desktop.setBackground(Color.white); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(desktop, BorderLayout.CENTER); + 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()); + + 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), + Integer.parseInt(width), Integer.parseInt(height)); + } + else + { + setBounds( (int) (screenSize.width - 900) / 2, + (int) (screenSize.height - 650) / 2, 900, 650); + } + + this.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + quit(); + } + }); + + this.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if(SwingUtilities.isRightMouseButton(evt)) + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + }); + + + this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); + + /////////Add a splashscreen on startup + /////////Add a splashscreen on startup + new SplashScreen(); + + + discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed. + } + + private void doVamsasClientCheck() + { + if (jalview.bin.Cache.vamsasJarsPresent()) + { + setupVamsasDisconnectedGui(); + VamsasMenu.setVisible(true); + final Desktop us = this; + VamsasMenu.addMenuListener(new MenuListener() { + // this listener remembers when the menu was first selected, and + // doesn't rebuild the session list until it has been cleared and + // reselected again. + boolean refresh=true; + public void menuCanceled(MenuEvent e) + { + refresh=true; + } + + public void menuDeselected(MenuEvent e) + { + refresh = true; + } + + public void menuSelected(MenuEvent e) + { + if (refresh) + { + us.buildVamsasStMenu(); + refresh=false; + } + } + }); + vamsasStart.setVisible(true); + } + } + + void showPasteMenu(int x, int y) + { + JPopupMenu popup = new JPopupMenu(); + JMenuItem item = new JMenuItem("Paste To New Window"); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + paste(); + } + }); + + popup.add(item); + popup.show(this, x, y); + } + + public void paste() + { + try + { + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents != null) + { + String file = (String) contents + .getTransferData(DataFlavor.stringFlavor); + + String format = new IdentifyFile().Identify(file, + FormatAdapter.PASTE); + + new FileLoader().LoadFile(file, FormatAdapter.PASTE, format); + + } + } + catch (Exception ex) + { + System.out.println("Unable to paste alignment from system clipboard:\n" + + ex); + } + } + + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + */ + public static synchronized void addInternalFrame(final JInternalFrame frame, + String title, int w, int h) + { + addInternalFrame(frame, title, w, h, true); + } + + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + * @param resizable DOCUMENT ME! + */ + public static synchronized void addInternalFrame(final JInternalFrame frame, + String title, int w, int h, boolean resizable) + { + + frame.setTitle(title); + if (frame.getWidth() < 1 || frame.getHeight() < 1) + { + frame.setSize(w, h); + } + // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN + // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN + // IF JALVIEW IS RUNNING HEADLESS + ///////////////////////////////////////////////// + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + return; + } + + openFrameCount++; + + frame.setVisible(true); + frame.setClosable(true); + frame.setResizable(resizable); + frame.setMaximizable(resizable); + frame.setIconifiable(resizable); + frame.setFrameIcon(null); + + if (frame.getX() < 1 && frame.getY() < 1) + { + frame.setLocation(xOffset * openFrameCount, + yOffset * ( (openFrameCount - 1) % 10) + yOffset); + } + + final JMenuItem menuItem = new JMenuItem(title); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameActivated(javax.swing.event. + InternalFrameEvent evt) + { + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } + + } + + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + PaintRefresher.RemoveComponent(frame); + openFrameCount--; + windowMenu.remove(menuItem); + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } + System.gc(); + } + ; + }); + + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + try + { + frame.setSelected(true); + frame.setIcon(false); + } + catch (java.beans.PropertyVetoException ex) + { + + } + } + }); + + windowMenu.add(menuItem); + + desktop.add(frame); + frame.toFront(); + try + { + frame.setSelected(true); + frame.requestFocus(); + } + catch (java.beans.PropertyVetoException ve) + {} + } + + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + if (!internalCopy) + { + Desktop.jalviewClipboard = null; + } + + internalCopy = false; + } + + public void dragEnter(DropTargetDragEvent evt) + {} + + public void dragExit(DropTargetEvent evt) + {} + + public void dragOver(DropTargetDragEvent evt) + {} + + public void dropActionChanged(DropTargetDragEvent evt) + {} + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void drop(DropTargetDropEvent evt) + { + Transferable t = evt.getTransferable(); + java.util.List files = null; + + try + { + DataFlavor uriListFlavor = new DataFlavor( + "text/uri-list;class=java.lang.String"); + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + //Works on Windows and MacOSX + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + files = (java.util.List) t.getTransferData(DataFlavor. + javaFileListFlavor); + } + else if (t.isDataFlavorSupported(uriListFlavor)) + { + // This is used by Unix drag system + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + String data = (String) t.getTransferData(uriListFlavor); + files = new java.util.ArrayList(1); + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, + "\r\n"); + st.hasMoreTokens(); ) + { + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + + java.net.URI uri = new java.net.URI(s); + java.io.File file = new java.io.File(uri); + files.add(file); + } + } + } + catch (Exception e) + {} + + if (files != null) + { + try + { + for (int i = 0; i < files.size(); i++) + { + String file = files.get(i).toString(); + String protocol = FormatAdapter.FILE; + String format = null; + + if (file.endsWith(".jar")) + { + format = "Jalview"; + + } + else + { + format = new IdentifyFile().Identify(file, + protocol); + } + + new FileLoader().LoadFile(file, protocol, format); + + } + } + catch (Exception ex) + {} + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), + jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, + jalview.io.AppletFormatAdapter.READABLE_FNAMES, + 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) + { + 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 = new IdentifyFile().Identify(choice, FormatAdapter.FILE); + } + + if (viewport != null) + { + new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format); + } + else + { + new FileLoader().LoadFile(choice, FormatAdapter.FILE, format); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputURLMenuItem_actionPerformed(AlignViewport viewport) + { + // This construct allows us to have a wider textfield + // for viewing + JLabel label = new JLabel("Enter URL of Input File"); + final JComboBox history = new JComboBox(); + + JPanel panel = new JPanel(new GridLayout(2, 1)); + panel.add(label); + panel.add(history); + history.setPreferredSize(new Dimension(400, 20)); + history.setEditable(true); + history.addItem("http://www."); + + String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); + + StringTokenizer st; + + if (historyItems != null) + { + st = new StringTokenizer(historyItems, "\t"); + + while (st.hasMoreTokens()) + { + history.addItem(st.nextElement()); + } + } + + int reply = JOptionPane.showInternalConfirmDialog(desktop, + panel, "Input Alignment From URL", + JOptionPane.OK_CANCEL_OPTION); + + if (reply != JOptionPane.OK_OPTION) + { + return; + } + + String url = history.getSelectedItem().toString(); + + if (url.toLowerCase().endsWith(".jar")) + { + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview"); + } + else + { + new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview"); + } + } + else + { + String format = new IdentifyFile().Identify(url, FormatAdapter.URL); + + if (format.equals("URL NOT FOUND")) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't locate " + url, + "URL not found", + JOptionPane.WARNING_MESSAGE); + + return; + } + + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format); + } + else + { + new FileLoader().LoadFile(url, FormatAdapter.URL, format); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(viewport); + Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); + } + + /* + * 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); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void aboutMenuItem_actionPerformed(ActionEvent e) + { + StringBuffer message = new StringBuffer("JalView version " + + jalview.bin.Cache.getProperty( + "VERSION") + + "; last updated: " + + jalview.bin. + Cache.getDefault("BUILD_DATE", + "unknown")); + + if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( + jalview.bin.Cache.getProperty("VERSION"))) + { + message.append("\n\n!! Jalview version " + + jalview.bin.Cache.getProperty("LATEST_VERSION") + + + " is available for download from http://www.jalview.org !!\n"); + + } + + message.append("\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 20;426-7."); + + JOptionPane.showInternalMessageDialog(Desktop.desktop, + + message.toString(), "About Jalview", + JOptionPane.INFORMATION_MESSAGE); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void documentationMenuItem_actionPerformed(ActionEvent e) + { + 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.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + {} + } + + public void closeAll_actionPerformed(ActionEvent e) + { + JInternalFrame[] frames = desktop.getAllFrames(); + for (int i = 0; i < frames.length; i++) + { + try + { + frames[i].setClosed(true); + } + catch (java.beans.PropertyVetoException ex) + {} + } + System.out.println("ALL CLOSED"); + + } + + public void raiseRelated_actionPerformed(ActionEvent e) + { + reorderAssociatedWindows(false, false); + } + + public void minimizeAssociated_actionPerformed(ActionEvent e) + { + reorderAssociatedWindows(true, false); + } + + void closeAssociatedWindows() + { + reorderAssociatedWindows(false, true); + } + + /* (non-Javadoc) + * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent) + */ + protected void garbageCollect_actionPerformed(ActionEvent e) + { + // We simply collect the garbage + jalview.bin.Cache.log.debug("Collecting garbage..."); + System.gc(); + jalview.bin.Cache.log.debug("Finished garbage collection."); + } + + /* (non-Javadoc) + * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent) + */ + protected void showMemusage_actionPerformed(ActionEvent e) + { + desktop.showMemoryUsage(showMemusage.isSelected()); + } + + void reorderAssociatedWindows(boolean minimize, boolean close) + { + JInternalFrame[] frames = desktop.getAllFrames(); + if (frames == null || frames.length < 1) + { + return; + } + + AlignViewport source = null, target = null; + if (frames[0] instanceof AlignFrame) + { + source = ( (AlignFrame) frames[0]).getCurrentView(); + } + else if (frames[0] instanceof TreePanel) + { + source = ( (TreePanel) frames[0]).getViewPort(); + } + else if (frames[0] instanceof PCAPanel) + { + source = ( (PCAPanel) frames[0]).av; + } + else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) + { + source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av; + } + + if (source != null) + { + for (int i = 0; i < frames.length; i++) + { + target = null; + if (frames[i] == null) + { + continue; + } + if (frames[i] instanceof AlignFrame) + { + target = ( (AlignFrame) frames[i]).getCurrentView(); + } + else if (frames[i] instanceof TreePanel) + { + target = ( (TreePanel) frames[i]).getViewPort(); + } + else if (frames[i] instanceof PCAPanel) + { + target = ( (PCAPanel) frames[i]).av; + } + else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) + { + target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av; + } + + if (source == target) + { + try + { + if (close) + { + frames[i].setClosed(true); + } + else + { + frames[i].setIcon(minimize); + if (!minimize) + { + frames[i].toFront(); + } + } + + } + catch (java.beans.PropertyVetoException ex) + {} + } + } + } + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void preferences_actionPerformed(ActionEvent e) + { + new Preferences(); + } + + /** + * 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"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + java.io.File choice = chooser.getSelectedFile(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + new Jalview2XML().SaveState(choice); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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) + { + String choice = chooser.getSelectedFile().getAbsolutePath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + new Jalview2XML().LoadJalviewAlign(choice); + } + } + + public void inputSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(null); + } + + JPanel progressPanel; + + public void startLoading(final String fileName) + { + if (fileLoadingCount == 0) + { + addProgressPanel("Loading File: " + fileName + " "); + + } + fileLoadingCount++; + } + private JProgressBar addProgressPanel(String string) + { + if (progressPanel==null) + { + progressPanel = new JPanel(new BorderLayout()); + totalProgressCount=0; + } + JProgressBar progressBar = new JProgressBar(); + progressBar.setIndeterminate(true); + + progressPanel.add(new JLabel(string), + BorderLayout.WEST); + + progressPanel.add(progressBar, BorderLayout.CENTER); + + instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + totalProgressCount++; + validate(); + return progressBar; + } + int totalProgressCount=0; + private void removeProgressPanel(JProgressBar progbar) + { + if (progressPanel!=null) + { + progressPanel.remove(progbar); + if (--totalProgressCount<1) + { + this.getContentPane().remove(progressPanel); + progressPanel = null; + } + } + validate(); + } + public void stopLoading() + { + fileLoadingCount--; + if (fileLoadingCount < 1) + { + if (progressPanel != null) + { + this.getContentPane().remove(progressPanel); + progressPanel = null; + } + fileLoadingCount = 0; + } + validate(); + } + public static int getViewCount(String viewId) + { + int count = 0; + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + for (int t = 0; t < frames.length; t++) + { + if (frames[t] instanceof AlignFrame) + { + AlignFrame af = (AlignFrame) frames[t]; + for (int a = 0; a < af.alignPanels.size(); a++) + { + if (viewId.equals( + ( (AlignmentPanel) af.alignPanels.elementAt(a)).av. + getSequenceSetId()) + ) + { + count++; + } + } + } + } + + return count; + } + + public void explodeViews(AlignFrame af) + { + int size = af.alignPanels.size(); + if (size < 2) + { + return; + } + + for (int i = 0; i < size; i++) + { + AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i); + AlignFrame newaf = new AlignFrame(ap); + if (ap.av.explodedPosition != null && + !ap.av.explodedPosition.equals(af.getBounds())) + { + newaf.setBounds(ap.av.explodedPosition); + } + + ap.av.gatherViewsHere = false; + + addInternalFrame(newaf, af.getTitle(), + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + + } + + public void gatherViews(AlignFrame source) + { + source.viewport.gatherViewsHere = true; + source.viewport.explodedPosition = source.getBounds(); + JInternalFrame[] frames = desktop.getAllFrames(); + String viewId = source.viewport.sequenceSetID; + + for (int t = 0; t < frames.length; t++) + { + if (frames[t] instanceof AlignFrame && frames[t] != source) + { + AlignFrame af = (AlignFrame) frames[t]; + boolean gatherThis = false; + for (int a = 0; a < af.alignPanels.size(); a++) + { + AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a); + if (viewId.equals(ap.av.getSequenceSetId())) + { + gatherThis = true; + ap.av.gatherViewsHere = false; + ap.av.explodedPosition = af.getBounds(); + source.addAlignmentPanel(ap, false); + } + } + + if (gatherThis) + { + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + } + } + } + + } + + jalview.gui.VamsasApplication v_client = null; + public void vamsasImport_actionPerformed(ActionEvent e) + { + if (v_client==null) + { + // Load and try to start a session. + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Open a saved VAMSAS session"); + chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session."); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + try { + v_client = new jalview.gui.VamsasApplication(this, + chooser.getSelectedFile()); + } catch (Exception ex) + { + jalview.bin.Cache.log.error("New vamsas session from existing session file failed:",ex); + return; + } + setupVamsasConnectedGui(); + v_client.initial_update(); // TODO: thread ? + } + }else { + jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported."); + } + } + + public void vamsasStart_actionPerformed(ActionEvent e) + { + if (v_client == null) + { + // Start a session. + // we just start a default session for moment. + /* + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Load Vamsas file"); + chooser.setToolTipText("Import"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + v_client = new jalview.gui.VamsasApplication(this, + chooser.getSelectedFile()); + * + */ + v_client = new VamsasApplication(this); + setupVamsasConnectedGui(); + v_client.initial_update(); // TODO: thread ? + } + else + { + // store current data in session. + v_client.push_update(); // TODO: thread + } + } + + protected void setupVamsasConnectedGui() + { + vamsasStart.setText("Session Update"); + vamsasSave.setVisible(true); + vamsasStop.setVisible(true); + vamsasImport.setVisible(false); // Document import to existing session is not possible for vamsas-client-1.0. + } + protected void setupVamsasDisconnectedGui() + { + vamsasSave.setVisible(false); + vamsasStop.setVisible(false); + vamsasImport.setVisible(true); + vamsasStart.setText("New Vamsas Session..."); + } + + public void vamsasStop_actionPerformed(ActionEvent e) + { + if (v_client != null) + { + v_client.end_session(); + v_client = null; + setupVamsasDisconnectedGui(); + } + } + protected void buildVamsasStMenu() + { + if (v_client == null) + { + String[] sess = null; + try + { + sess = VamsasApplication.getSessionList(); + } catch (Exception e) + { + jalview.bin.Cache.log.warn( + "Problem getting current sessions list.", e); + sess = null; + } + if (sess != null) + { + jalview.bin.Cache.log.debug("Got current sessions list: " + + sess.length + " entries."); + VamsasStMenu.removeAll(); + for (int i = 0; i < sess.length; i++) + { + JMenuItem sessit = new JMenuItem(); + sessit.setText(sess[i]); + sessit.setToolTipText("Connect to session " + sess[i]); + final Desktop dsktp = this; + final String mysesid = sess[i]; + sessit.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + if (dsktp.v_client == null) + { + Thread rthr = new Thread(new Runnable() { + + public void run() + { + dsktp.v_client = new VamsasApplication(dsktp, mysesid); + dsktp.setupVamsasConnectedGui(); + dsktp.v_client.initial_update(); + } + + }); + rthr.start(); + } + }; + }); + VamsasStMenu.add(sessit); + } + // don't show an empty menu. + VamsasStMenu.setVisible(sess.length>0); + + } + else + { + jalview.bin.Cache.log.debug("No current vamsas sessions."); + VamsasStMenu.removeAll(); + VamsasStMenu.setVisible(false); + } + } else { + // Not interested in the content. Just hide ourselves. + VamsasStMenu.setVisible(false); + } + } + public void vamsasSave_actionPerformed(ActionEvent e) + { + if (v_client != null) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), new String[] + {"vdj"}, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + new String[] + {"Vamsas Document"}, "Vamsas Document"); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save Vamsas Document Archive"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + java.io.File choice = chooser.getSelectedFile(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + String warnmsg=null; + String warnttl=null; + try { + v_client.vclient.storeDocument(choice); + } + catch (Error ex) + { + warnttl = "Serious Problem saving Vamsas Document"; + warnmsg = ex.toString(); + jalview.bin.Cache.log.error("Error Whilst saving document to "+choice,ex); + + } + catch (Exception ex) + { + warnttl = "Problem saving Vamsas Document."; + warnmsg = ex.toString(); + jalview.bin.Cache.log.warn("Exception Whilst saving document to "+choice,ex); + + } + if (warnmsg!=null) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + + warnmsg, warnttl, + JOptionPane.ERROR_MESSAGE); + } + } + } + } + JProgressBar vamUpdate = null; + /** + * hide vamsas user gui bits when a vamsas document event is being handled. + * @param b true to hide gui, false to reveal gui + */ + public void setVamsasUpdate(boolean b) + { + jalview.bin.Cache.log.debug("Setting gui for Vamsas update " + + (b ? "in progress" : "finished")); + + if (vamUpdate!=null) + { + this.removeProgressPanel(vamUpdate); + } + if (b) + { + vamUpdate = this.addProgressPanel("Updating vamsas session"); + } + vamsasStart.setVisible(!b); + vamsasStop.setVisible(!b); + vamsasSave.setVisible(!b); + } + + public JInternalFrame[] getAllFrames() + { + return desktop.getAllFrames(); + } + + + /** + * Checks the given url to see if it gives a response indicating that + * the user should be informed of a new questionnaire. + * @param url + */ + public void checkForQuestionnaire(String url) + { + UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); + javax.swing.SwingUtilities.invokeLater(jvq); + } + /** + * Proxy class for JDesktopPane which optionally + * displays the current memory usage and highlights + * the desktop area with a red bar if free memory runs low. + * @author AMW + */ + class MyDesktopPane extends JDesktopPane implements Runnable + { + + boolean showMemoryUsage = false; + Runtime runtime; + java.text.NumberFormat df; + + float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage; + + public MyDesktopPane(boolean showMemoryUsage) + { + showMemoryUsage(showMemoryUsage); + } + + public void showMemoryUsage(boolean showMemoryUsage) + { + this.showMemoryUsage = showMemoryUsage; + if (showMemoryUsage) + { + Thread worker = new Thread(this); + worker.start(); + } + } + + public void run() + { + df = java.text.NumberFormat.getNumberInstance(); + df.setMaximumFractionDigits(2); + runtime = Runtime.getRuntime(); + + while (showMemoryUsage) + { + try + { + Thread.sleep(3000); + maxMemory = runtime.maxMemory() / 1048576f; + allocatedMemory = runtime.totalMemory() / 1048576f; + freeMemory = runtime.freeMemory() / 1048576f; + totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); + + percentUsage = (totalFreeMemory / maxMemory) * 100; + + // if (percentUsage < 20) + { + // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red); + // instance.set.setBorder(border1); + } + repaint(); + + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + public void paintComponent(Graphics g) + { + if(showMemoryUsage) + { + if (percentUsage < 20) + g.setColor(Color.red); + + g.drawString("Total Free Memory: " + df.format(totalFreeMemory) + + "MB; Max Memory: " + df.format(maxMemory) + + "MB; " + df.format(percentUsage) + "%", 10, + getHeight() - g.getFontMetrics().getHeight()); + } + } + + + + } + protected JMenuItem groovyShell; + public void doGroovyCheck() { + if (jalview.bin.Cache.groovyJarsPresent()) + { + groovyShell = new JMenuItem(); + groovyShell.setText("Groovy Console..."); + groovyShell.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) { + groovyShell_actionPerformed(e); + } + }); + toolsMenu.add(groovyShell); + groovyShell.setVisible(true); + } + } + /** + * Accessor method to quickly get all the AlignmentFrames + * loaded. + */ + public static AlignFrame[] getAlignframes() { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + + if (frames == null) + { + return null; + } + Vector avp=new Vector(); + try + { + //REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) + { + AlignFrame af = (AlignFrame) frames[i]; + avp.addElement(af); + } + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + if (avp.size()==0) + { + return null; + } + AlignFrame afs[] = new AlignFrame[avp.size()]; + for (int i=0,j=avp.size(); i