X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=263eb1876260d2a832528d2ea99538b57a157335;hb=495723ac6f2a30ba8d7f5e65b0723e2ba8f121e1;hp=037a7a9928b9f304d7235a87374fd0d4aa1aa662;hpb=1ee3386743590a8b6d98f6c8839eae1b390c7f3b;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 037a7a9..263eb18 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -19,529 +19,1147 @@ 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.*; - /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ -public class Desktop extends jalview.jbgui.GDesktop - implements DropTargetListener +public class Desktop + extends jalview.jbgui.GDesktop implements DropTargetListener, + ClipboardOwner { - /** DOCUMENT ME!! */ - public static JDesktopPane desktop; - static int openFrameCount = 0; - static final int xOffset = 30; - static final int yOffset = 30; - public static jalview.ws.Discoverer discoverer; - /** - * Creates a new Desktop object. - */ - public Desktop() - { - Image image = null; + /** DOCUMENT ME!! */ + public static Desktop instance; - try - { - java.net.URL url = getClass().getResource("/images/logo.gif"); + //Need to decide if the Memory Usage is to be included in + //Next release or not. + // public static MyDesktopPane desktop; + public static JDesktopPane desktop; - if (url != null) - { - image = java.awt.Toolkit.getDefaultToolkit().createImage(url); - MediaTracker mt = new MediaTracker(this); - mt.addImage(image, 0); - mt.waitForID(0); - setIconImage(image); + 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); + + desktop = new JDesktopPane(); + 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()); } - } - catch (Exception ex) + } + }); + + + 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()) + { + VamsasMenu.setVisible(true); + vamsasLoad.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(); } - 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"); + 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(); + } + ; + }); - if ((x != null) && (y != null) && (width != null) && (height != null)) + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + try { - setBounds(Integer.parseInt(x), Integer.parseInt(y), - Integer.parseInt(width), Integer.parseInt(height)); + frame.setSelected(true); + frame.setIcon(false); } - else + catch (java.beans.PropertyVetoException ex) { - setBounds((int) (screenSize.width - 900) / 2, - (int) (screenSize.height - 650) / 2, 900, 650); + } + } + }); - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - quit(); - } - }); + 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; + } - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); + public void dragEnter(DropTargetDragEvent evt) + {} - /////////Add a splashscreen on startup - /////////Add a splashscreen on startup - JInternalFrame frame = new JInternalFrame(); + public void dragExit(DropTargetEvent evt) + {} - SplashScreen splash = new SplashScreen(frame, image); - frame.setContentPane(splash); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.setLocation((int) ((getWidth() - 750) / 2), - (int) ((getHeight() - 160) / 2)); + public void dragOver(DropTargetDragEvent evt) + {} - addInternalFrame(frame, "", 750, 160, false); + public void dropActionChanged(DropTargetDragEvent evt) + {} - discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed. + /** + * 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) + {} - /** - * 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) + if (files != null) { - addInternalFrame(frame, title, w, h, true); + 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"), + 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"); - /** - * 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) + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - frame.setTitle(title); - if(frame.getWidth()<1 || frame.getHeight()<1) + String format = null; + if (chooser.getSelectedFormat().equals("Jalview")) { - frame.setSize(w, h); + format = "Jalview"; } - // 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")) + else { - return; + 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"); - openFrameCount++; - - frame.setVisible(true); - frame.setClosable(true); - frame.setResizable(resizable); - frame.setMaximizable(resizable); - frame.setIconifiable(resizable); - frame.setFrameIcon(null); + while (st.hasMoreTokens()) + { + history.addItem(st.nextElement()); + } + } - if (frame.getX()<1 && frame.getY()<1) - { - frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset); - } + int reply = JOptionPane.showInternalConfirmDialog(desktop, + panel, "Input Alignment From URL", + JOptionPane.OK_CANCEL_OPTION); - 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); - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - itf.requestFocus(); - } - ; - }); - - 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); - }catch(java.beans.PropertyVetoException ve) - {} + if (reply != JOptionPane.OK_OPTION) + { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void dragEnter(DropTargetDragEvent evt) + 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); - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void dragExit(DropTargetEvent evt) + 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"); + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void dragOver(DropTargetDragEvent evt) + 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"); + + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void dropActionChanged(DropTargetDragEvent evt) + public void raiseRelated_actionPerformed(ActionEvent e) + { + reorderAssociatedWindows(false, false); + } + + public void minimizeAssociated_actionPerformed(ActionEvent e) + { + reorderAssociatedWindows(true, false); + } + + void closeAssociatedWindows() + { + reorderAssociatedWindows(false, true); + } + + void reorderAssociatedWindows(boolean minimize, boolean close) + { + JInternalFrame[] frames = desktop.getAllFrames(); + if (frames == null || frames.length < 1) { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void drop(DropTargetDropEvent evt) + 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) { - Transferable t = evt.getTransferable(); + source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av; + } - if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + if (source != null) + { + for (int i = 0; i < frames.length; i++) + { + target = null; + if (frames[i] == null) { - return; + continue; } - - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - - try + if (frames[i] instanceof AlignFrame) { - 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); - } + target = ( (AlignFrame) frames[i]).getCurrentView(); } - catch (Exception ex) + else if (frames[i] instanceof TreePanel) { - ex.printStackTrace(); + target = ( (TreePanel) frames[i]).getViewPort(); } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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) + else if (frames[i] instanceof PCAPanel) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + target = ( (PCAPanel) frames[i]).av; + } + else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) + { + target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av; + } - String format = null; - if (chooser.getSelectedFormat().equals("Jalview")) + if (source == target) + { + try + { + if (close) { - format = "Jalview"; + frames[i].setClosed(true); } else { - format = IdentifyFile.Identify(choice, "File"); + frames[i].setIcon(minimize); + if (!minimize) + { + frames[i].toFront(); + } } - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); - LoadFile(choice, "File", format); + } + catch (java.beans.PropertyVetoException ex) + {} } + } } - - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - * @param protocol DOCUMENT ME! - * @param format DOCUMENT ME! - */ - public void LoadFile(String file, String protocol, String format) + } + + /** + * 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) { - FileLoader fileLoader = new FileLoader(); - fileLoader.LoadFile(file, protocol, format); + String choice = chooser.getSelectedFile().getAbsolutePath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + new Jalview2XML().LoadJalviewAlign(choice); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void inputURLMenuItem_actionPerformed(ActionEvent e) + /* public void vamsasLoad_actionPerformed(ActionEvent e) { - Object reply = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Enter url of input file", "Input alignment from URL", - JOptionPane.QUESTION_MESSAGE, null, null, "http://www."); + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); - if (reply == null) - { - return; - } + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Load Vamsas file"); + chooser.setToolTipText("Import"); - String url = reply.toString().trim(); + int value = chooser.showOpenDialog(this); - if (url.toLowerCase().endsWith(".jar")) - { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview"); - Jalview2XML.LoadJalviewAlign(url); - } - else - { + if (value == JalviewFileChooser.APPROVE_OPTION) + { + jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null); + vs.load( + chooser.getSelectedFile().getAbsolutePath() + ); + } - 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; - } + public void inputSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(null); + } - LoadFile(url, "URL", format); - } - } + JPanel progressPanel; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void inputTextboxMenuItem_actionPerformed(ActionEvent e) + public void startLoading(final String fileName) + { + if (fileLoadingCount == 0) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(); - Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); - } + progressPanel = new JPanel(new BorderLayout()); + JProgressBar progressBar = new JProgressBar(); + progressBar.setIndeterminate(true); + + progressPanel.add(new JLabel("Loading File: " + fileName + " "), + BorderLayout.WEST); - /* - * Exit the program - */ - public void quit() + progressPanel.add(progressBar, BorderLayout.CENTER); + + instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + } + fileLoadingCount++; + validate(); + } + + public void stopLoading() + { + fileLoadingCount--; + if (fileLoadingCount < 1) { - 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); + 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++; + } + } + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void aboutMenuItem_actionPerformed(ActionEvent e) + return count; + } + + public void explodeViews(AlignFrame af) + { + int size = af.alignPanels.size(); + if (size < 2) { - StringBuffer message = new StringBuffer("JalView 2005 version " + - jalview.bin.Cache.getProperty( - "VERSION") + - "; last updated: " + - jalview.bin. - Cache.getDefault("BUILD_DATE", "unknown")); + return; + } - if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( - jalview.bin.Cache.getProperty("VERSION"))) + 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())) { - message.append("\n\n!! Jalview version " - + jalview.bin.Cache.getProperty("LATEST_VERSION") - + " is available for download from http://www.jalview.org !!\n"); - + newaf.setBounds(ap.av.explodedPosition); } - 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 12;426-7."); + ap.av.gatherViewsHere = false; - JOptionPane.showInternalMessageDialog(Desktop.desktop, - - message.toString(), "About Jalview", - JOptionPane.INFORMATION_MESSAGE); + addInternalFrame(newaf, af.getTitle(), + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void documentationMenuItem_actionPerformed(ActionEvent e) + 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++) { - try + 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++) { - 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); + 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); + } } - catch (Exception ex) + + if (gatherThis) { - ex.printStackTrace(); + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); } + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void preferences_actionPerformed(ActionEvent e) + } + + jalview.gui.VamsasClient v_client = null; + public void vamsasLoad_actionPerformed(ActionEvent e) + { + if (v_client == null) { - new Preferences(); + // Start a session. + 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.VamsasClient(this, + chooser.getSelectedFile()); + this.vamsasLoad.setText("Session Update"); + this.vamsasStop.setVisible(true); + v_client.initial_update(); + v_client.startWatcher(); + } + } + else + { + // store current data in session. + v_client.push_update(); + } + } + + public void vamsasStop_actionPerformed(ActionEvent e) + { + if (v_client != null) + { + v_client.end_session(); + v_client = null; + this.vamsasStop.setVisible(false); + this.vamsasLoad.setText("Start Vamsas Session..."); + } + } + + /** + * 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")); + vamsasLoad.setVisible(!b); + vamsasStop.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); + } + + /*DISABLED + 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(); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveState_actionPerformed(ActionEvent e) + public void run() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "jar" }, - new String[] { "Jalview Project" }, "Jalview Project"); + df = java.text.NumberFormat.getNumberInstance(); + df.setMaximumFractionDigits(2); + runtime = Runtime.getRuntime(); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save State"); + while (showMemoryUsage) + { + try + { + Thread.sleep(3000); + maxMemory = runtime.maxMemory() / 1048576f; + allocatedMemory = runtime.totalMemory() / 1048576f; + freeMemory = runtime.freeMemory() / 1048576f; + totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); - int value = chooser.showSaveDialog(this); + percentUsage = (totalFreeMemory / maxMemory) * 100; - if (value == JalviewFileChooser.APPROVE_OPTION) + // if (percentUsage < 20) + { + // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red); + // instance.set.setBorder(border1); + } + repaint(); + + } + catch (Exception ex) { - java.io.File choice = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - Jalview2XML.SaveState(choice); + ex.printStackTrace(); } + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void loadState_actionPerformed(ActionEvent e) + public void paintComponent(Graphics g) { - 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(showMemoryUsage) + { + if (percentUsage < 20) + g.setColor(Color.red); - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - Jalview2XML.LoadJalviewAlign(choice); - } + 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 Shell..."); + 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. + */ + protected 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