X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9d58c7badef5f205da54936e314b68d820a49115;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=05486468880ba3346b0493cd433f1073ab66deea;hpb=b618755c67d798ace34ebd6d0f384e913e8574c9;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 0548646..9d58c7b 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,401 +1,669 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * - * AM Waterhouse - *******************/ - - + * 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.gui.*; import jalview.io.*; -import jalview.datamodel.*; -import javax.swing.*; + import java.awt.*; -import java.awt.event.*; +import java.awt.datatransfer.*; import java.awt.dnd.*; +import java.awt.event.*; +import java.util.*; + import javax.swing.*; -import java.awt.datatransfer.*; -import jalview.bin.Cache; -public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Desktop extends jalview.jbgui.GDesktop + implements DropTargetListener, ClipboardOwner { - 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) + /** DOCUMENT ME!! */ + public static Desktop instance; + 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; + + static int fileLoadingCount= 0; + + /** + * Creates a new Desktop object. + */ + public Desktop() + { + instance = this; + + 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 "+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.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); + frame.setLocation((int) ((getWidth() - 750) / 2), + (int) ((getHeight() - 160) / 2)); + + addInternalFrame(frame, "", 750, 160, false); + + discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed. + + } + + /** + * 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")) { - image = java.awt.Toolkit.getDefaultToolkit().createImage(url); - MediaTracker mt = new MediaTracker(this); - mt.addImage(image, 0); - mt.waitForID(0); - setIconImage(image); + return; } - }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); + 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) + { + 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); + frame.requestFocus(); + }catch(java.beans.PropertyVetoException ve) + {} + } + + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + Desktop.jalviewClipboard = null; + } + public void dragEnter(DropTargetDragEvent evt) + {} - // This line prevents Windows Look&Feel resizing all new windows to maximum - // if previous window was maximised - desktop.setDesktopManager( new DefaultDesktopManager() ); + public void dragExit(DropTargetEvent evt) + {} + public void dragOver(DropTargetDragEvent evt) + {} - 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 dropActionChanged(DropTargetDragEvent evt) + {} - if(x!=null && y!=null && width!=null && height!=null) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void drop(DropTargetDropEvent evt) { - setBounds( Integer.parseInt(x), Integer.parseInt(y), - Integer.parseInt(width), Integer.parseInt(height)); + 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) + { + e.printStackTrace(); + } + + 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) + { + ex.printStackTrace(); + } + } } - 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() + /** + * 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"); + + 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) { - public void actionPerformed(ActionEvent e) + // 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) { - try{ frame.setSelected(true); frame.setIcon(false); } - catch(java.beans.PropertyVetoException ex){}; + st = new StringTokenizer(historyItems, "\t"); + + while (st.hasMoreTokens()) + { + history.addItem(st.nextElement()); + } } - }); - frame.setVisible(true); - windowMenu.add(menuItem); - } + 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); + } - 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 + /* + * 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"))) { - String format = jalview.io.IdentifyFile.Identify(file, protocol); - LoadFile(file, protocol, format); + message.append("\n\n!! Jalview version " + + jalview.bin.Cache.getProperty("LATEST_VERSION") + + " is available for download from http://www.jalview.org !!\n"); + } - } - - }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(); - int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File", - JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.PLAIN_MESSAGE, - null, - new Object[]{"Accept", "Cancel", }, null); - - - if(accept == JOptionPane.YES_OPTION) - { - String format = IdentifyFile.Identify(cap.getText(), "Paste"); - SequenceI [] sequences = null; - - if (FormatAdapter.formats.contains( format )) - sequences = FormatAdapter.readFile(cap.getText(), "Paste", format); - - - if(sequences!=null) + + 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) + { + ex.printStackTrace(); + } + } + + /** + * 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 vamsasLoad_actionPerformed(ActionEvent e) + { + 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) { - AlignFrame af = new AlignFrame(new Alignment(sequences)); - af.currentFileFormat = format; - addInternalFrame(af, "Cut & Paste input - "+format, - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); - af.statusBar.setText("Successfully pasted alignment file"); + jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null); + vs.load( + chooser.getSelectedFile().getAbsolutePath() + ); } - else - JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n" - +"Formats currently supported are\n" - +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM", - "Error parsing text", JOptionPane.WARNING_MESSAGE); - } - } + }*/ -/* -* 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." - +"\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); - } - } -} + public void inputSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(null); + } + + JPanel progressPanel; + + public void startLoading(final String fileName) + { + if (fileLoadingCount == 0) + { + progressPanel = new JPanel(new BorderLayout()); + JProgressBar progressBar = new JProgressBar(); + progressBar.setIndeterminate(true); + + progressPanel.add(new JLabel("Loading File: " + fileName + " "), + BorderLayout.WEST); + + progressPanel.add(progressBar, BorderLayout.CENTER); + + instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + } + fileLoadingCount++; + validate(); + } + + public void stopLoading() + { + fileLoadingCount--; + if (fileLoadingCount < 1) + { + if(progressPanel!=null) + { + this.getContentPane().remove(progressPanel); + progressPanel = null; + } + fileLoadingCount = 0; + } + validate(); + } + +}