-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.io.*;\r
-\r
-import java.awt.*;\r
-import java.awt.datatransfer.*;\r
-import java.awt.dnd.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Desktop extends jalview.jbgui.GDesktop\r
- implements DropTargetListener, ClipboardOwner\r
-{\r
- /** DOCUMENT ME!! */\r
- public static Desktop instance;\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30;\r
- static final int yOffset = 30;\r
- public static jalview.ws.Discoverer discoverer;\r
-\r
- public static Object [] jalviewClipboard;\r
-\r
-\r
- /**\r
- * Creates a new Desktop object.\r
- */\r
- public Desktop()\r
- {\r
- instance = this;\r
-\r
- Image image = null;\r
-\r
- try\r
- {\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\r
-\r
- if (url != null)\r
- {\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
-\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- setIconImage(image);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- desktop = new JDesktopPane();\r
- desktop.setBackground(Color.white);\r
- setContentPane(desktop);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
-\r
- // This line prevents Windows Look&Feel resizing all new windows to maximum\r
- // if previous window was maximised\r
- desktop.setDesktopManager(new DefaultDesktopManager());\r
-\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
-\r
- if ((x != null) && (y != null) && (width != null) && (height != null))\r
- {\r
- setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
- Integer.parseInt(width), Integer.parseInt(height));\r
- }\r
- else\r
- {\r
- setBounds((int) (screenSize.width - 900) / 2,\r
- (int) (screenSize.height - 650) / 2, 900, 650);\r
- }\r
-\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- quit();\r
- }\r
- });\r
-\r
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
-\r
- /////////Add a splashscreen on startup\r
- /////////Add a splashscreen on startup\r
- JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.setLocation((int) ((getWidth() - 750) / 2),\r
- (int) ((getHeight() - 160) / 2));\r
-\r
- addInternalFrame(frame, "", 750, 160, false);\r
-\r
- discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- */\r
- public static synchronized void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h)\r
- {\r
- addInternalFrame(frame, title, w, h, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- * @param resizable DOCUMENT ME!\r
- */\r
- public static synchronized void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h, boolean resizable)\r
- {\r
-\r
- frame.setTitle(title);\r
- if(frame.getWidth()<1 || frame.getHeight()<1)\r
- {\r
- frame.setSize(w, h);\r
- }\r
- // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
- // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
- // IF JALVIEW IS RUNNING HEADLESS\r
- /////////////////////////////////////////////////\r
- if (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true"))\r
- {\r
- return;\r
- }\r
-\r
-\r
- openFrameCount++;\r
-\r
- frame.setVisible(true);\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
-\r
- if (frame.getX()<1 && frame.getY()<1)\r
- {\r
- frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);\r
- }\r
-\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameActivated(javax.swing.event.\r
- InternalFrameEvent evt)\r
- {\r
- JInternalFrame itf = desktop.getSelectedFrame();\r
- if (itf != null)\r
- itf.requestFocus();\r
-\r
- }\r
-\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- JInternalFrame itf = desktop.getSelectedFrame();\r
- if (itf != null)\r
- itf.requestFocus();\r
- }\r
- ;\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setSelected(true);\r
- frame.setIcon(false);\r
- }\r
- catch (java.beans.PropertyVetoException ex)\r
- {\r
-\r
- }\r
- }\r
- });\r
-\r
- windowMenu.add(menuItem);\r
-\r
- desktop.add(frame);\r
- frame.toFront();\r
- try{\r
- frame.setSelected(true);\r
- frame.requestFocus();\r
- }catch(java.beans.PropertyVetoException ve)\r
- {}\r
- }\r
-\r
- public void lostOwnership(Clipboard clipboard, Transferable contents)\r
- {\r
- Desktop.jalviewClipboard = null;\r
- }\r
-\r
- public void dragEnter(DropTargetDragEvent evt)\r
- {}\r
-\r
- public void dragExit(DropTargetEvent evt)\r
- {}\r
-\r
- public void dragOver(DropTargetDragEvent evt)\r
- {}\r
-\r
- public void dropActionChanged(DropTargetDragEvent evt)\r
- {}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void drop(DropTargetDropEvent evt)\r
- {\r
- Transferable t = evt.getTransferable();\r
- java.util.List files = null;\r
-\r
- try\r
- {\r
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- {\r
- //Works on Windows and MacOSX\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
- }\r
- else if (t.isDataFlavorSupported(uriListFlavor))\r
- {\r
- // This is used by Unix drag system\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- String data = (String) t.getTransferData(uriListFlavor);\r
- files = new java.util.ArrayList(1);\r
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
- data,\r
- "\r\n");\r
- st.hasMoreTokens(); )\r
- {\r
- String s = st.nextToken();\r
- if (s.startsWith("#"))\r
- {\r
- // the line is a comment (as per the RFC 2483)\r
- continue;\r
- }\r
-\r
- java.net.URI uri = new java.net.URI(s);\r
- java.io.File file = new java.io.File(uri);\r
- files.add(file);\r
- }\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- if (files != null)\r
- {\r
- try\r
- {\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = FormatAdapter.FILE;\r
- String format = null;\r
-\r
- if (file.endsWith(".jar"))\r
- {\r
- format = "Jalview";\r
-\r
- }\r
- else\r
- {\r
- format = new IdentifyFile().Identify(file,\r
- protocol);\r
- }\r
-\r
-\r
- new FileLoader().LoadFile(file, protocol, format);\r
-\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- String format = null;\r
- if (chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- format = "Jalview";\r
- }\r
- else\r
- {\r
- format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
- }\r
-\r
- if (alignment != null)\r
- new FileLoader().LoadFile(alignment, choice, FormatAdapter.FILE, format);\r
- else\r
- new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
- {\r
- // This construct allows us to have a wider textfield\r
- // for viewing\r
- JLabel label = new JLabel("Enter URL of Input File");\r
- final JComboBox history = new JComboBox();\r
-\r
- JPanel panel = new JPanel(new GridLayout(2,1));\r
- panel.add(label);\r
- panel.add(history);\r
- history.setPreferredSize(new Dimension(400,20));\r
- history.setEditable(true);\r
- history.addItem("http://www.");\r
-\r
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");\r
-\r
- StringTokenizer st;\r
-\r
- if (historyItems != null)\r
- {\r
- st = new StringTokenizer(historyItems, "\t");\r
-\r
- while (st.hasMoreTokens())\r
- {\r
- history.addItem(st.nextElement());\r
- }\r
- }\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(desktop,\r
- panel, "Input Alignment From URL",\r
- JOptionPane.OK_CANCEL_OPTION );\r
-\r
-\r
- if (reply != JOptionPane.OK_OPTION )\r
- {\r
- return;\r
- }\r
-\r
- String url = history.getSelectedItem().toString();\r
-\r
- if (url.toLowerCase().endsWith(".jar"))\r
- {\r
- if (alignment != null)\r
- new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, "Jalview");\r
- else\r
- new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");\r
- }\r
- else\r
- {\r
- String format = new IdentifyFile().Identify(url, FormatAdapter.URL);\r
-\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- if (alignment != null)\r
- new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, format);\r
- else\r
- new FileLoader().LoadFile(url, FormatAdapter.URL, format);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(alignment);\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r
-\r
- /*\r
- * Exit the program\r
- */\r
- public void quit()\r
- {\r
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
- System.exit(0);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- StringBuffer message = new StringBuffer("JalView version " +\r
- jalview.bin.Cache.getProperty(\r
- "VERSION") +\r
- "; last updated: " +\r
- jalview.bin.\r
- Cache.getDefault("BUILD_DATE", "unknown"));\r
-\r
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(\r
- jalview.bin.Cache.getProperty("VERSION")))\r
- {\r
- message.append("\n\n!! Jalview version "\r
- + jalview.bin.Cache.getProperty("LATEST_VERSION")\r
- + " is available for download from http://www.jalview.org !!\n");\r
-\r
- }\r
-\r
- message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +\r
- "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +\r
- "\nFor all issues relating to Jalview, email help@jalview.org" +\r
- "\n\nIf you use JalView, please cite:" +\r
- "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +\r
- "\nBioinformatics, 2004 12;426-7.");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-\r
- message.toString(), "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
-\r
- javax.help.HelpBroker hb = hs.createHelpBroker();\r
- hb.setCurrentID("home");\r
- hb.setDisplayed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- new Preferences();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save State");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- java.io.File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- new Jalview2XML().SaveState(choice);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Restore state");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
- new Jalview2XML().LoadJalviewAlign(choice);\r
- }\r
- }\r
-\r
- /* public void vamsasLoad_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Load Vamsas file");\r
- chooser.setToolTipText("Import");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);\r
- vs.load(\r
- chooser.getSelectedFile().getAbsolutePath()\r
- );\r
- }\r
-\r
- }*/\r
-\r
-\r
- public void inputSequence_actionPerformed(ActionEvent e)\r
- {\r
- SequenceFetcher sf = new SequenceFetcher(null);\r
- }\r
-}\r
-\r
+/*
+ * 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<j; i++) {
+ afs[i] = (AlignFrame) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
+
+ /**
+ * Add Groovy Support to Jalview
+ */
+ public void groovyShell_actionPerformed(ActionEvent e) {
+ // use reflection to avoid creating compilation dependency.
+ if (!jalview.bin.Cache.groovyJarsPresent())
+ {
+ throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+ }
+ try {
+ Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
+ Constructor gccons = gcClass.getConstructor(null);
+ java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
+ java.lang.reflect.Method run = gcClass.getMethod("run", null);
+ Object gc = gccons.newInstance(null);
+ setvar.invoke(gc, new Object[] { "Jalview", this});
+ run.invoke(gc, null);
+ }
+ catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff