-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-package jalview.gui;\r
-\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class Desktop extends jalview.jbgui.GDesktop\r
-{\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30, yOffset = 30;\r
- static boolean splashScreenVisible = false;\r
-\r
- public Desktop()\r
- {\r
- Image image =null;\r
- try{\r
- java.net.URL url = getClass().getResource("/BartonGroupBanner.gif");\r
- if(url!=null)\r
- {\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\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
- setTitle("Jalview 2005");\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- setVisible(true);\r
- desktop = new JDesktopPane();\r
- setContentPane(desktop);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
-\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- setBounds( (int)(screenSize.getWidth()-1200)/2,\r
- (int)(screenSize.getHeight()-800)/2,\r
- 1200 ,\r
- 800);\r
-\r
-\r
- /////////Add a splashscreen on startup\r
- JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- addInternalFrame(frame, "",820,200);\r
- splashScreenVisible = true;\r
-\r
- frame.setLocation( (int)((getWidth()-820) /2), (int)((getHeight()-240) /2));\r
- frame.setClosable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
- frame.setFrameIcon(null);\r
- splashScreenVisible = false;\r
-\r
- }\r
-\r
- public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
- {\r
- if(!splashScreenVisible)\r
- frame.setVisible(true); //necessary as of 1.3\r
- desktop.add(frame);\r
- openFrameCount++;\r
- try {\r
- frame.setSelected(true);\r
- } catch (java.beans.PropertyVetoException e) {}\r
- frame.setTitle(title);\r
- frame.setResizable(true);\r
- frame.setSize(w,h);\r
- frame.setClosable(true);\r
- frame.setMaximizable(true);\r
- frame.setIconifiable(true);\r
- frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
- frame.toFront();\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- };\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- try{ frame.setSelected(true); frame.setIcon(false); }\r
- catch(java.beans.PropertyVetoException ex){};\r
- }\r
- });\r
-\r
- windowMenu.add(menuItem);\r
- }\r
-\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
- String format = IdentifyFile.Identify(choice, "File");\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains(format))\r
- sequences = FormatAdapter.read(file, protocol, format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, 700, 500);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
-\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(this, "Couldn't open file.\n"\r
- + "Formats currently supported are\n"\r
- + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(this,"Enter url of input file",\r
- "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE);\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- System.out.println(format +" format");\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(this,"Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- LoadFile(url, "URL", format);\r
- }\r
-\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- int accept = JOptionPane.showInternalOptionDialog(desktop, cap, "Cut & paste Alignment File",\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- new Object[]{"Accept", "Cancel", }, null);\r
-\r
-\r
- if(accept == JOptionPane.YES_OPTION)\r
- {\r
- String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains( format ))\r
- sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
-\r
-\r
- if(sequences!=null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(this, "Couldn't read the pasted text.\n"\r
- +"Formats currently supported are\n"\r
- +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
- "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
-\r
-\r
- }\r
- }\r
-\r
-/*\r
-* Exit the program\r
-*/\r
- public void quit_actionPerformed(ActionEvent e)\r
- {\r
- this.setVisible(false);\r
- System.exit(0);\r
- }\r
-\r
-\r
- protected void colourIndexMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey(null);\r
- addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
- }\r
-\r
-\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(desktop,\r
- "JalView 2005"\r
- +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and Geoff Barton."\r
- +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
- +"\nIf you use JalView, please cite: \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- jalview.util.BrowserLauncher.openURL("http://jalview.org/documentation.html");\r
- }catch(Exception ex){}\r
- }\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.*;
+
+/**
+ * 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);
+
+ 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());
+ }
+ }
+ });
+
+
+ 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();
+ }
+
+ }
+
+ 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"),
+ 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)
+ {
+ // 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);
+ }
+
+ 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 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)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+ vs.load(
+ chooser.getSelectedFile().getAbsolutePath()
+ );
+ }
+
+ }*/
+
+
+ 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();
+ }
+
+ 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.VamsasClient v_client = null;
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ if (v_client == null)
+ {
+ // 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();
+ }
+ }
+
+ 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 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<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