-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener
-{
- /** DOCUMENT ME!! */
- public static JDesktopPane desktop;
- static int openFrameCount = 0;
- static final int xOffset = 30;
- static final int yOffset = 30;
- public static jalview.ws.Discoverer discoverer;
-
- public static Object [] jalviewClipboard;
-
-
- /**
- * Creates a new Desktop object.
- */
- public Desktop()
- {
- Image image = null;
-
-
- try
- {
- java.net.URL url = getClass().getResource("/images/logo.gif");
-
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(image, 0);
- mt.waitForID(0);
- setIconImage(image);
- }
- }
- catch (Exception ex)
- {
- }
-
- setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- desktop = new JDesktopPane();
- desktop.setBackground(Color.white);
- setContentPane(desktop);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
-
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- String x = jalview.bin.Cache.getProperty("SCREEN_X");
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
-
- if ((x != null) && (y != null) && (width != null) && (height != null))
- {
- setBounds(Integer.parseInt(x), Integer.parseInt(y),
- Integer.parseInt(width), Integer.parseInt(height));
- }
- else
- {
- setBounds((int) (screenSize.width - 900) / 2,
- (int) (screenSize.height - 650) / 2, 900, 650);
- }
-
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- 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"))
- {
- 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)
- {
- 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)
- {}
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragEnter(DropTargetDragEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragExit(DropTargetEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragOver(DropTargetDragEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dropActionChanged(DropTargetDragEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- 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";
- String format = null;
-
- if (file.endsWith(".jar"))
- {
- format = "Jalview";
-
- }
- else
- {
- format = jalview.io.IdentifyFile.Identify(file,
- protocol);
- }
- LoadFile(file, protocol, format);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"),
- new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
- new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open local file");
- chooser.setToolTipText("Open");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- 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 = IdentifyFile.Identify(choice, "File");
- }
-
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
- LoadFile(choice, "File", format);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- * @param protocol DOCUMENT ME!
- * @param format DOCUMENT ME!
- */
- public void LoadFile(String file, String protocol, String format)
- {
- FileLoader fileLoader = new FileLoader();
- fileLoader.LoadFile(file, protocol, format);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
- {
- Object reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter url of input file", "Input alignment from URL",
- JOptionPane.QUESTION_MESSAGE, null, null, "http://www.");
-
- if (reply == null)
- {
- return;
- }
-
- String url = reply.toString().trim();
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
- Jalview2XML.LoadJalviewAlign(url);
- }
- else
- {
-
- 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);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput();
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
- }
-
- /*
- * Exit the program
- */
- public void quit()
- {
- 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 12;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());
- 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());
- 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)
- {
- SequenceFetcher sf = new SequenceFetcher(null);
- }
-}
-
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
+ static int fileLoadingCount= 0;\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
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(desktop, BorderLayout.CENTER);\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(AlignViewport viewport)\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 (viewport != null)\r
+ new FileLoader().LoadFile(viewport, 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(AlignViewport viewport)\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 (viewport != null)\r
+ new FileLoader().LoadFile(viewport, 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 (viewport != null)\r
+ new FileLoader().LoadFile(viewport, 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(AlignViewport viewport)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(viewport);\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 20;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
+ new SequenceFetcher(null);\r
+ }\r
+\r
+ JPanel progressPanel;\r
+\r
+ public void startLoading(final String fileName)\r
+ {\r
+ if (fileLoadingCount == 0)\r
+ {\r
+ progressPanel = new JPanel(new BorderLayout());\r
+ JProgressBar progressBar = new JProgressBar();\r
+ progressBar.setIndeterminate(true);\r
+\r
+ progressPanel.add(new JLabel("Loading File: " + fileName + " "),\r
+ BorderLayout.WEST);\r
+\r
+ progressPanel.add(progressBar, BorderLayout.CENTER);\r
+\r
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);\r
+ }\r
+ fileLoadingCount++;\r
+ validate();\r
+ }\r
+\r
+ public void stopLoading()\r
+ {\r
+ fileLoadingCount--;\r
+ if (fileLoadingCount < 1)\r
+ {\r
+ if(progressPanel!=null)\r
+ {\r
+ this.getContentPane().remove(progressPanel);\r
+ progressPanel = null;\r
+ }\r
+ fileLoadingCount = 0;\r
+ }\r
+ validate();\r
+ }\r
+\r
+}\r
+\r
git://source.jalview.org / jalview.git / blobdiff