*/\r
package jalview.gui;\r
\r
+import jalview.datamodel.*;\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
+\r
import javax.swing.*;\r
\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
\r
-public class Desktop\r
- extends jalview.jbgui.GDesktop implements DropTargetListener\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class Desktop extends jalview.jbgui.GDesktop\r
+ implements DropTargetListener\r
{\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30;\r
- static final int yOffset = 30;\r
-\r
- public Desktop()\r
- {\r
- Image image = null;\r
-\r
- try\r
+ /** DOCUMENT ME!! */\r
+ public static JDesktopPane desktop;\r
+ static int openFrameCount = 0;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
+\r
+ /**\r
+ * Creates a new Desktop object.\r
+ */\r
+ public Desktop()\r
{\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\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
+ 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
+ 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 2005");\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
+ setTitle("Jalview 2005");\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
+ // 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
+ 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
+ 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
+ }\r
+ else\r
+ {\r
+ setBounds((int) (screenSize.width - 900) / 2,\r
(int) (screenSize.height - 650) / 2, 900, 650);\r
- }\r
+ }\r
\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- quit();\r
- }\r
- });\r
- setVisible(true);\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
- addInternalFrame(frame, "", 750, 160, false);\r
- frame.setLocation( (int) ( (getWidth() - 750) / 2),\r
- (int) ( (getHeight() - 160) / 2));\r
- }\r
-\r
- public static void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h)\r
- {\r
- addInternalFrame(frame, title, w, h, true);\r
- }\r
-\r
- public static void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h,\r
- boolean resizable)\r
- {\r
- desktop.add(frame);\r
- openFrameCount++;\r
-\r
- try\r
- {\r
- frame.setSelected(true);\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
+ addInternalFrame(frame, "", 750, 160, false);\r
+ frame.setLocation((int) ((getWidth() - 750) / 2),\r
+ (int) ((getHeight() - 160) / 2));\r
}\r
- catch (java.beans.PropertyVetoException e)\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 void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
{\r
+ addInternalFrame(frame, title, w, h, true);\r
}\r
\r
- frame.setTitle(title);\r
- frame.setSize(w, h);\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
- frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
- frame.toFront();\r
-\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\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 void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h, boolean resizable)\r
{\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- }\r
- ;\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
+ desktop.add(frame);\r
+ openFrameCount++;\r
+\r
try\r
{\r
- frame.setSelected(true);\r
- frame.setIcon(false);\r
+ frame.setSelected(true);\r
}\r
- catch (java.beans.PropertyVetoException ex)\r
+ catch (java.beans.PropertyVetoException e)\r
{\r
}\r
\r
- ;\r
- }\r
- });\r
-\r
- frame.setVisible(true);\r
- windowMenu.add(menuItem);\r
- }\r
-\r
- public void dragEnter(DropTargetDragEvent evt)\r
- {\r
- }\r
-\r
- public void dragExit(DropTargetEvent evt)\r
- {\r
- }\r
-\r
- public void dragOver(DropTargetDragEvent evt)\r
- {\r
- }\r
+ frame.setTitle(title);\r
+ frame.setSize(w, h);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
+ frame.toFront();\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\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
+\r
+ frame.setVisible(true);\r
+ windowMenu.add(menuItem);\r
+ }\r
\r
- public void dropActionChanged(DropTargetDragEvent evt)\r
- {\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {\r
+ }\r
\r
- public void drop(DropTargetDropEvent evt)\r
- {\r
- Transferable t = evt.getTransferable();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragExit(DropTargetEvent evt)\r
+ {\r
+ }\r
\r
- if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragOver(DropTargetDragEvent evt)\r
{\r
- return;\r
}\r
\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {\r
+ }\r
\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void drop(DropTargetDropEvent evt)\r
{\r
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.\r
- javaFileListFlavor);\r
+ Transferable t = evt.getTransferable();\r
\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = "File";\r
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ return;\r
+ }\r
+\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
\r
- if (file.endsWith(".jar"))\r
+ try\r
{\r
- Jalview2XML.LoadJalviewAlign(file);\r
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = "File";\r
+ String format = null;\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+\r
+ }\r
+ else\r
+ {\r
+ format = jalview.io.IdentifyFile.Identify(file,\r
+ protocol);\r
+ }\r
+ LoadFile(file, protocol, format);\r
+ }\r
}\r
- else\r
+ catch (Exception ex)\r
{\r
- String format = jalview.io.IdentifyFile.Identify(file,\r
- protocol);\r
- LoadFile(file, protocol, format);\r
+ ex.printStackTrace();\r
}\r
- }\r
}\r
- catch (Exception ex)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
{\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\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
- "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
+ 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 = IdentifyFile.Identify(choice, "File");\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
+ LoadFile(choice, "File", format);\r
+ }\r
+ }\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ */\r
+ public void LoadFile(String file, String protocol, String format)\r
{\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- if (chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- else\r
- {\r
- String format = IdentifyFile.Identify(choice, "File");\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\r
- }\r
+ LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ loader.start();\r
}\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter url of input file", "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
- .toString();\r
-\r
- if (url == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ */\r
+ public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)\r
{\r
- return;\r
- }\r
+ LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ loader.start();\r
+\r
+ while (loader.isAlive())\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(50);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
\r
- String format = IdentifyFile.Identify(url, "URL");\r
+ return loader.af;\r
+ }\r
\r
- if (format.equals("URL NOT FOUND"))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
+ String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter url of input file", "Input alignment from URL",\r
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
+ .toString();\r
+\r
+ if (url == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (url.trim().toLowerCase().endsWith(".jar"))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");\r
+ Jalview2XML.LoadJalviewAlign(url);\r
+ }\r
+ else\r
+ {\r
\r
- return;\r
+ String format = IdentifyFile.Identify(url, "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
+ LoadFile(url, "URL", format);\r
+ }\r
}\r
\r
- LoadFile(url, "URL", format);\r
- }\r
-\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput();\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r
-\r
- /*\r
- * Exit the program\r
- */\r
- public void quit()\r
- {\r
- if (jalview.bin.Jalview.applet != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.Jalview.applet.destroy();\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput();\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
}\r
- else\r
+\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit()\r
{\r
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x +\r
- "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y +\r
- "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH",\r
- getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT",\r
- getHeight() + "");\r
- System.exit(0);\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
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "JalView 2005 version " +\r
- jalview.bin.Cache.VERSION +\r
- "; last updated: " +\r
- jalview.bin.Cache.BUILD_DATE +\r
- "\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
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\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.setLocation(new Point(200, 50));\r
- hb.setSize(new Dimension(800, 700));\r
- hb.setCurrentID("home");\r
- hb.setDisplayed(true);\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "JalView 2005 version " + jalview.bin.Cache.VERSION +\r
+ "; last updated: " + jalview.bin.Cache.BUILD_DATE +\r
+ "\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.", "About Jalview",\r
+ JOptionPane.INFORMATION_MESSAGE);\r
}\r
- catch (Exception ex)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void documentationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- ex.printStackTrace();\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.setLocation(new Point(200, 50));\r
+ hb.setSize(new Dimension(800, 700));\r
+ hb.setCurrentID("home");\r
+ hb.setDisplayed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- }\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- Preferences pref = new Preferences();\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
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"jar"},\r
- new String[]\r
- {"Jalview Project"}, "Jalview Project");\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
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save State");\r
\r
- int value = chooser.showSaveDialog(this);\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
- Jalview2XML.SaveState(choice);\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ java.io.File choice = chooser.getSelectedFile();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ Jalview2XML.SaveState(choice);\r
+ }\r
}\r
- }\r
-\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"jar"},\r
- new String[]\r
- {"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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void loadState_actionPerformed(ActionEvent e)\r
{\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\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
- class LoadingThread\r
- extends Thread\r
- {\r
- String file;\r
- String protocol;\r
- String format;\r
+ int value = chooser.showOpenDialog(this);\r
\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\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
+ Jalview2XML.LoadJalviewAlign(choice);\r
+ }\r
}\r
\r
- public void run()\r
+ class LoadingThread extends Thread\r
{\r
- SequenceI[] sequences = null;\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ AlignFrame af;\r
\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
- }\r
-\r
- if ( (sequences != null) && (sequences.length > 0))\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
- try\r
+ public LoadingThread(String file, String protocol, String format)\r
{\r
- af.setMaximum(Preferences.showFullscreen);\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
}\r
- catch (Exception ex)\r
+\r
+ public void run()\r
{\r
+ SequenceI[] sequences = null;\r
+\r
+ if(format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
+ }\r
+ else\r
+ {\r
+ if (FormatAdapter.formats.contains(format))\r
+ {\r
+ sequences = FormatAdapter.readFile(file, protocol, format);\r
+ }\r
+\r
+ if ( (sequences != null) && (sequences.length > 0))\r
+ {\r
+ af = new AlignFrame(new Alignment(sequences));\r
+ addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.currentFileFormat = format;\r
+ af.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ try\r
+ {\r
+ af.setMaximum(Preferences.showFullscreen);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't open file.\n" +\r
+ "Formats currently supported are\n" +\r
+ "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
+ , "Error loading file", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
}\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't open file.\n" +\r
- "Formats currently supported are\n" +\r
- "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
- , "Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
}\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff