/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\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
+import java.util.*;\r
\r
import javax.swing.*;\r
\r
* @version $Revision$\r
*/\r
public class Desktop extends jalview.jbgui.GDesktop\r
- implements DropTargetListener\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
MediaTracker mt = new MediaTracker(this);\r
mt.addImage(image, 0);\r
mt.waitForID(0);\r
- // setIconImage(image);\r
+ setIconImage(image);\r
}\r
}\r
catch (Exception ex)\r
{\r
}\r
\r
- setTitle("Jalview 2005");\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
+ 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
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
+ addInternalFrame(frame, "", 750, 160, false);\r
+\r
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.\r
+\r
}\r
\r
/**\r
* @param w DOCUMENT ME!\r
* @param h DOCUMENT ME!\r
*/\r
- public static void addInternalFrame(final JInternalFrame frame,\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
* @param h DOCUMENT ME!\r
* @param resizable DOCUMENT ME!\r
*/\r
- public static void addInternalFrame(final JInternalFrame frame,\r
+ public static synchronized void addInternalFrame(final JInternalFrame frame,\r
String title, int w, int h, boolean resizable)\r
{\r
- desktop.add(frame);\r
- openFrameCount++;\r
\r
- try\r
- {\r
- frame.setSelected(true);\r
- }\r
- catch (java.beans.PropertyVetoException e)\r
- {\r
- }\r
-\r
- frame.setTitle(title);\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
- frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
- frame.toFront();\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
catch (java.beans.PropertyVetoException ex)\r
{\r
- }\r
\r
- ;\r
+ }\r
}\r
});\r
\r
- frame.setVisible(true);\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void dragEnter(DropTargetDragEvent evt)\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
{\r
+ Desktop.jalviewClipboard = null;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {}\r
+\r
public void dragExit(DropTargetEvent evt)\r
- {\r
- }\r
+ {}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
public void dragOver(DropTargetDragEvent evt)\r
- {\r
- }\r
+ {}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
public void dropActionChanged(DropTargetDragEvent evt)\r
- {\r
- }\r
+ {}\r
\r
/**\r
* DOCUMENT ME!\r
public void drop(DropTargetDropEvent evt)\r
{\r
Transferable t = evt.getTransferable();\r
+ java.util.List files = null;\r
\r
- if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ try\r
{\r
- return;\r
- }\r
-\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\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
- try\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
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\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 = "File";\r
- String format = null;\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
+ 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
- else\r
- {\r
- format = jalview.io.IdentifyFile.Identify(file,\r
- protocol);\r
- }\r
- LoadFile(file, protocol, format);\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
+ }\r
}\r
}\r
\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
"LAST_DIRECTORY"),\r
String format = null;\r
if (chooser.getSelectedFormat().equals("Jalview"))\r
{\r
- format = "Jalview";\r
+ format = "Jalview";\r
}\r
else\r
{\r
- format = IdentifyFile.Identify(choice, "File");\r
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
}\r
\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\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 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
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- * @param protocol DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
+ * @param e DOCUMENT ME!\r
*/\r
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)\r
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)\r
{\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\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 (loader.isAlive())\r
+ while (st.hasMoreTokens())\r
{\r
- try\r
- {\r
- Thread.sleep(50);\r
- }\r
- catch (Exception ex)\r
- {}\r
+ history.addItem(st.nextElement());\r
}\r
+ }\r
\r
- return loader.af;\r
- }\r
+ int reply = JOptionPane.showInternalConfirmDialog(desktop,\r
+ panel, "Input Alignment From URL",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
+ if (reply != JOptionPane.OK_OPTION )\r
{\r
return;\r
}\r
\r
- if (url.trim().toLowerCase().endsWith(".jar"))\r
+ String url = history.getSelectedItem().toString();\r
+\r
+ if (url.toLowerCase().endsWith(".jar"))\r
{\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");\r
- Jalview2XML.LoadJalviewAlign(url);\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
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);\r
\r
if (format.equals("URL NOT FOUND"))\r
{\r
return;\r
}\r
\r
- LoadFile(url, "URL", format);\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
* @param e DOCUMENT ME!\r
*/\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput();\r
+ cap.setForInput(viewport);\r
Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
}\r
\r
*/\r
public void aboutMenuItem_actionPerformed(ActionEvent e)\r
{\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
+ 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.", "About Jalview",\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
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
{\r
java.io.File choice = chooser.getSelectedFile();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- Jalview2XML.SaveState(choice);\r
+ new Jalview2XML().SaveState(choice);\r
}\r
}\r
\r
String choice = chooser.getSelectedFile().getAbsolutePath();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
chooser.getSelectedFile().getParent());\r
- Jalview2XML.LoadJalviewAlign(choice);\r
+ new Jalview2XML().LoadJalviewAlign(choice);\r
}\r
}\r
\r
- class LoadingThread extends Thread\r
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
- String file;\r
- String protocol;\r
- String format;\r
- AlignFrame af;\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- }\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Load Vamsas file");\r
+ chooser.setToolTipText("Import");\r
\r
- public void run()\r
- {\r
- SequenceI[] sequences = null;\r
+ int value = chooser.showOpenDialog(this);\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
+ 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
- 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
\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
+ 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