/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.util.*;
import javax.swing.*;
+import org.vamsas.test.simpleclient.ArchiveClient;
/**
* DOCUMENT ME!
* @version $Revision$
*/
public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener
+ implements DropTargetListener, ClipboardOwner
{
/** DOCUMENT ME!! */
+ public static Desktop instance;
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;
+
+ static int fileLoadingCount= 0;
+
/**
* Creates a new Desktop object.
*/
public Desktop()
{
+ instance = this;
+
Image image = null;
try
{
}
- setTitle("Jalview 2005");
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
desktop = new JDesktopPane();
desktop.setBackground(Color.white);
- setContentPane(desktop);
+ 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
SplashScreen splash = new SplashScreen(frame, image);
frame.setContentPane(splash);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- addInternalFrame(frame, "", 750, 160, false);
frame.setLocation((int) ((getWidth() - 750) / 2),
(int) ((getHeight() - 160) / 2));
- discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+
+ addInternalFrame(frame, "", 750, 160, false);
+
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+
}
/**
* @param w DOCUMENT ME!
* @param h DOCUMENT ME!
*/
- public static void addInternalFrame(final JInternalFrame frame,
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
String title, int w, int h)
{
addInternalFrame(frame, title, w, h, true);
* @param h DOCUMENT ME!
* @param resizable DOCUMENT ME!
*/
- public static void addInternalFrame(final JInternalFrame frame,
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
String title, int w, int h, boolean resizable)
{
frame.setTitle(title);
- if(w!=AlignFrame.NEW_WINDOW_WIDTH &&
- h!=AlignFrame.NEW_WINDOW_HEIGHT)
- frame.setSize(w, h);
-
+ 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
}
- desktop.add(frame);
openFrameCount++;
- try
- {
- frame.setSelected(true);
- }
- catch (java.beans.PropertyVetoException e)
- {
- }
-
+ frame.setVisible(true);
frame.setClosable(true);
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
frame.setFrameIcon(null);
- if (w != AlignFrame.NEW_WINDOW_WIDTH &&
- h != AlignFrame.NEW_WINDOW_HEIGHT)
- frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);
- frame.toFront();
+
+ 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();
}
;
});
}
catch (java.beans.PropertyVetoException ex)
{
- }
- ;
+ }
}
});
- frame.setVisible(true);
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)
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
{
+ Desktop.jalviewClipboard = null;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
+ public void dragEnter(DropTargetDragEvent evt)
+ {}
+
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!
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
+ java.util.List files = null;
- if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ try
{
- return;
+ 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);
+ }
+ }
}
-
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-
- try
+ catch (Exception e)
{
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ e.printStackTrace();
+ }
+ if (files != null)
+ {
+ try
+ {
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
- String protocol = "File";
- String format = null;
+ String file = files.get(i).toString();
+ String protocol = FormatAdapter.FILE;
+ String format = null;
- if (file.endsWith(".jar"))
- {
- format = "Jalview";
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+
+ }
+ else
+ {
+ format = new IdentifyFile().Identify(file,
+ protocol);
+ }
+
+
+ new FileLoader().LoadFile(file, protocol, format);
- }
- else
- {
- format = jalview.io.IdentifyFile.Identify(file,
- protocol);
- }
- LoadFile(file, protocol, format);
}
- }
- catch (Exception ex)
- {
+ }
+ catch (Exception ex)
+ {
ex.printStackTrace();
+ }
}
}
*
* @param e DOCUMENT ME!
*/
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
"LAST_DIRECTORY"),
String format = null;
if (chooser.getSelectedFormat().equals("Jalview"))
{
- format = "Jalview";
+ format = "Jalview";
}
else
{
- format = IdentifyFile.Identify(choice, "File");
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
}
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
- LoadFile(choice, "File", format);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+ else
+ new FileLoader().LoadFile(choice, FormatAdapter.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)
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter url of input file", "Input alignment from URL",
- JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
- .toString();
+ // 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();
- if (url == null)
+ 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;
}
- if (url.trim().toLowerCase().endsWith(".jar"))
+ String url = history.getSelectedItem().toString();
+
+ if (url.toLowerCase().endsWith(".jar"))
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
- Jalview2XML.LoadJalviewAlign(url);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
}
else
{
-
- String format = IdentifyFile.Identify(url, "URL");
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
if (format.equals("URL NOT FOUND"))
{
return;
}
- LoadFile(url, "URL", format);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, format);
}
}
*
* @param e DOCUMENT ME!
*/
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput();
+ cap.setForInput(viewport);
Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
}
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = new StringBuffer("JalView 2005 version " +
+ StringBuffer message = new StringBuffer("JalView version " +
jalview.bin.Cache.getProperty(
"VERSION") +
"; last updated: " +
"\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.");
+ "\nBioinformatics, 2004 20;426-7.");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setLocation(new Point(200, 50));
- hb.setSize(new Dimension(800, 700));
hb.setCurrentID("home");
hb.setDisplayed(true);
}
{
java.io.File choice = chooser.getSelectedFile();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- Jalview2XML.SaveState(choice);
+ new Jalview2XML().SaveState(choice);
}
}
String choice = chooser.getSelectedFile().getAbsolutePath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
- Jalview2XML.LoadJalviewAlign(choice);
+ 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();
}
+ 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);
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff