*/
package jalview.gui;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.UrlConstants;
import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.UrlDownloadClient;
import jalview.ws.params.ParamManager;
import java.awt.BorderLayout;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.ListIterator;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
+import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
showNews.setVisible(false);
+ getIdentifiersOrgData();
+
+ checkURLLinks();
+
this.addWindowListener(new WindowAdapter()
{
@Override
@Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isPopupTrigger())
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
{
showPasteMenu(evt.getX(), evt.getY());
}
});
}
+ public void getIdentifiersOrgData()
+ {
+ // Thread off the identifiers fetcher
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Downloading data from identifiers.org");
+ UrlDownloadClient client = new UrlDownloadClient();
+ try
+ {
+ client.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ Cache.log.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
+ }
+ });
+ }
+
@Override
protected void showNews_actionPerformed(ActionEvent e)
{
* ((openFrameCount - 1) % 10) + yOffset);
}
+ /*
+ * add an entry for the new frame in the Window menu
+ * (and remove it when the frame is closed)
+ */
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameActivated(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameActivated(InternalFrameEvent evt)
{
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
}
-
}
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameClosed(InternalFrameEvent evt)
{
PaintRefresher.RemoveComponent(frame);
- openFrameCount--;
+
+ /*
+ * defensive check to prevent frames being
+ * added half off the window
+ */
+ if (openFrameCount > 0)
+ {
+ openFrameCount--;
+ }
+
+ /*
+ * ensure no reference to alignFrame retained by menu item listener
+ */
+ if (menuItem.getActionListeners().length > 0)
+ {
+ menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+ }
windowMenu.remove(menuItem);
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
+ if (itf instanceof AlignFrame)
+ {
+ Jalview.setCurrentAlignFrame((AlignFrame) itf);
+ }
}
System.gc();
};
}
}
});
- menuItem.addMouseListener(new MouseListener()
- {
-
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- @Override
- public void mousePressed(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- try
- {
- frame.setSelected(false);
- } catch (PropertyVetoException e1)
- {
- }
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- try
- {
- frame.setSelected(true);
- } catch (PropertyVetoException e1)
- {
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
-
- }
- });
windowMenu.add(menuItem);
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
java.util.List<String> files = new ArrayList<String>();
java.util.List<String> protocols = new ArrayList<String>();
dialogExecutor.shutdownNow();
}
closeAll_actionPerformed(null);
+
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
System.exit(0);
}
@Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ // TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
{
}
}
+ Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
if (v_client != null)
{
{
ssm.resetAll();
}
+ System.gc();
}
@Override
*
* @param af
*/
- public void explodeViews(AlignFrame af)
+ public static void explodeViews(AlignFrame af)
{
int size = af.alignPanels.size();
if (size < 2)
new Thread(jvq).start();
}
+ public void checkURLLinks()
+ {
+ // Thread off the URL link checker
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (Cache.getDefault("CHECKURLLINKS", true))
+ {
+ // check what the actual links are - if it's just the default don't
+ // bother with the warning
+ Vector<String> links = Preferences.sequenceUrlLinks
+ .getLinksForMenu();
+
+ // only need to check links if there is one with a
+ // SEQUENCE_ID which is not the default EMBL_EBI link
+ ListIterator<String> li = links.listIterator();
+ boolean check = false;
+ List<JLabel> urls = new ArrayList<JLabel>();
+ while (li.hasNext())
+ {
+ String link = li.next();
+ if (link.contains(SEQUENCE_ID)
+ && !link.equals(UrlConstants.DEFAULT_STRING))
+ {
+ check = true;
+ int barPos = link.indexOf("|");
+ String urlMsg = barPos == -1 ? link : link.substring(0,
+ barPos) + ": " + link.substring(barPos + 1);
+ urls.add(new JLabel(urlMsg));
+ }
+ }
+ if (!check)
+ {
+ return;
+ }
+
+ // ask user to check in case URL links use old style tokens
+ // ($SEQUENCE_ID$ for sequence id _or_ accession id)
+ JPanel msgPanel = new JPanel();
+ msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
+ msgPanel.add(Box.createVerticalGlue());
+ JLabel msg = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ msgPanel.add(msg);
+ for (JLabel url : urls)
+ {
+ msgPanel.add(url);
+ }
+ msgPanel.add(msg2);
+
+ final JCheckBox jcb = new JCheckBox(
+ MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // update Cache settings for "don't show this again"
+ boolean showWarningAgain = !jcb.isSelected();
+ Cache.setProperty("CHECKURLLINKS",
+ Boolean.valueOf(showWarningAgain).toString());
+ }
+ });
+ msgPanel.add(jcb);
+
+ JOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ }
+
/**
* Proxy class for JDesktopPane which optionally displays the current memory
* usage and highlights the desktop area with a red bar if free memory runs
*/
void openGroovyConsole()
{
- groovyConsole = new groovy.ui.Console();
+ if (groovyConsole == null)
+ {
+ groovyConsole = new groovy.ui.Console();
+ groovyConsole.setVariable("Jalview", this);
+ groovyConsole.run();
- /*
- * bind groovy variable 'Jalview' to the Desktop object
- */
- groovyConsole.setVariable("Jalview", this);
+ /*
+ * We allow only one console at a time, so that AlignFrame menu option
+ * 'Calculate | Run Groovy script' is unambiguous.
+ * Disable 'Groovy Console', and enable 'Run script', when the console is
+ * opened, and the reverse when it is closed
+ */
+ Window window = (Window) groovyConsole.getFrame();
+ window.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ /*
+ * rebind CMD-Q from Groovy Console to Jalview Quit
+ */
+ addQuitHandler();
+ enableExecuteGroovy(false);
+ }
+ });
+ }
/*
- * start the console
+ * show Groovy console window (after close and reopen)
*/
- groovyConsole.run();
+ ((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * Allow only one console at a time, so that the AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'new console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus
+ * and disable opening a second console
*/
- Window window = (Window) groovyConsole.getFrame();
- window.addWindowListener(new WindowAdapter()
+ enableExecuteGroovy(true);
+ }
+
+ /**
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
+ */
+ protected void addQuitHandler()
+ {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
- public void windowClosed(WindowEvent e)
+ public void actionPerformed(ActionEvent e)
{
- enableExecuteGroovy(false);
+ quit();
}
});
-
- /*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
- */
- enableExecuteGroovy(true);
}
/**
{
// Works on Windows and MacOSX
Cache.log.debug("Drop handled as javaFileListFlavor");
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
- files.add(((File)file).toString());
+ files.add(((File) file).toString());
protocols.add(FormatAdapter.FILE);
}
}
{
Cache.log.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null)
{
Cache.log.debug("Supported transfer dataflavor: "
+ fl.toString());
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Object df = t.getTransferData(fl);
if (df != null)
{