/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
import jalview.bin.Cache;
import jalview.io.*;
+import jalview.ws.params.ParamManager;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import javax.swing.event.MenuListener;
/**
- * DOCUMENT ME!
+ * Jalview Desktop
+ *
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop implements
- DropTargetListener, ClipboardOwner, IProgressIndicator
+ DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider
{
- /** DOCUMENT ME!! */
+
+ private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+
+ /**
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(listener);
+ }
+
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
+ }
+
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void removeJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName,
+ listener);
+ }
+
+ /** Singleton Desktop instance */
public static Desktop instance;
- // Need to decide if the Memory Usage is to be included in
- // Next release or not.
public static MyDesktopPane desktop;
- // public static JDesktopPane desktop;
-
static int openFrameCount = 0;
static final int xOffset = 30;
static int fileLoadingCount = 0;
+ class MyDesktopManager implements DesktopManager
+ {
+
+ private DesktopManager delegate;
+
+ public MyDesktopManager(DesktopManager delegate)
+ {
+ this.delegate = delegate;
+ }
+
+ public void activateFrame(JInternalFrame f)
+ {
+ try
+ {
+ delegate.activateFrame(f);
+ } catch (NullPointerException npe)
+ {
+ Point p = getMousePosition();
+ instance.showPasteMenu(p.x, p.y);
+ }
+ }
+
+ public void beginDraggingFrame(JComponent f)
+ {
+ delegate.beginDraggingFrame(f);
+ }
+
+ public void beginResizingFrame(JComponent f, int direction)
+ {
+ delegate.beginResizingFrame(f, direction);
+ }
+
+ public void closeFrame(JInternalFrame f)
+ {
+ delegate.closeFrame(f);
+ }
+
+ public void deactivateFrame(JInternalFrame f)
+ {
+ delegate.deactivateFrame(f);
+ }
+
+ public void deiconifyFrame(JInternalFrame f)
+ {
+ delegate.deiconifyFrame(f);
+ }
+
+ public void dragFrame(JComponent f, int newX, int newY)
+ {
+ delegate.dragFrame(f, newX, newY);
+ }
+
+ public void endDraggingFrame(JComponent f)
+ {
+ delegate.endDraggingFrame(f);
+ }
+
+ public void endResizingFrame(JComponent f)
+ {
+ delegate.endResizingFrame(f);
+ }
+
+ public void iconifyFrame(JInternalFrame f)
+ {
+ delegate.iconifyFrame(f);
+ }
+
+ public void maximizeFrame(JInternalFrame f)
+ {
+ delegate.maximizeFrame(f);
+ }
+
+ public void minimizeFrame(JInternalFrame f)
+ {
+ delegate.minimizeFrame(f);
+ }
+
+ public void openFrame(JInternalFrame f)
+ {
+ delegate.openFrame(f);
+ }
+
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight)
+ {
+ delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight)
+ {
+ delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ // All other methods, simply delegate
+
+ }
+
/**
* Creates a new Desktop object.
*/
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
-
+ desktop.setDesktopManager(new MyDesktopManager(
+ new DefaultDesktopManager()));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
{
setBounds((int) (screenSize.width - 900) / 2,
(int) (screenSize.height - 650) / 2, 900, 650);
}
- jconsole = new Console(this);
- // immediately output essential build information
- System.out.println("Jalview Desktop "
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Desktop "
+ jalview.bin.Cache.getProperty("VERSION") + "\n"
+ "Build Date: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
}
});
- discoverer = new jalview.ws.jws1.Discoverer(); // Only gets started if gui is
// displayed.
// Thread off a new instance of the file chooser - this reduces the time it
// takes to open it later on.
Cache.log.debug("Filechooser init thread finished.");
}
}).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+
+ });
}
/**
iw = (int) (iw * sw);
iy = (int) (iy * sh);
ih = (int) (ih * sh);
+ while (ix >= screenSize.width)
+ {
+ jalview.bin.Cache.log
+ .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ ix -= screenSize.width;
+ }
+ while (iy >= screenSize.height)
+ {
+ jalview.bin.Cache.log
+ .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ iy -= screenSize.height;
+ }
jalview.bin.Cache.log.debug("Got last known dimensions for "
+ windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ " height:" + ih);
}
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();
- }
+ 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)
- {
- PaintRefresher.RemoveComponent(frame);
- openFrameCount--;
- windowMenu.remove(menuItem);
- JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- {
- itf.requestFocus();
- }
- System.gc();
- };
- });
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ PaintRefresher.RemoveComponent(frame);
+ openFrameCount--;
+ windowMenu.remove(menuItem);
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ {
+ itf.requestFocus();
+ }
+ System.gc();
+ };
+ });
menuItem.addActionListener(new ActionListener()
{
}
}
});
+ 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 inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"),
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.READABLE_FNAMES,
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
}
// TODO: update this text for each release or centrally store it for lite
// and application
- message
- .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
- + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
- + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
- + "\nIf you use Jalview, please cite:"
- + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
+ message.append("\nAuthors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
+ + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+ + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+ + "\nIf you use Jalview, please cite:"
+ + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
*/
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");
+ 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");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JProgressBar progpanel = addProgressPanel("Saving jalview project "
- + choice.getName());
+ setProgressBar("Saving jalview project " + choice.getName(),
+ choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
// TODO catch and handle errors for savestate
- new Jalview2XML().SaveState(choice);
- removeProgressPanel(progpanel);
+ try
+ {
+ new Jalview2XML().SaveState(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning(
+ "Whilst saving current state to " + choice.getName(), oom);
+ } catch (Exception ex)
+ {
+ Cache.log
+ .error("Problems whilst trying to save to "
+ + choice.getName(), ex);
+ JOptionPane.showMessageDialog(this,
+ "Error whilst saving current state to " + choice.getName(),
+ "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
}
}
*/
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");
+ 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");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getAbsolutePath();
- setProgressBar("loading jalview project "
- + chooser.getSelectedFile().getName(), choice.hashCode());
+ final String choice = chooser.getSelectedFile().getAbsolutePath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
- new Jalview2XML().LoadJalviewAlign(choice);
- setProgressBar(null, choice.hashCode());
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ setProgressBar("loading jalview project " + choice,
+ choice.hashCode());
+ try
+ {
+ new Jalview2XML().LoadJalviewAlign(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Problems whilst loading project from "
+ + choice, ex);
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Error whilst loading project from " + choice,
+ "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
}
}
validate();
}
- public static int getViewCount(String viewId)
+ public static int getViewCount(String alignmentId)
{
- AlignViewport[] aps = getViewports(viewId);
+ AlignViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
- * @param viewId
- * @return all AlignmentPanels concerning the viewId sequence set
+ * @param alignmentId
+ * @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String viewId)
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
int count = 0;
if (Desktop.desktop == null)
AlignFrame af = (AlignFrame) frames[t];
for (int a = 0; a < af.alignPanels.size(); a++)
{
- if (viewId
+ if (alignmentId
.equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
.getSequenceSetId()))
{
if (v_client == null)
{
// Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open a saved VAMSAS session");
- chooser
- .setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+ chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
int value = chooser.showOpenDialog(this);
}
bis.close();
fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file, url
- .toExternalForm());
+ v_client = new jalview.gui.VamsasApplication(this, file,
+ url.toExternalForm());
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
return false;
}
- setProgressBar("Importing VAMSAS session from " + file.getName(), file
- .hashCode());
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
}
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
- setProgressBar("Importing VAMSAS session from " + file.getName(), file
- .hashCode());
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
return v_client.inSession();
}
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
new String[]
{ "Vamsas Document" }, "Vamsas Document");
public void paintComponent(Graphics g)
{
- if (showMemoryUsage && g != null)
+ if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
g.setColor(Color.red);
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
- + df.format(percentUsage) + "%", 10, getHeight()
- - fm.getHeight());
+ g.drawString(
+ "Total Free Memory: " + df.format(totalFreeMemory)
+ + "MB; Max Memory: " + df.format(maxMemory)
+ + "MB; " + df.format(percentUsage) + "%", 10,
+ getHeight() - fm.getHeight());
}
}
}
avp.clear();
return afs;
}
+ public AppJmol[] getJmols()
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ Vector avp = new Vector();
+ try
+ {
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ AppJmol af = (AppJmol) frames[i];
+ avp.addElement(af);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ AppJmol afs[] = new AppJmol[avp.size()];
+ for (int i = 0, j = avp.size(); i < j; i++)
+ {
+ afs[i] = (AppJmol) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
/**
* Add Groovy Support to Jalview
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar("Cancelled "
- + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
+ /**
+ * flag set if jalview GUI is being operated programmatically
+ */
+ private boolean inBatchMode = false;
+
+ /**
+ * check if jalview GUI is being operated programmatically
+ *
+ * @return inBatchMode
+ */
+ public boolean isInBatchMode()
+ {
+ return inBatchMode;
+ }
+
+ /**
+ * set flag if jalview GUI is being operated programmatically
+ *
+ * @param inBatchMode
+ */
+ public void setInBatchMode(boolean inBatchMode)
+ {
+ this.inBatchMode = inBatchMode;
+ }
+
public void startServiceDiscovery()
{
- discoverer.start();
- new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()).start();
+ startServiceDiscovery(false);
+ }
+
+ public void startServiceDiscovery(boolean blocking)
+ {
+ boolean alive = true;
+ Thread t0 = null, t1 = null, t2 = null;
+
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+ {
+ (t0 = new Thread(discoverer)).start();
+ }
+
+ try
+ {
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ // EnfinEnvision web service menu entries are rebuild every time the
+ // menu is shown, so no changeSupport events are needed.
+ jalview.ws.EnfinEnvision2OneWay.getInstance();
+ (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+ .start();
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .info("Exception when trying to launch Envision2 workflow discovery.",
+ e);
+ Cache.log.info(e.getStackTrace());
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+ }
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+ changeSupport);
+
+ }
+ Thread t3=null;
+ {
+ // TODO: do rest service discovery
+ }
+ if (blocking)
+ {
+ while (alive)
+ {
+ try
+ {
+ Thread.sleep(15);
+ } catch (Exception e)
+ {
+ }
+ alive = (t1 != null && t1.isAlive())
+ || (t2 != null && t2.isAlive())
+ || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
+ }
+ }
+ }
+
+ /**
+ * called to check if the service discovery process completed successfully.
+ *
+ * @param evt
+ */
+ protected void JalviewServicesChanged(PropertyChangeEvent evt)
+ {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+ {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .getErrorMessages();
+ if (ermsg != null)
+ {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+ {
+ if (serviceChangedDialog == null)
+ {
+ // only run if we aren't already displaying one of these.
+ javax.swing.SwingUtilities
+ .invokeLater(serviceChangedDialog = new Runnable()
+ {
+ public void run()
+ {
+
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ ermsg
+ + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n",
+ "Preferences Problem",
+ JOptionPane.WARNING_MESSAGE);
+ serviceChangedDialog = null;
+
+ }
+ });
+ }
+ }
+ else
+ {
+ Cache.log
+ .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+ + ermsg);
+ }
+ }
+ }
+ }
+
+ private Runnable serviceChangedDialog = null;
+
+ /**
+ * start a thread to open a URL in the configured browser. Pops up a warning
+ * dialog to the user if there is an exception when calling out to the browser
+ * to open the URL.
+ *
+ * @param url
+ */
+ public static void showUrl(final String url)
+ {
+ showUrl(url, Desktop.instance);
+ }
+ /**
+ * Like showUrl but allows progress handler to be specified
+ * @param url
+ * @param progress (null) or object implementing IProgressIndicator
+ */
+ public static void showUrl(final String url, final IProgressIndicator progress)
+ {
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ try
+ {
+ if (progress!=null) {
+ progress.setProgressBar("Opening "+url, this.hashCode());
+ }
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Unixers: Couldn't find default web browser."
+ + "\nAdd the full path to your browser in Preferences.",
+ "Web browser not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ if (progress!=null) {
+ progress.setProgressBar(null, this.hashCode());
+ }
+ }
+ }).start();
+ }
+
+ public static WsParamSetManager wsparamManager = null;
+
+ public static ParamManager getUserParameterStore()
+ {
+ if (wsparamManager == null)
+ {
+ wsparamManager = new WsParamSetManager();
+ }
+ return wsparamManager;
}
+
+
}
git://source.jalview.org / jalview.git / blobdiff