X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ec9974ca73b1b6733c0450bcdfcc2a4f9e3faefb;hb=cf25e4f4f7d2cb2a7847a01d7cbe52003b46bf54;hp=3ba50c53fce289cebf681cdd7ad0c0cbf5af5f72;hpb=8a33c09bdd60c4b0f1c85136d1f8596240151c67;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 3ba50c5..ec9974c 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,5 +1,5 @@ /* - * 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. @@ -19,11 +19,14 @@ package jalview.gui; 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.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.File; @@ -40,7 +43,8 @@ import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; /** - * DOCUMENT ME! + * Jalview Desktop + * * * @author $author$ * @version $Revision$ @@ -48,15 +52,115 @@ import javax.swing.event.MenuListener; public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator { - /** DOCUMENT ME!! */ + + private class JalviewChangeSupport implements PropertyChangeListener + { + public void propertyChange(PropertyChangeEvent evt) + { + // Handle change events - most are simply routed to other sources + changeSupport.firePropertyChange(evt); + } + + /** + * change listeners are notified of changes to resources so they can update + * their state. E.g. - the 'services' property notifies when the available + * set of web service endpoints have changed. + */ + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); + + /** + * @param propertyName + * @param listener + * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String, + * java.beans.PropertyChangeListener) + */ + public void addJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(propertyName, listener); + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addJalviewPropertyChangeListener( + PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /* + * @param propertyName + * + * @param oldValue + * + * @param newValue + * + * @see + * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String, + * java.lang.Object, java.lang.Object) public void firePropertyChange(String + * propertyName, Object oldValue, Object newValue) { + * changeSupport.firePropertyChange(propertyName, oldValue, newValue); } + */ + + /** + * @param propertyName + * @param listener + * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String, + * java.beans.PropertyChangeListener) + */ + public void removeJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(propertyName, listener); + } + + } + + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); + + /** + * @param listener + * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addJalviewPropertyChangeListener( + PropertyChangeListener listener) + { + changeSupport.addJalviewPropertyChangeListener(listener); + } + + /** + * @param propertyName + * @param listener + * @see jalview.gui.Desktop.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.Desktop.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; @@ -70,84 +174,105 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static boolean internalCopy = false; 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 - - } + + 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. */ @@ -177,7 +302,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised - desktop.setDesktopManager(new MyDesktopManager(new DefaultDesktopManager())); + desktop.setDesktopManager(new MyDesktopManager( + new DefaultDesktopManager())); Rectangle dims = getLastKnownDimensions(""); if (dims != null) { @@ -231,7 +357,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - 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. @@ -288,6 +413,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -450,34 +587,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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() { @@ -629,8 +765,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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")); @@ -810,22 +946,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -1038,10 +1172,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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"); @@ -1051,12 +1185,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); } } @@ -1069,10 +1218,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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"); @@ -1080,13 +1229,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); } } @@ -1329,13 +1497,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -1390,8 +1557,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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( @@ -1420,8 +1587,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -1435,8 +1602,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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(); } @@ -1586,9 +1753,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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"); @@ -1752,17 +1919,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); } } } @@ -1926,8 +2094,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -1963,17 +2133,135 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + /** + * 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(); - - try { - new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()).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("Exception when trying to launch Envision2 workflow discovery.", + e); Cache.log.info(e.getStackTrace()); } - new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()).start(); + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + .addPropertyChangeListener(changeSupport); + (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer())) + .start(); + } + if (blocking) + { + while (alive) + { + try + { + Thread.sleep(15); + } catch (Exception e) + { + } + alive = (t1 != null && t1.isAlive()) + || (t2 != null && t2.isAlive()) + || (t0 != null && t0.isAlive()); + } + } + } + + /** + * 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) + { + new Thread(new Runnable() + { + public void run() + { + try + { + 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(); + } + } + }).start(); + } + + public static WsParamSetManager wsparamManager = null; + + public static ParamManager getUserParameterStore() + { + if (wsparamManager == null) + { + wsparamManager = new WsParamSetManager(); + } + return wsparamManager; } + }