import javax.swing.event.MenuEvent;
import jalview.analysis.*;
+import jalview.bin.Cache;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.io.*;
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener, thatListener;
+ final java.beans.PropertyChangeListener thisListener;
// Do this once to get current state
BuildWebServiceMenu();
- Desktop.discoverer
- .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+ Desktop.instance.addJalviewPropertyChangeListener("services",
+ thisListener=new java.beans.PropertyChangeListener()
{
public void propertyChange(PropertyChangeEvent evt)
{
- // System.out.println("Discoverer property change.");
- if (evt.getPropertyName().equals("services"))
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
System.err
- .println("Change support JWS1: build services again.");
+ .println("Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
}
}
});
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .addPropertyChangeListener(
- thatListener = new java.beans.PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- System.err
- .println("Change support JWS2: build services again.");
- BuildWebServiceMenu();
- }
- });
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
- Desktop.discoverer.removePropertyChangeListener(thisListener);
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .removePropertyChangeListener(thatListener);
+ System.out.println("deregistering discoverer listener");
+ Desktop.instance.removeJalviewPropertyChangeListener("services",thisListener);
closeMenuItem_actionPerformed(true);
};
});
// object broker mechanism.
Vector wsmenu = new Vector();
final IProgressIndicator af = this;
- if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
+ if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ && Discoverer.services != null
+ && (Discoverer.services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to be
// stored or retrieved from elsewhere
}
// TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
jws2servs.attachWSMenuEntry(jws2men, this);
wsmenu.add(jws2men);
}
- else
- {
- if (!jws2servs.isRunning())
- {
- new Thread(jws2servs).start();
- }
- }
}
}
resetWebServiceMenu();
*/
private void build_urlServiceMenu(JMenu webService)
{
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+ webService, this);
+ }
}
/*
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;
import javax.swing.event.MenuListener;
/**
- * DOCUMENT ME!
+ * Jalview Desktop
+ *
*
* @author $author$
* @version $Revision$
public class Desktop extends jalview.jbgui.GDesktop implements
DropTargetListener, ClipboardOwner, IProgressIndicator
{
- /** DOCUMENT ME!! */
+
+ private class JalviewChangeSupport implements PropertyChangeListener
+ {
+ @Override
+ 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;
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.
*/
// 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)
{
}
});
- 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.
public void paintComponent(Graphics g)
{
- if (showMemoryUsage && g != null)
+ if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
g.setColor(Color.red);
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_ENVISION2_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());
+ }
+ }
}
+
}
import java.beans.PropertyChangeListener;
import java.net.ConnectException;
import java.util.HashSet;
+import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JMenu;
}
boolean running = false;
-
+ Thread oldthread=null;
@Override
public void run()
{
- if (running)
+ if (running && oldthread!=null && oldthread.isAlive())
{
return;
}
running = true;
+ oldthread = Thread.currentThread();
try
{
Class foo = getClass().getClassLoader().loadClass(
{
System.err
.println("Not enabling Jalview Webservices version 2: client jar is not available."
- +"\nPlease check that your webstart JNLP file is up to date!");
+ + "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
}
- // Cache.initLogger();
- // Cache.log.setLevel(Level.DEBUG);
- // TODO: Document and PACK JWS2
- String jwsservers = Cache.getDefault("JWS2HOSTURLS",
- "http://webservices.compbio.dundee.ac.uk:8084/jws2");
- try
+ if (services != null)
{
- if (Jws2Base.validURL(jwsservers))
+ services.removeAllElements();
+ }
+ for (String jwsservers : getServiceUrls())
+ {
+ try
{
- // look for services
- for (Services srv : Jws2Base.Services.values())
+ if (Jws2Base.validURL(jwsservers))
{
- MsaWS service = null;
- try
- {
- service = Jws2Base.connect(jwsservers, srv);
- } catch (Exception e)
+ // look for services
+ for (Services srv : Jws2Base.Services.values())
{
- System.err.println("Jws2 Discoverer: Problem with "
- + jwsservers + " with service " + srv + ":\n"
- + e.getMessage());
- if (!(e instanceof javax.xml.ws.WebServiceException))
+ MsaWS service = null;
+ try
{
- e.printStackTrace();
+ service = Jws2Base.connect(jwsservers, srv);
+ } catch (Exception e)
+ {
+ System.err.println("Jws2 Discoverer: Problem on "
+ + jwsservers + " with service " + srv + ":\n"
+ + e.getMessage());
+ if (!(e instanceof javax.xml.ws.WebServiceException))
+ {
+ e.printStackTrace();
+ }
+ }
+ ;
+ if (service != null)
+ {
+ addService(jwsservers, srv, service);
}
}
- ;
- if (service != null)
- {
- addService(jwsservers, srv, service);
- }
- }
- }
- else
+ }
+ else
+ {
+ Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Cache.log.warn("Exception when discovering Jws2 services.", e);
+ } catch (Error e)
{
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ Cache.log.error("Exception when discovering Jws2 services.", e);
}
- } catch (Exception e)
- {
- e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- } catch (Error e)
- {
- Cache.log.error("Exception when discovering Jws2 services.", e);
}
+ oldthread = null;
running = false;
changeSupport.firePropertyChange("services", new Vector(), services);
}
return running;
}
+ /**
+ * the jalview .properties entry for JWS2 URLS
+ */
+ final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ public static void setServiceUrls(Vector<String> urls)
+ {
+ if (urls != null)
+ {
+ StringBuffer urlbuffer = new StringBuffer();
+ String sep = "";
+ for (String url : urls)
+ {
+ urlbuffer.append(sep);
+ urlbuffer.append(url);
+ sep = ",";
+ }
+ Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ }
+ else
+ {
+ Cache.removeProperty(JWS2HOSTURLS);
+ }
+ }
+
+ public static Vector<String> getServiceUrls()
+ {
+ String surls = Cache.getDefault(JWS2HOSTURLS,
+ "http://webservices.compbio.dundee.ac.uk:8084/jws2");
+ Vector<String> urls = new Vector<String>();
+ try
+ {
+ StringTokenizer st = new StringTokenizer(surls, ",");
+ while (st.hasMoreElements())
+ {
+ String url = null;
+ try
+ {
+ java.net.URL u = new java.net.URL(url = st.nextToken());
+ if (!urls.contains(url))
+ {
+ urls.add(url);
+ }
+ else
+ {
+ jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ + JWS2HOSTURLS + " list");
+ }
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log
+ .warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
+ jalview.bin.Cache.log
+ .warn("This was probably due to a malformed comma separated list"
+ + " in the "
+ + JWS2HOSTURLS
+ + " entry of $(HOME)/.jalview_properties)");
+ jalview.bin.Cache.log.debug("Exception was ", ex);
+ }
+ }
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.warn(
+ "Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
+ }
+ if (urls.size() >= 0)
+ {
+ return urls;
+ }
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff