<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
- <offline_allowed />
+ <icon href="JalviewLogo_big.png" />
+ <offline_allowed/>
</information>
<resources>
<j2se version="${j2sev}" initial_heap_size="10M" />
<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
+ <icon href="JalviewLogo_big.png" />
<offline_allowed />
</information>
<resources>
<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
+ <icon href="JalviewLogo_big.png" />
<offline_allowed />
</information>
<resources>
<head><title>Jalview Documentation</title></head>
<body>
-<IMG src="align.jpg"><font size="4">
+<IMG src="Jalview_Logo.png"><font size="4">
<br><br>
<strong>Jalview Documentation</strong></font>
<br><br>
<strong>What's new ?</strong>
</p>
<p>
- The Jalview 2.8 release features (tbc)
- <br /> For full
- details see the <a href="releases.html#Jalview2.7.1">Jalview 2.7.1
- release history</a>.
+ Jalview 2.8 includes a brand new logo, which you'll see in file browsers, splash screens, and also on the new look Jalview site.
</p>
<p>
- <strong>Highlights in Jalview Desktop Version 2.7.1</strong>
+ In addition to our new look, Jalview 2.8 includes a number of new
+ features.. some of which have been in development since July 2010. The
+ highlights are below, and - as usual, for a comprehensive list, take a
+ look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
+ Notes</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Desktop Version 2.8</strong>
</p>
<ul>
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = getAboutMessage(false);
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+// StringBuffer message = getAboutMessage(false);
+// JOptionPane.showInternalMessageDialog(Desktop.desktop,
+//
+// message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ new Thread(new Runnable() { public void run() {new SplashScreen(true);}}).start();
}
public StringBuffer getAboutMessage(boolean shortv)
message.append("<html>");
if (shortv)
{
- message.append("<h1><strong>Jalview "
+ message.append("<h1><strong>Version: "
+ jalview.bin.Cache.getProperty("VERSION")
+ "</strong></h1><br>");
message.append("<strong>Last Updated: <em>"
else
{
- message.append("<strong>Jalview version "
+ message.append("<strong>Version "
+ jalview.bin.Cache.getProperty("VERSION")
+ "; last updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Jalview version "
+ message.append("<br>!! Version "
+ jalview.bin.Cache.getDefault("LATEST_VERSION",
"..Checking..")
+ " is available for download from "
"AUTHORNAMES",
"Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
+ "<br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br>For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br>For help, see the FAQ at <a href=\"http://www.jalview.org\">www.jalview.org</a> and/or join the jalview-discuss@jalview.org mailing list"
+ "<br>If you use Jalview, please cite:"
+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
return wsparamManager;
}
+ /**
+ * static hyperlink handler proxy method for use by Jalview's internal windows
+ * @param e
+ */
+ public static void hyperlinkUpdate(HyperlinkEvent e)
+ {
+ if (e.getEventType() == EventType.ACTIVATED)
+ {
+ String url=null;
+ try
+ {
+ url = e.getURL().toString();
+ Desktop.showUrl(url);
+ } catch (Exception x)
+ {
+ if (url!=null) {
+ if (Cache.log!=null) {
+ Cache.log.error("Couldn't handle string "+url+" as a URL.");
+ } else {
+ System.err.println("Couldn't handle string "+url+" as a URL.");
+ }
+ }
+ // ignore any exceptions due to dud links.
+ }
+
+ }
+ }
+
}
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class SplashScreen extends JPanel implements Runnable
+public class SplashScreen extends JPanel implements Runnable, HyperlinkListener
{
boolean visible = true;
*/
public SplashScreen()
{
+ this(false);
+ }
+ private boolean interactiveDialog=false;
+ /**
+ *
+ * @param interactive if true - an internal dialog is opened rather than a free-floating splash screen
+ */
+ public SplashScreen(boolean interactive)
+ {
+ this.interactiveDialog=interactive;
+ // show a splashscreen that will disapper
Thread t = new Thread(this);
t.start();
}
+
MouseAdapter closer = new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
try
{
- visible = false;
- closeSplash();
+ if (!interactiveDialog)
+ {
+ visible = false;
+ closeSplash();
+ }
} catch (Exception ex)
{
}
addMouseListener(closer);
try
{
- java.net.URL url = getClass().getResource("/images/logo.gif");
+ java.net.URL url = getClass().getResource("/images/Jalview_Logo.png");
if (url != null)
{
iframe = new JInternalFrame();
iframe.setFrameIcon(null);
- iframe.setClosable(false);
+ iframe.setClosable(interactiveDialog);
this.setLayout(new BorderLayout());
iframe.setContentPane(this);
iframe.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.desktop.add(iframe);
SplashImage splashimg = new SplashImage(image);
iconimg.add(splashimg, BorderLayout.CENTER);
- add(iconimg, BorderLayout.WEST);
+ add(iconimg, BorderLayout.NORTH);
add(authlist, BorderLayout.CENTER);
authlist.setEditable(false);
authlist.addMouseListener(closer);
protected boolean refreshText()
{
String newtext = Desktop.instance.getAboutMessage(true).toString();
- System.err.println("Text found: \n"+newtext+"\nEnd of newtext.");
+ //System.err.println("Text found: \n"+newtext+"\nEnd of newtext.");
if (oldtext != newtext.length())
{
iframe.setVisible(false);
authlist=new JTextPane();
authlist.setEditable(false);
authlist.addMouseListener(closer);
+ authlist.addHyperlinkListener(this);
authlist.setContentType("text/html");
authlist.setText(newtext);
authlist.setVisible(true);
add(authlist, BorderLayout.CENTER);
- iframe.pack();
- iframe.setVisible(true);
iframe.setBounds((int) ((Desktop.instance.getWidth() - 750) / 2),
(int) ((Desktop.instance.getHeight() - 160) / 2), 750,
iframe.getPreferredSize().height);
- System.err.println("New preferred size: "+iframe.getPreferredSize().height);
+ //System.err.println("New preferred size: "+iframe.getPreferredSize().height);
+ iframe.validate();
+ iframe.setVisible(true);
return true;
}
while (visible)
{
+ iframe.repaint();
try
{
Thread.sleep(500);
} catch (Exception ex)
{
}
-
- if (((System.currentTimeMillis() / 1000) - startTime) > 5)
+
+ if (!interactiveDialog && ((System.currentTimeMillis() / 1000) - startTime) > 5)
{
visible = false;
}
if (visible && refreshText())
{
- repaint();
+// if (interactiveDialog) {
+ iframe.repaint();
+// } else {
+// iframe.repaint();
+// };
+ }
+ if (interactiveDialog)
+ {
+ return;
}
}
if (image != null)
{
- g.drawImage(image, 4, (getHeight() - image.getHeight(this)) / 2,
+ g.drawImage(image, (getWidth() - image.getWidth(this)) / 2, (getHeight() - image.getHeight(this)) / 2,
this);
}
}
* += fontSize + 4); }
*/
}
+ @Override
+ public void hyperlinkUpdate(HyperlinkEvent e)
+ {
+ Desktop.hyperlinkUpdate(e);
+
+ }
}
\ No newline at end of file
* @version $Revision$
*/
public class WebserviceInfo extends GWebserviceInfo implements
- HyperlinkListener
+ HyperlinkListener, IProgressIndicator
{
/** Job is Queued */
this.title = title;
setInfoText(info);
- java.net.URL url = getClass().getResource("/images/logo.gif");
+ java.net.URL url = getClass().getResource("/images/Jalview_Logo_small.png");
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
MediaTracker mt = new MediaTracker(this);
if (image != null)
{
- g.rotate(Math.toRadians(angle), 28, 28);
+ int x=image.getWidth(this)/2,y=image.getHeight(this)/2;
+ g.rotate(Math.toRadians(angle), 10+x, 10+y);
g.drawImage(image, 10, 10, this);
- g.rotate(-Math.toRadians(angle), 28, 28);
+ g.rotate(-Math.toRadians(angle), 10+x, 10+y);
}
}
public void hyperlinkUpdate(HyperlinkEvent e)
{
- if (e.getEventType() == EventType.ACTIVATED)
+ Desktop.hyperlinkUpdate(e);
+ }
+
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
+ Hashtable progressBars, progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
{
- String url=null;
- try
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
+
+ JPanel progressPanel;
+ Long lId = new Long(id);
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if (progressBars.get(lId) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(lId);
+ progressPanel = null;
+ if (message != null)
{
- url = e.getURL().toString();
- Desktop.showUrl(url);
- } catch (Exception x)
+ statusBar.setText(message);
+ }
+ if (progressBarHandlers.contains(lId))
{
- if (url!=null) {
- Cache.log.error("Couldn't handle string "+url+" as a URL.");
- }
- // ignore any exceptions due to dud links.
+ progressBarHandlers.remove(lId);
}
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(lId, progressPanel);
+ }
+ // update GUI
+ // setMenusForViewport();
+ validate();
+ }
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
}
+ return false;
}
}
public JButton mergeResults = new JButton();
GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+ public JPanel statusPanel = new JPanel(new GridLayout());
+ public JLabel statusBar = new JLabel();
/**
* Creates a new GWebserviceInfo object.
buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(
19, 6, 16, 4), 0, 0));
+ this.add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
}
/**
jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
}
// Decide on overall state based on collected jobs[] states
- if (jstate.running > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- }
- else if (jstate.queuing > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- }
- else
- {
- jobComplete = true;
- if (jstate.finished > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (jstate.error > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- else if (jstate.serror > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
+ updateGlobalStatus(jstate);
if (!jobComplete)
{
try
}
}
+ protected void updateGlobalStatus(JobStateSummary jstate)
+ {
+ if (jstate.running > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ else if (jstate.queuing > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+ else
+ {
+ jobComplete = true;
+ if (jstate.finished > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ }
+
public AWSThread()
{
super();
try
{
boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
- if (cancelledJob || true)
+ if (true) // cancelledJob || true)
{
// CANCELLED_JOB
// if the Jaba server indicates the job can't be cancelled, its
.pullExecStatistics(j.getJobId(), lastchunk);
if (chunk != null)
{
- changed=chunk.getChunk().length()>0;
+ changed|=chunk.getChunk().length()>0;
response.append(chunk.getChunk());
lastchunk = chunk.getNextPosition();
+ try {
+ Thread.sleep(50);
+ } catch (InterruptedException x){};
}
;
} while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
public void parseResult()
{
+ long progbar=System.currentTimeMillis();
+ wsInfo.setProgressBar("Collecting job results.", progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
if (jobs[j].isFinished() && msjob.alignment == null)
{
+ int nunchanged=3,nexcept=3;
boolean jpchanged=false,jpex=false;
do {
try
{
jpchanged = updateJobProgress(msjob);
jpex=false;
+ if (jpchanged) {
+ nexcept=3;
+ }
} catch (Exception e)
{
.warn("Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
- if (jpex) {
- // give up polling after two consecutive exceptions
- jpchanged=false;
- } else {
- jpchanged=true;
- }
+ nexcept--;
+ nunchanged=3;
// set flag remember that we've had an exception.
jpex=true;
+ jpchanged=false;
}
- if (jpchanged)
+ if (!jpchanged)
{
try
{
- Thread.sleep(jpex ? 400 : 200); // wait a bit longer if we experienced an exception.
+ Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we experienced an exception.
} catch (Exception ex)
{
}
;
- }
- } while (jpchanged);
+ nunchanged--;
+ }
+ } while (nunchanged>0 && nexcept>0);
if (Cache.log.isDebugEnabled())
{
Cache.log
.debug("Results not available for finished job - marking as broken job.",
e);
+ msjob.jobProgress
+ .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ + e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
}
else
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
+ wsInfo.setProgressBar(null, progbar);
}
void displayResults(boolean newFrame)
git://source.jalview.org / jalview.git / commitdiff
