Version "
- + Cache.getProperty("VERSION")
- + "; last updated: "
- + Cache.getDefault("BUILD_DATE", "unknown"));
- }
+ StringBuilder message = new StringBuilder(1024);
+ message.append("Version: ")
+ .append(Cache.getProperty("VERSION")).append("
")
+ .append("Built: ")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append(" from ").append(Cache.getBuildDetailsForSplash())
+ .append("");
- if (Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking"))
{
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("
...Checking latest version...");
}
- else if (!Cache.getDefault("LATEST_VERSION", "Checking")
- .equals(Cache.getProperty("VERSION")))
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
if (Cache.getProperty("VERSION").toLowerCase()
@@ -1408,29 +1389,22 @@ public class Desktop extends jalview.jbgui.GDesktop
message.append("");
}
- message.append("
!! Version "
- + Cache.getDefault("LATEST_VERSION",
- "..Checking..")
- + " is available for download from "
- + Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + " !!");
+ message.append("
!! Version ")
+ .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org"))
+ .append(" !!");
if (red)
{
message.append("
");
}
}
- message.append("
Authors: " + Cache.getDefault(
- "AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
- + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
- + "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
- + "
If you use Jalview, please cite:"
- + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"
- + "");
- return message;
+ message.append("
Authors: ");
+ message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
+ message.append(CITATION);
+
+ return message.toString();
}
/**
@@ -1574,7 +1548,8 @@ public class Desktop extends jalview.jbgui.GDesktop
return;
}
- AlignmentViewport source = null, target = null;
+ AlignViewportI source = null;
+ AlignViewportI target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
@@ -1794,7 +1769,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
try
{
- new Jalview2XML().loadJalviewAlign(choice);
+ new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
@@ -2001,11 +1976,28 @@ public class Desktop extends jalview.jbgui.GDesktop
return;
}
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen())
+ ? af.featureSettings
+ : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = af.alignPanels.get(i);
+
AlignFrame newaf = new AlignFrame(ap);
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
+
/*
* Restore the view's last exploded frame geometry if known. Multiple
* views from one exploded frame share and restore the same (frame)
@@ -2021,8 +2013,17 @@ public class Desktop extends jalview.jbgui.GDesktop
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ // and materialise a new feature settings dialog instance for the new alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
+ }
}
+ af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
@@ -2042,7 +2043,6 @@ public class Desktop extends jalview.jbgui.GDesktop
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
-
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
@@ -2063,11 +2063,33 @@ public class Desktop extends jalview.jbgui.GDesktop
if (gatherThis)
{
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
}
}
+
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null
+ && source.featureSettings.isOpen())
+ {
+ source.showFeatureSettingsUI();
+ }
}
public JInternalFrame[] getAllFrames()
@@ -2469,7 +2491,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void setProgressBar(String message, long id)
{
- Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+ // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
if (progressBars == null)
{
@@ -2610,7 +2632,7 @@ public class Desktop extends jalview.jbgui.GDesktop
public void startServiceDiscovery(boolean blocking)
{
boolean alive = true;
- Thread t0 = null, t1 = null, t2 = null;
+ Thread t0 = null, t1 = null, t2 = null, t3 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
@@ -2628,12 +2650,14 @@ public class Desktop extends jalview.jbgui.GDesktop
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .startDiscoverer(changeSupport);
+ t2 = startServiceDiscovery(
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer(), false);
}
- Thread t3 = null;
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- // TODO: do rest service discovery
+ // start slivka discovery
+ t3 = startServiceDiscovery(
+ jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance(), false);
}
if (blocking)
{
@@ -2645,11 +2669,29 @@ public class Desktop extends jalview.jbgui.GDesktop
} catch (Exception e)
{
}
+ // FIXME: Condition should check the discoverer's isRunning rather than
+ // threads
alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
+ || (t3 != null && t3.isAlive()) || (t0 != null && t0.isAlive());
+ }
+ }
+ }
+
+ public Thread startServiceDiscovery(WSDiscovererI discoverer,
+ boolean blocking)
+ {
+ Thread thread = discoverer.startDiscoverer(changeSupport);
+ if (blocking)
+ {
+ try
+ {
+ thread.join();
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
}
}
+ return thread;
}
/**
@@ -2661,8 +2703,9 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
{
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .getErrorMessages();
+ final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer
+ .getDiscoverer();
+ final String ermsg = discoverer.getErrorMessages();
if (ermsg != null)
{
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))