JAL-1159 Merging 2.8.1 patches and Anne Menards work from 2012 into development branch

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f77e64d..345c529 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -648,8 +648,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
+    if (instance == null || (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true")))
     {
       return;
     }
@@ -913,7 +913,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .getSelectedFile().getParent());
 
       String format = null;
-      if (chooser.getSelectedFormat().equals("Jalview"))
+      if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview"))
       {
         format = "Jalview";
       }
@@ -1510,6 +1510,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressPanel != null)
     {
+      synchronized(progressPanel) {
       progressPanel.remove(progbar);
       GridLayout gl = (GridLayout) progressPanel.getLayout();
       gl.setRows(gl.getRows() - 1);
@@ -1518,6 +1519,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         this.getContentPane().remove(progressPanel);
         progressPanel = null;
       }
+      }
     }
     validate();
   }
@@ -1527,9 +1529,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     fileLoadingCount--;
     if (fileLoadingCount < 1)
     {
-      for (JPanel flp : fileLoadingPanels)
+      while (fileLoadingPanels.size()>0)
       {
-        removeProgressPanel(flp);
+        removeProgressPanel(fileLoadingPanels.remove(0));
       }
       fileLoadingPanels.clear();
       fileLoadingCount = 0;
@@ -2435,7 +2437,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     boolean alive = true;
     Thread t0 = null, t1 = null, t2 = null;
-
+    // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+    if (true)
+    {
     // todo: changesupport handlers need to be transferred
     if (discoverer == null)
     {
@@ -2445,28 +2449,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     // JAL-940 - disabled JWS1 service configuration - always start discoverer
     // until we phase out completely
-    if (true)
-    {
       (t0 = new Thread(discoverer)).start();
     }
 
-    try
+    // ENFIN services are EOLed as of Jalview 2.8.1 release
+    if (false)
     {
-      if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+      try
       {
-        // 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();
+        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());
       }
-    } 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())