X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=21a0e37ca8435e267a74176b3571eae20ba2e988;hb=70c875f4c2db626298097acd47f31db9115fcea8;hp=ed9ed504c9cb312e17688761266f7bcb0ceb2ffa;hpb=1b378087ec2d5be9b290cd63c45bfdb9e75269fb;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ed9ed50..21a0e37 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -143,7 +143,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
 
-  public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
+  public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
@@ -559,26 +559,27 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public void getIdentifiersOrgData()
   {
-    // Thread off the identifiers fetcher
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+    {// Thread off the identifiers fetcher
+      new Thread(new Runnable()
       {
-        Cache.log.debug("Downloading data from identifiers.org");
-        UrlDownloadClient client = new UrlDownloadClient();
-        try
-        {
-          client.download(IdOrgSettings.getUrl(),
-                  IdOrgSettings.getDownloadLocation());
-        } catch (IOException e)
+        @Override
+        public void run()
         {
-          Cache.log.debug("Exception downloading identifiers.org data"
-                  + e.getMessage());
+          Cache.log.debug("Downloading data from identifiers.org");
+          try
+          {
+            UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                    IdOrgSettings.getDownloadLocation());
+          } catch (IOException e)
+          {
+            Cache.log.debug("Exception downloading identifiers.org data"
+                    + e.getMessage());
+          }
         }
-      }
-    }).start();
-    ;
+      }).start();
+      ;
+    }
   }
 
   @Override
@@ -927,7 +928,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (java.lang.ClassCastException cex)
     {
       Cache.log.warn(
-              "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
               cex);
     }
   }
@@ -1135,7 +1136,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     panel.add(history);
     history.setPreferredSize(new Dimension(400, 20));
     history.setEditable(true);
-    history.addItem("http://www.");
+    history.addItem("https://www.");
 
     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
 
@@ -1351,7 +1352,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                       "..Checking..")
               + " is available for download from "
               + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
+                      "https://www.jalview.org")
               + " !!");
       if (red)
       {
@@ -1362,7 +1363,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             "AUTHORFNAMES",
             "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
-            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
             + "<br><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"
@@ -1924,7 +1925,10 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
 
     // FIXME: ideally should use UI interface API
-    FeatureSettings viewFeatureSettings = af.featureSettings;
+    FeatureSettings viewFeatureSettings = (af.featureSettings != null
+            && af.featureSettings.isOpen())
+            ? af.featureSettings
+            : null;
     Rectangle fsBounds = af.getFeatureSettingsGeometry();
     for (int i = 0; i < size; i++)
     {
@@ -1935,9 +1939,10 @@ public class Desktop extends jalview.jbgui.GDesktop
       // transfer reference for existing feature settings to new alignFrame
       if (ap == af.alignPanel)
       {
-        newaf.featureSettings = (viewFeatureSettings.fr.ap == ap)
-                ? viewFeatureSettings
-                : null;
+        if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+        {
+          newaf.featureSettings = viewFeatureSettings;
+        }
         newaf.setFeatureSettingsGeometry(fsBounds);
       }
 
@@ -1966,6 +1971,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     }
 
+    af.featureSettings = null;
     af.alignPanels.clear();
     af.closeMenuItem_actionPerformed(true);
 
@@ -2566,13 +2572,36 @@ public class Desktop extends jalview.jbgui.GDesktop
     this.inBatchMode = inBatchMode;
   }
 
+  /**
+   * start service discovery and wait till it is done
+   */
   public void startServiceDiscovery()
   {
     startServiceDiscovery(false);
   }
 
+  /**
+   * start service discovery threads - blocking or non-blocking
+   * 
+   * @param blocking
+   */
   public void startServiceDiscovery(boolean blocking)
   {
+    startServiceDiscovery(blocking,false);
+  }
+
+  /**
+   * start service discovery threads
+   * 
+   * @param blocking
+   *          - false means call returns immediately
+   * @param ignore_SHOW_JWS2_SERVICES_preference
+   *          - when true JABA services are discovered regardless of user's JWS2
+   *          discovery preference setting
+   */
+  public void startServiceDiscovery(boolean blocking,
+          boolean ignore_SHOW_JWS2_SERVICES_preference)
+  {
     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
@@ -2590,7 +2619,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       (t0 = new Thread(discoverer)).start();
     }
 
-    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    if (ignore_SHOW_JWS2_SERVICES_preference
+            || Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
               .startDiscoverer(changeSupport);