X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=f06adc4cad82042fc2b809c7a3b4cb13447fb6b0;hp=7564dda8f9171496a7fc55727552619dd84cb45a;hb=8dadf27423ca69874dc6a3c9d416974ba5ae767f;hpb=31e884303f1da48817451195d7be98633ab93427

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7564dda..f06adc4 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -927,7 +927,7 @@ 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 +1135,7 @@ 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 +1351,7 @@ 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 +1362,7 @@ 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"
@@ -2571,13 +2571,36 @@ 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
@@ -2595,7 +2618,8 @@ 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);