From 5f631be878dd25f9b73d4ba09083e0fd3df8d153 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 23 Mar 2017 14:56:17 +0000
Subject: [PATCH] JAL-2314 Tidies

---
 src/jalview/gui/Desktop.java            |    5 ----
 src/jalview/ws/jws2/Jws2Discoverer.java |   46 +++++++++++++++----------------
 2 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index dc16a57..7d0eb7f 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2854,13 +2854,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
-      {
-        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
-      }
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
               changeSupport);
-
     }
     Thread t3 = null;
     {
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 1b2c708..adca0fa 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -67,7 +67,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   /*
    * the .jalview_properties entry for JWS2 URLS
    */
-  final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+  private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
 
   /*
    * Singleton instance
@@ -85,12 +85,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
-  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
-          validServiceUrls = null;
+  private Vector<String> invalidServiceUrls = null;
 
-  boolean running = false, aborted = false;
+  private Vector<String> urlsWithoutServices = null;
 
-  Thread oldthread = null;
+  private Vector<String> validServiceUrls = null;
+
+  private volatile boolean running = false;
+
+  private volatile boolean aborted = false;
+
+  private Thread oldthread = null;
 
   /**
    * holds list of services.
@@ -143,9 +148,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public void setAborted(boolean aborted)
   {
     this.aborted = aborted;
-
   }
 
+  @Override
   public void run()
   {
 
@@ -179,7 +184,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       ignoredServices.add(ignored);
     }
 
-    changeSupport.firePropertyChange("services", services, new Vector());
+    changeSupport.firePropertyChange("services", services,
+            new Vector<Jws2Instance>());
     oldthread = Thread.currentThread();
     try
     {
@@ -263,7 +269,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     if (!aborted)
     {
       // resort services according to order found in jabaws service list
-      // also ensure servics for each host are ordered in same way.
+      // also ensure services for each host are ordered in same way.
 
       if (services != null && services.size() > 0)
       {
@@ -290,7 +296,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
     oldthread = null;
     running = false;
-    changeSupport.firePropertyChange("services", new Vector(), services);
+    changeSupport.firePropertyChange("services",
+            new Vector<Jws2Instance>(), services);
   }
 
   /**
@@ -321,7 +328,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector();
+      validServiceUrls = new Vector<String>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -330,6 +337,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * attach all available web services to the appropriate submenu in the given
    * JMenu
    */
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
     // dynamically regenerate service list.
@@ -348,8 +356,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       return;
     }
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", false);
+
     /**
      * eventually, JWS2 services will appear under the same align/etc submenus.
      * for moment we keep them separate.
@@ -442,27 +449,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             {
               new Thread(new Runnable()
               {
+                @Override
                 public void run()
                 {
                   setPreferredServiceFor(alignFrame, sv.serviceType,
                           sv.action, sv);
                   changeSupport.firePropertyChange("services",
-                          new Vector(), services);
+                          new Vector<Jws2Instance>(), services);
                 };
               }).start();
 
             }
           });
         }
-        /*
-         * hitm.addActionListener(new ActionListener() {
-         * 
-         * @Override public void actionPerformed(ActionEvent arg0) { new
-         * Thread(new Runnable() {
-         * 
-         * @Override public void run() { new SetPreferredServer(alignFrame,
-         * service.serviceType, service.action); } }).start(); } });
-         */
       }
     }
   }
@@ -481,7 +480,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    MsaWSClient msacl = new MsaWSClient();
+
     List<String> hostLabels = new ArrayList<String>();
     Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
     Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
@@ -590,6 +589,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             new PropertyChangeListener()
             {
 
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 if (getDiscoverer().services != null)
-- 
1.7.10.2