clean up implicit object refs

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ef57d5f..270023e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -153,12 +153,15 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
+import ext.vamsas.ServiceHandle;
+
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
  * @version $Revision$
  */
+@SuppressWarnings("serial")
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
@@ -2081,7 +2084,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
-        Vector newDs = (importDs) ? new Vector() : null; // used to create
+        Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+                                                                      // create
         // minimum dataset set
 
         for (int i = 0; i < sequences.length; i++)
@@ -3029,7 +3033,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param toggleSeqs
    * @param toggleCols
    */
-  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+  protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
   {
 
     boolean hide = false;
@@ -3809,7 +3813,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       sortByAnnotScore.removeAll();
       // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
+      Hashtable<String, String> scoreSorts = new Hashtable<>();
       AlignmentAnnotation aann[];
       for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
@@ -3822,11 +3826,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         }
       }
-      Enumeration labels = scoreSorts.keys();
+      Enumeration<String> labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {
         addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
+                labels.nextElement());
       }
       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();
@@ -4154,14 +4158,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // No MSAWS used any more:
             // Vector msaws = null; // (Vector)
             // Discoverer.services.get("MsaWS");
-            Vector secstrpr = (Vector) Discoverer.services
+            Vector<ServiceHandle> secstrpr = Discoverer.services
                     .get("SecStrPred");
             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
               for (int i = 0, j = secstrpr.size(); i < j; i++)
               {
-                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+                final ext.vamsas.ServiceHandle sh = secstrpr
                         .get(i);
                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
                         .getServiceClient(sh);
@@ -4271,7 +4275,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param webService
    */
-  private void build_urlServiceMenu(JMenu webService)
+  protected void build_urlServiceMenu(JMenu webService)
   {
     // TODO: remove this code when 2.7 is released
     // DEBUG - alignmentView

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index ea883c8..bee9fad 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -23,6 +23,7 @@ package jalview.ws.jws1;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
+import java.net.URL;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -111,21 +112,20 @@ public class Discoverer implements Runnable
 
   static private java.net.URL RootServiceURL = null;
 
-  static public Vector ServiceURLList = null;
+  static public Vector<URL> ServiceURLList = null;
 
   static private boolean reallyDiscoverServices = true;
 
-  public static java.util.Hashtable services = null; // vectors of services
-
+  public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
   // stored by
   // abstractServiceType
   // string
 
-  public static java.util.Vector serviceList = null; // flat list of services
+  public static java.util.Vector<ServiceHandle> serviceList = null;
 
-  static private Vector getDiscoveryURLS()
+  static private Vector<URL> getDiscoveryURLS()
   {
-    Vector urls = new Vector();
+    Vector<URL> urls = new Vector<>();
     String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
             "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
 
@@ -189,7 +189,7 @@ public class Discoverer implements Runnable
       else
       {
         jalview.bin.Cache.log.debug("Setting default services");
-        services = new Hashtable();
+        services = new Hashtable<>();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
                 "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
@@ -217,8 +217,8 @@ public class Discoverer implements Runnable
                             + "\ndoi://10.1093/nar/gkv332",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
                     "JPred Secondary Structure Prediction") };
-        services = new Hashtable();
-        serviceList = new Vector();
+        services = new Hashtable<>();
+        serviceList = new Vector<>();
         buildServiceLists(defServices, serviceList, services);
       }
 
@@ -284,8 +284,9 @@ public class Discoverer implements Runnable
    *          Hashtable
    * @return boolean
    */
-  static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
-          Hashtable sscat)
+  static private boolean buildServiceLists(ServiceHandle[] sh,
+          Vector<ServiceHandle> cat,
+          Hashtable<String, Vector<ServiceHandle>> sscat)
   {
     boolean seenNewDiscovery = false;
     for (int i = 0, j = sh.length; i < j; i++)
@@ -297,11 +298,11 @@ public class Discoverer implements Runnable
                 + sh[i].getEndpointURL() + "\n");
         if (!sscat.containsKey(sh[i].getAbstractName()))
         {
-          sscat.put(sh[i].getAbstractName(), cat = new Vector());
+          sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
         }
         else
         {
-          cat = (Vector) sscat.get(sh[i].getAbstractName());
+          cat = sscat.get(sh[i].getAbstractName());
         }
         cat.add(sh[i]);
         if (sh[i].getAbstractName().equals("Registry"))
@@ -334,8 +335,8 @@ public class Discoverer implements Runnable
 
   public void discoverServices()
   {
-    Hashtable sscat = new Hashtable();
-    Vector cat = new Vector();
+    Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
+    Vector<ServiceHandle> cat = new Vector<>();
     ServiceHandle sh[] = null;
     int s_url = 0;
     if (ServiceURLList == null)
@@ -347,7 +348,7 @@ public class Discoverer implements Runnable
     while (s_url < ServiceURLList.size())
     {
       if ((sh = getServices(
-              (java.net.URL) ServiceURLList.get(s_url))) != null)
+              ServiceURLList.get(s_url))) != null)
       {
 
         buildServiceLists(sh, cat, sscat);
@@ -365,7 +366,7 @@ public class Discoverer implements Runnable
     // so no need to access original discovery thread.
     // Curent decision is to change properties then notify listeners with old
     // and new values.
-    Hashtable oldServices = services;
+    Hashtable<String, Vector<ServiceHandle>> oldServices = services;
     // Vector oldServicelist = serviceList;
     services = sscat;
     serviceList = cat;
@@ -384,7 +385,7 @@ public class Discoverer implements Runnable
       @Override
       public void run()
       {
-        discoverer.doDiscovery();
+        Discoverer.doDiscovery();
         discoverer.discoverServices();
       }
     };
@@ -394,19 +395,19 @@ public class Discoverer implements Runnable
   /**
    * binding service abstract name to handler class
    */
-  private static Hashtable serviceClientBindings;
+  private static Hashtable<String, WS1Client> serviceClientBindings;
 
   public static WS1Client getServiceClient(ServiceHandle sh)
   {
     if (serviceClientBindings == null)
     {
       // get a list from Config or create below
-      serviceClientBindings = new Hashtable();
+      serviceClientBindings = new Hashtable<>();
       serviceClientBindings.put("MsaWS", new MsaWSClient());
       serviceClientBindings.put("SecStrPred", new JPredClient());
       serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
     }
-    WS1Client instance = (WS1Client) serviceClientBindings
+    WS1Client instance = serviceClientBindings
             .get(sh.getAbstractName());
     if (instance == null)
     {