X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b655b2e60fa3369533ca61bcbb87806bb8a6d1b4;hb=02cd62bf5796571c15a9d42774291bfa74b6b31c;hp=ef57d5f5eaf530d45eaf5c905ea5343073035b46;hpb=d9f0a24d9662a0b530fd79b51108dd074d03d6e0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ef57d5f..b655b2e 100644
--- 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;
@@ -3321,7 +3325,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       JEditorPane editPane = new JEditorPane("text/html", "");
@@ -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