JAL-1499 MEGA format, JAL-1421 List<String> url links

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index fee47e5..8953487 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -33,7 +33,6 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -62,6 +61,7 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Hashtable;
@@ -215,19 +215,6 @@ public class PopupMenu extends JPopupMenu
   JMenuItem hideInsertions = new JMenuItem();
 
   /**
-   * Creates a new PopupMenu object.
-   * 
-   * @param ap
-   *          DOCUMENT ME!
-   * @param seq
-   *          DOCUMENT ME!
-   */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
-  {
-    this(ap, seq, links, null);
-  }
-
-  /**
    * 
    * @param ap
    * @param seq
@@ -235,7 +222,7 @@ public class PopupMenu extends JPopupMenu
    * @param groupLinks
    */
   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
-          Vector links, Vector groupLinks)
+          List<String> links, List<String> groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -616,10 +603,10 @@ public class PopupMenu extends JPopupMenu
     {
 
       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-      Vector linkset = new Vector();
+      List<String> linkset = new ArrayList<String>();
       for (int i = 0; i < links.size(); i++)
       {
-        String link = links.elementAt(i).toString();
+        String link = links.get(i);
         UrlLink urlLink = null;
         try
         {
@@ -670,7 +657,7 @@ public class PopupMenu extends JPopupMenu
                 {
                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                   {
-                    linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                    linkset.add(urls[u] + "|" + urls[u + 1]);
                     addshowLink(linkMenu, label + "|" + urls[u],
                             urls[u + 1]);
                   }
@@ -688,7 +675,7 @@ public class PopupMenu extends JPopupMenu
               {
                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                  linkset.add(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
@@ -706,7 +693,7 @@ public class PopupMenu extends JPopupMenu
               {
                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                  linkset.add(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
@@ -717,7 +704,7 @@ public class PopupMenu extends JPopupMenu
         {
           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
           {
-            linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+            linkset.add(label + "|" + urlLink.getUrl_prefix());
             // Add a non-dynamic link
             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
           }
@@ -861,7 +848,7 @@ public class PopupMenu extends JPopupMenu
     showOrHideMenu.add(item);
   }
 
-  private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+  private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
   {
 
     // TODO: usability: thread off the generation of group url content so root
@@ -929,7 +916,7 @@ public class PopupMenu extends JPopupMenu
                              // to user
     for (int i = 0; i < groupLinks.size(); i++)
     {
-      String link = groupLinks.elementAt(i).toString();
+      String link = groupLinks.get(i);
       GroupUrlLink urlLink = null;
       try
       {