X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=480b1959d49250a5db6c3130ba530e43a1fd7b64;hb=c5aa740f1fff4c8caee4ccf0c0e0de517ca4dcb8;hp=968262bf9ef69e6d157aeea79a7e9821247431f0;hpb=10b678ebd64a6ae54d45d1c92acf8de2fb3133ff;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 968262b..480b195 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -32,6 +32,8 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.Vector;
+
 
 /**
  * DOCUMENT ME!
@@ -68,11 +70,12 @@ public class PopupMenu extends JPopupMenu
     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-  JMenu jMenu1 = new JMenu();
+  JMenu editMenu = new JMenu();
   JMenuItem cut = new JMenuItem();
   JMenuItem copy = new JMenuItem();
   JMenuItem upperCase = new JMenuItem();
   JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -80,7 +83,7 @@ public class PopupMenu extends JPopupMenu
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(final AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -233,7 +236,10 @@ public class PopupMenu extends JPopupMenu
             showBoxes.setSelected(sg.getDisplayBoxes());
         }
         else
+        {
           groupMenu.setVisible(false);
+          editMenu.setVisible(false);
+        }
 
         if (!ap.av.alignment.getGroups().contains(sg))
         {
@@ -248,24 +254,31 @@ public class PopupMenu extends JPopupMenu
         {
             sequenceMenu.setVisible(false);
         }
-        else
-        {
-          java.util.Vector links = Preferences.sequenceURLLinks;
 
+        if(links != null && links.size()>0)
+        {
           JMenu linkMenu = new JMenu("Link");
           JMenuItem item;
           for(int i=0; i<links.size(); i++)
           {
             String link = links.elementAt(i).toString();
+            final String label = link.substring(0, link.indexOf("|"));
+            item = new JMenuItem(label);
+            final String url;
 
-            item = new JMenuItem(link.substring(0, link.indexOf("|")));
-            String id = sequence.getName();
-            if(id.indexOf("|")>-1)
-              id = id.substring(id.lastIndexOf("|")+1);
-
-            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + id +
-                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            if (link.indexOf("$SEQUENCE_ID$") > -1)
+            {
+              String id = seq.getName();
+              if (id.indexOf("|") > -1)
+                id = id.substring(id.lastIndexOf("|") + 1);
+
+              url = link.substring(link.indexOf("|") + 1,
+                                   link.indexOf("$SEQUENCE_ID$"))
+                  + id +
+                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            }
+            else
+              url = link.substring(link.lastIndexOf("|")+1);
 
 
             item.addActionListener(new java.awt.event.ActionListener()
@@ -362,7 +375,7 @@ public class PopupMenu extends JPopupMenu
                     showColourText_actionPerformed(e);
                 }
             });
-    jMenu1.setText("Edit");
+    editMenu.setText("Edit");
     cut.setText("Cut");
     cut.addActionListener(new ActionListener()
     {
@@ -395,9 +408,17 @@ public class PopupMenu extends JPopupMenu
         lowerCase_actionPerformed(e);
       }
     });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        toggle_actionPerformed(e);
+      }
+    });
     add(groupMenu);
         add(sequenceMenu);
-    this.add(jMenu1);
+    this.add(editMenu);
     groupMenu.add(groupName);
         groupMenu.addSeparator();
         groupMenu.add(unGroupMenuItem);
@@ -447,10 +468,11 @@ public class PopupMenu extends JPopupMenu
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
-    jMenu1.add(copy);
-    jMenu1.add(cut);
-    jMenu1.add(upperCase);
-    jMenu1.add(lowerCase);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
@@ -1069,4 +1091,18 @@ public class PopupMenu extends JPopupMenu
     ap.repaint();
   }
 
+  public void toggle_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+      return;
+
+    for (int g = 0; g < sg.getSize(); g++)
+    {
+      sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+    }
+
+    ap.repaint();
+  }
+
 }