From c5aa740f1fff4c8caee4ccf0c0e0de517ca4dcb8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 7 Jun 2006 12:59:07 +0000
Subject: [PATCH] PopupMenu displays URL links

---
 src/jalview/gui/IdPanel.java   |    3 ++-
 src/jalview/gui/PopupMenu.java |   33 +++++++++++++++++++++------------
 2 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index eb6c3bc..9e0ed33 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -279,7 +279,8 @@ public class IdPanel extends JPanel implements MouseListener,
         if (javax.swing.SwingUtilities.isRightMouseButton(e))
         {
             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-                    (Sequence) av.getAlignment().getSequenceAt(seq));
+                    (Sequence) av.getAlignment().getSequenceAt(seq),
+                    Preferences.sequenceURLLinks);
             pop.show(this, e.getX(), y);
 
             return;
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index f99b1ed..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!
@@ -81,7 +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
@@ -252,24 +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()
-- 
1.7.10.2