From a3b90af5d2d63a54e94e827022325c3c0313384c Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 4 Nov 2016 14:28:57 +0000
Subject: [PATCH] JAL-2282 Better check for existing url links

---
 src/jalview/gui/Desktop.java |   24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4d10cc8..d06dd26 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -77,6 +78,7 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.concurrent.ExecutorService;
@@ -2276,20 +2278,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           // check what the actual links are - if it's just the default don't
           // bother with the warning
           Vector<String> links = Preferences.sequenceURLLinks;
-          if (links == null || links.size() < 1)
+
+          // only need to check links if there is one with a
+          // SEQUENCE_ID which is not the default EMBL_EBI link
+          ListIterator<String> li = links.listIterator();
+          Boolean check = false;
+          while (li.hasNext() && !check)
           {
-            // there are no links
-            return;
+            String link = li.next();
+            check = (link.contains(SEQUENCE_ID) && !link
+                    .equals(EMBLEBI_STRING));
           }
-          else if ((links.size() == 1)
-                  && links.get(0).equals(EMBLEBI_STRING))
+          if (!check)
           {
-            // the only link is the default EMBL-EBI link
             return;
           }
 
-          // check in case URL links use old style tokens ($SEQUENCE_ID$ for
-          // sequence id _or_ accession id)
+          // ask user to check in case URL links use old style tokens
+          // ($SEQUENCE_ID$ for sequence id _or_ accession id)
           JPanel msgPanel = new JPanel();
           msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
           msgPanel.add(Box.createVerticalGlue());
@@ -2306,7 +2312,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                   MessageManager.getString("label.do_not_display_again"));
           jcb.addActionListener(new ActionListener()
           {
-
             @Override
             public void actionPerformed(ActionEvent e)
             {
@@ -2327,7 +2332,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                   MessageManager
                           .getString("label.SEQUENCE_ID_no_longer_used"),
                   JOptionPane.WARNING_MESSAGE);
-
         }
       }
     });
-- 
1.7.10.2