From 86b0e83560beed0d399802f866762b3532c6c468 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 7 Nov 2016 11:52:23 +0000
Subject: [PATCH] JAL-2282 show url links that need checked; remove 'www' from
 default

---
 src/jalview/gui/Desktop.java         |   32 +++++++++++++++++++-------------
 src/jalview/jbgui/GSequenceLink.java |    2 +-
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d06dd26..28606f1 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2282,12 +2282,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           // 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)
+          boolean check = false;
+          List<JLabel> urls = new ArrayList<JLabel>();
+          while (li.hasNext())
           {
             String link = li.next();
-            check = (link.contains(SEQUENCE_ID) && !link
-                    .equals(EMBLEBI_STRING));
+            if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+            {
+              check = true;
+              int barPos = link.indexOf("|");
+              String urlMsg = barPos == -1 ? link : link.substring(0,
+                      barPos) + ": " + link.substring(barPos + 1);
+              urls.add(new JLabel(urlMsg));
+            }
           }
           if (!check)
           {
@@ -2306,6 +2313,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                   MessageManager
                           .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
           msgPanel.add(msg);
+          for (JLabel url : urls)
+          {
+            msgPanel.add(url);
+          }
           msgPanel.add(msg2);
 
           final JCheckBox jcb = new JCheckBox(
@@ -2315,15 +2326,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              // update Cache settings if checkbox is selected
-              if (jcb.isSelected())
-              {
-                Cache.setProperty("CHECKURLLINKS", "false");
-              }
-              else
-              {
-                Cache.setProperty("CHECKURLLINKS", "true");
-              }
+              // update Cache settings for "don't show this again"
+              boolean showWarningAgain = !jcb.isSelected();
+              Cache.setProperty("CHECKURLLINKS",
+                      Boolean.valueOf(showWarningAgain).toString());
             }
           });
           msgPanel.add(jcb);
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index b27752e..2689946 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -67,7 +67,7 @@ public class GSequenceLink extends Panel
       }
     });
     urlTB.setFont(JvSwingUtils.getLabelFont());
-    urlTB.setText("http://www.");
+    urlTB.setText("http://");
     urlTB.setBounds(new Rectangle(78, 40, 309, 23));
     urlTB.addKeyListener(new KeyAdapter()
     {
-- 
1.7.10.2