From ff513732821cba597d07b4fc19a1f7805b3412c1 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 12 Dec 2016 13:43:16 +0000
Subject: [PATCH] JAL-2316 Missed change from previous checkin

---
 src/jalview/urls/CustomUrlProvider.java |   31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
index f4dcc0c..dae9ccd 100644
--- a/src/jalview/urls/CustomUrlProvider.java
+++ b/src/jalview/urls/CustomUrlProvider.java
@@ -76,7 +76,8 @@ public class CustomUrlProvider extends UrlProviderImpl
       nonselectedUrls = parseUrlStrings(storedUrlList);
     } catch (Exception ex)
     {
-      System.out.println(ex + "\nError parsing sequence links");
+      System.out
+              .println(ex.getMessage() + "\nError parsing sequence links");
     }
   }
 
@@ -98,7 +99,8 @@ public class CustomUrlProvider extends UrlProviderImpl
       nonselectedUrls = parseUrlList(storedUrlList);
     } catch (Exception ex)
     {
-      System.out.println(ex + "\nError parsing sequence links");
+      System.out
+              .println(ex.getMessage() + "\nError parsing sequence links");
     }
   }
 
@@ -138,6 +140,11 @@ public class CustomUrlProvider extends UrlProviderImpl
   private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
   {
     HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+    if (urlList == null)
+    {
+      return urls;
+    }
+
     Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
     while (it.hasNext())
     {
@@ -194,10 +201,6 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public boolean setDefaultUrl(String id)
   {
-    /*if (id == null)
-    {
-      defaultUrl = null;
-    }*/
     if (selectedUrls.containsKey(id))
     {
       defaultUrl = id;
@@ -315,14 +318,8 @@ public class CustomUrlProvider extends UrlProviderImpl
   public String chooseDefaultUrl()
   {
     // unilaterally set the default id to the EMBL_EBI link
-    
-    if (nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
-    {
-      // default key must be selected so remove from nonselected list
-      nonselectedUrls.remove(UrlConstants.DEFAULT_LABEL);
-    }
-
-    if (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
+    if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
+            && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
     {
       selectedUrls.put(UrlConstants.DEFAULT_LABEL, new UrlLink(
               UrlConstants.DEFAULT_STRING));
@@ -331,4 +328,10 @@ public class CustomUrlProvider extends UrlProviderImpl
     return UrlConstants.DEFAULT_LABEL;
   }
 
+  @Override
+  public boolean contains(String id)
+  {
+    return (selectedUrls.containsKey(id) || nonselectedUrls.containsKey(id));
+  }
+
 }
-- 
1.7.10.2