X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FCustomUrlProvider.java;h=d23f771fea5a72bb5dbee6e5bf19fde81def4096;hb=refs%2Fheads%2FJalview-JS%2Fdevelop_j2s_v3_2_9_j11;hp=0d5ef990ce6260f0b82f8c55360fb408ccc82251;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
index 0d5ef99..d23f771 100644
--- a/src/jalview/urls/CustomUrlProvider.java
+++ b/src/jalview/urls/CustomUrlProvider.java
@@ -107,12 +107,12 @@ public class CustomUrlProvider extends UrlProviderImpl
   {
     // cachedUrlList is in form <label>|<url>|<label>|<url>...
     // parse cachedUrlList into labels (used as id) and url links
-    HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> urls = new HashMap<>();
 
     StringTokenizer st = new StringTokenizer(urlStrings, SEP);
     while (st.hasMoreElements())
     {
-      String name = st.nextToken();
+      String name = st.nextToken().trim();
 
       if (!isMiriamId(name))
       {
@@ -129,6 +129,7 @@ public class CustomUrlProvider extends UrlProviderImpl
         {
           url = url + SEP + st.nextToken();
         }
+        url = url.trim();
         urls.put(name, new UrlLink(name, url, name));
       }
     }
@@ -138,7 +139,7 @@ public class CustomUrlProvider extends UrlProviderImpl
 
   private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
   {
-    HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> urls = new HashMap<>();
     if (urlList == null)
     {
       return urls;
@@ -160,10 +161,24 @@ public class CustomUrlProvider extends UrlProviderImpl
    */
   private void upgradeOldLinks(HashMap<String, UrlLink> urls)
   {
+    boolean upgrade = false;
     // upgrade old SRS link
     if (urls.containsKey(SRS_LABEL))
     {
       urls.remove(SRS_LABEL);
+      upgrade = true;
+    }
+    // upgrade old EBI link - easier just to remove and re-add than faffing
+    // around checking exact url
+    if (urls.containsKey(UrlConstants.DEFAULT_LABEL))
+    {
+      // note because this is called separately for selected and nonselected
+      // urls, the default url will not always be present
+      urls.remove(UrlConstants.DEFAULT_LABEL);
+      upgrade = true;
+    }
+    if (upgrade)
+    {
       UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
       link.setLabel(UrlConstants.DEFAULT_LABEL);
       urls.put(UrlConstants.DEFAULT_LABEL, link);
@@ -173,7 +188,7 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public List<String> getLinksForMenu()
   {
-    List<String> links = new ArrayList<String>();
+    List<String> links = new ArrayList<>();
     Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
             .iterator();
     while (it.hasNext())
@@ -187,7 +202,7 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public List<UrlLinkDisplay> getLinksForTable()
   {
-    ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+    ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<>();
     displayLinks = getLinksForTable(selectedUrls, true);
     displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
     return displayLinks;
@@ -275,8 +290,8 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public void setUrlData(List<UrlLinkDisplay> links)
   {
-    HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
-    HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> unselurls = new HashMap<>();
+    HashMap<String, UrlLink> selurls = new HashMap<>();
 
     Iterator<UrlLinkDisplay> it = links.iterator();
     while (it.hasNext())