X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FCustomUrlProvider.java;h=d23f771fea5a72bb5dbee6e5bf19fde81def4096;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=b10d8167fb4e16b8dfa9bae9d1bf320746e6142e;hpb=40f8e76e5d28e2c2fe5fddab72fe797a696bed8a;p=jalview.git

diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
index b10d816..d23f771 100644
--- a/src/jalview/urls/CustomUrlProvider.java
+++ b/src/jalview/urls/CustomUrlProvider.java
@@ -37,7 +37,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 /**
  * 
@@ -108,12 +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))
       {
@@ -130,6 +129,7 @@ public class CustomUrlProvider extends UrlProviderImpl
         {
           url = url + SEP + st.nextToken();
         }
+        url = url.trim();
         urls.put(name, new UrlLink(name, url, name));
       }
     }
@@ -139,7 +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;
@@ -150,8 +150,7 @@ public class CustomUrlProvider extends UrlProviderImpl
     {
       Map.Entry<String, String> pair = it.next();
       urls.put(pair.getKey(),
- new UrlLink(pair.getKey(), pair.getValue(),
-              pair.getKey()));
+              new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
     }
     upgradeOldLinks(urls);
     return urls;
@@ -162,20 +161,34 @@ 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.setDescription(UrlConstants.DEFAULT_LABEL);
+      link.setLabel(UrlConstants.DEFAULT_LABEL);
       urls.put(UrlConstants.DEFAULT_LABEL, link);
     }
   }
 
   @Override
-  public Vector<String> getLinksForMenu()
+  public List<String> getLinksForMenu()
   {
-    Vector<String> links = new Vector<String>();
+    List<String> links = new ArrayList<>();
     Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
             .iterator();
     while (it.hasNext())
@@ -189,7 +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;
@@ -277,8 +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())
@@ -297,15 +310,13 @@ public class CustomUrlProvider extends UrlProviderImpl
         }
         if (link.getIsSelected())
         {
-          selurls.put(link.getId(),
-                  new UrlLink(link.getName(), link.getUrl(), link.getName()));
+          selurls.put(link.getId(), new UrlLink(link.getDescription(),
+                  link.getUrl(), link.getDescription()));
         }
         else
         {
-          unselurls
-                  .put(link.getId(),
-                          new UrlLink(link.getName(), link.getUrl(), link
-                                  .getName()));
+          unselurls.put(link.getId(), new UrlLink(link.getDescription(),
+                  link.getUrl(), link.getDescription()));
         }
         // sort out primary and selected ids
         if (link.getIsPrimary())
@@ -327,7 +338,7 @@ public class CustomUrlProvider extends UrlProviderImpl
             && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
     {
       UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
-      link.setDescription(UrlConstants.DEFAULT_LABEL);
+      link.setLabel(UrlConstants.DEFAULT_LABEL);
       selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
     }
     primaryUrl = UrlConstants.DEFAULT_LABEL;
@@ -337,7 +348,8 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public boolean contains(String id)
   {
-    return (selectedUrls.containsKey(id) || nonselectedUrls.containsKey(id));
+    return (selectedUrls.containsKey(id)
+            || nonselectedUrls.containsKey(id));
   }
 
 }