Merge branch 'releases/Release_2_11_4_Branch'

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index b125ba5..89c92d4 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -49,6 +49,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.HttpUtils;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 import jalview.xml.binding.uniprot.DbReferenceType;
@@ -68,7 +69,7 @@ import jalview.xml.binding.uniprot.PropertyType;
  */
 public class Uniprot extends DbSourceProxyImpl
 {
-  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://rest.uniprot.org";
 
   private static final String BAR_DELIMITER = "|";
 
@@ -144,10 +145,12 @@ public class Uniprot extends DbSourceProxyImpl
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
-      String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
+      String downloadstring = getDomain() + "/uniprotkb/" + queries
+              + ".xml";
 
       URL url = new URL(downloadstring);
-      HttpURLConnection urlconn = (HttpURLConnection) url.openConnection();
+      HttpURLConnection urlconn = (HttpURLConnection) HttpUtils
+              .openConnection(url);
       // anything other than 200 means we don't have data
       // TODO: JAL-3882 reuse the EnsemblRestClient's fair
       // use/backoff logic to retry when the server tells us to go away
@@ -298,7 +301,7 @@ public class Uniprot extends DbSourceProxyImpl
         if (location.getPosition() != null)
         {
           if (location.getPosition().getPosition() == null
-                  || !"unknown".equals(location.getPosition().getStatus()))
+                  || "unknown".equals(location.getPosition().getStatus()))
           {
             Console.warn(
                     "Ignoring single position feature with uncertain location "