X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Falphafold%2FAlphafoldRestClient.java;h=a63190266db8bc145856dfaaad2fb22d9689031c;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=6b855fcdfaea983217d5e54cc280e1c27254cf05;hpb=6d03a7bc7ca503f0e845dcbc568e44a39c842612;p=jalview.git

diff --git a/src/jalview/fts/service/alphafold/AlphafoldRestClient.java b/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
index 6b855fc..a631902 100644
--- a/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
+++ b/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
@@ -1,13 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.service.alphafold;
 
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
-import java.util.Map;
 import java.util.Objects;
 
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -48,7 +67,8 @@ public class AlphafoldRestClient
       String alphaFoldId = "AF-" + upref.getAccessionId() + "-F1";
       try
       {
-        String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId);
+        String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId,
+                null);
         URL url = new URL(urls);
         if (!HttpUtils.checkUrlAvailable(url, 50))
         {
@@ -56,7 +76,7 @@ public class AlphafoldRestClient
         }
       } catch (Exception mfe)
       {
-        jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
+        Console.debug("Exception accessing urls", mfe);
         continue;
       }
       int colCounter = 0;
@@ -98,7 +118,7 @@ public class AlphafoldRestClient
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+            jalview.bin.Console.outPrintln("offending value:" + fieldData);
           }
         }
       }