Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

[jalview.git] / src / jalview / fts / service / threedbeacons / TDBeaconsFTSRestClient.java

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index ccdc525..ac02a5f 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * 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.threedbeacons;
 
 import java.net.URI;
@@ -37,18 +57,21 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
   /**
    * production server URI
    */
-  private static String TDB_PROD_API="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+  private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
   /**
    * dev server URI
    */
-  private static String TDB_DEV_API="https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
-  private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API; 
+  private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+  private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
 
   public static FTSRestClientI instance = null;
 
   protected TDBeaconsFTSRestClient()
   {
   }
+
   @SuppressWarnings("unchecked")
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
@@ -77,14 +100,15 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       }
 
       WebResource webResource;
-      webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN+query);
+      webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
 
       URI uri = webResource.getURI();
       System.out.println(uri.toString());
 
       // Execute the REST request
       ClientResponse clientResponse;
-      if (isMocked()) { 
+      if (isMocked())
+      {
         clientResponse = null;
       }
       else
@@ -99,7 +123,9 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       String responseString = null;
 
       // Check the response status and report exception if one occurs
-      int responseStatus = isMocked() ? (mockQueries.containsKey(query) ? 200 : 404) : clientResponse.getStatus();
+      int responseStatus = isMocked()
+              ? (mockQueries.containsKey(query) ? 200 : 404)
+              : clientResponse.getStatus();
       switch (responseStatus)
       {
       // if success
@@ -110,7 +136,8 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
         }
         else
         {
-          responseString = isMocked() ? mockQueries.get(query): clientResponse.getEntity(String.class);
+          responseString = isMocked() ? mockQueries.get(query)
+                  : clientResponse.getEntity(String.class);
         }
         break;
       case 400:
@@ -143,14 +170,14 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
         }
       }
       throw e;
-      
+
     }
 
   }
 
   /**
    * returns response for when the 3D-Beacons service doesn't have a record for
-   * the given query - in 2.11.2 this triggers a failover to the PDBe FTS 
+   * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
    * 
    * @return null
    */
@@ -228,14 +255,14 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
     SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
     int colCounter = 0;
     summaryRowData = new Object[(associatedSeq != null)
-                                ? displayFields.size() + 1
-                                : displayFields.size()];
-                        if (associatedSeq != null)
-                        {
-                          associatedSequence = associatedSeq;
-                          summaryRowData[0] = associatedSequence;
-                          colCounter = 1;
-                        }
+            ? displayFields.size() + 1
+            : displayFields.size()];
+    if (associatedSeq != null)
+    {
+      associatedSequence = associatedSeq;
+      summaryRowData[0] = associatedSequence;
+      colCounter = 1;
+    }
 
     for (FTSDataColumnI field : displayFields)
     {
@@ -339,8 +366,8 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       columnNames = new String[] { "", "Display", "Group" };
       break;
     case PREFERENCES:
-      columnNames = new String[] { "3DB Beacons Field", "Show in search summary",
-          "Show in structure summary" };
+      columnNames = new String[] { "3DB Beacons Field",
+          "Show in search summary", "Show in structure summary" };
       break;
     default:
       break;