X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FRemoteFormatTest.java;h=d48ff918c5928b48d5872aa58a62cb5841dbad8e;hb=e3e0829f9fb59144a1ce6e3ae99f25dc2641ecb2;hp=90d4472246f64bd27e65346ae9cfa2d5336cf455;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/test/jalview/ws/dbsources/RemoteFormatTest.java b/test/jalview/ws/dbsources/RemoteFormatTest.java
index 90d4472..d48ff91 100644
--- a/test/jalview/ws/dbsources/RemoteFormatTest.java
+++ b/test/jalview/ws/dbsources/RemoteFormatTest.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.ws.dbsources;
 
 import static org.testng.Assert.assertEquals;
@@ -51,14 +71,15 @@ public class RemoteFormatTest
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
 
-    sf = new SequenceFetcher(false);
+    sf = new SequenceFetcher();
   }
 
   @DataProvider(name = "AccessionData")
   protected Object[][] getAccessions()
   {
     return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
-        { DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
+        { DBRefSource.PDB, "1QIP" },
+        { DBRefSource.EMBL, "X53828" },
         { DBRefSource.EMBLCDS, "CAA37824" },
         { DBRefSource.ENSEMBL, "ENSG00000157764" },
         { new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
@@ -80,7 +101,7 @@ public class RemoteFormatTest
     SequenceI sq = al.getSequenceAt(0);
     // suppress this check as only Uniprot and PDB acquire PDB refs
     // assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
-    assertTrue(sq.getDBRefs().length > 0, "No DBRef on sequence.");
+    assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
     // suppress this test as only certain databases provide 'primary' dbrefs
     // assertFalse(sq.getPrimaryDBRefs().isEmpty());
     int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
@@ -92,21 +113,21 @@ public class RemoteFormatTest
   @Test(groups = { "Network" })
   public void testUniprotFreeTextSearch() throws Exception
   {
-    List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+    List<FTSDataColumnI> wantedFields = new ArrayList<>();
     FTSRestClientI client = UniProtFTSRestClient.getInstance();
     wantedFields.add(client.getDataColumnByNameOrCode("id"));
     wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
     wantedFields.add(client.getDataColumnByNameOrCode("organism"));
     wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
     wantedFields.add(client.getDataColumnByNameOrCode("length"));
-  
+
     FTSRestRequest request = new FTSRestRequest();
     request.setAllowEmptySeq(false);
     request.setResponseSize(100);
     request.setFieldToSearchBy("Search All");
     request.setSearchTerm("metanephrops"); // lobster!
     request.setWantedFields(wantedFields);
-  
+
     FTSRestResponse response;
     response = client.executeRequest(request);
     assertTrue(response.getNumberOfItemsFound() > 20);