JAL-1270 set Cache properties in setUp to ensure test success

[jalview.git] / test / jalview / ws / PDBSequenceFetcherTest.java

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 35de214..778fc18 100644 (file)
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -1,47 +1,67 @@
+/*
+ * 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;
 
-import static org.junit.Assert.*;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import static org.junit.Assert.assertTrue;
 
 import java.util.List;
 
 import org.junit.Before;
 import org.junit.Test;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
 public class PDBSequenceFetcherTest
 {
 
   SequenceFetcher sf;
+
   @Before
   public void setUp() throws Exception
   {
+    // ensure 'add annotation from structure' is selected
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+
     sf = new SequenceFetcher(false);
   }
 
   @Test
-  public void testPdbPerChainRetrieve() throws Exception
-  {
-    List<DbSourceProxy> sps = sf
-    .getSourceProxy("PDB");
-    AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
-    assertTrue(response!=null);
-    assertTrue(response.getHeight()==1);
-  }
-  @Test
   public void testRnaSeqRetrieve() throws Exception
   {
-    List<DbSourceProxy> sps = sf
-    .getSourceProxy("PDB");
+    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
-    assertTrue(response!=null);
-    assertTrue(response.getHeight()==1);
-    for (SequenceI sq:response.getSequences())
+    assertTrue(response != null);
+    assertTrue(response.getHeight() == 1);
+    for (SequenceI sq : response.getSequences())
     {
-      assertTrue("No annotation transfered to sequence.",sq.getAnnotation().length>0);
-      assertTrue("No PDBEntry on sequence.",sq.getPDBId().size()>0);
-      assertTrue("No RNA annotation on sequence.", sq.getRNA()!=null);
+      assertTrue("No annotation transfered to sequence.",
+              sq.getAnnotation().length > 0);
+      assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
+      assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);
     }
   }