X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=778fc188a5f02ceb70e48eb30307aad83c4750f3;hb=1e13e955bb673692c0c122f6a6e3415981a6e64d;hp=f5913e6040c03491955ebc9d6da3049d05c8b798;hpb=3b94f01f4edf56896ae3b5f0ce6cb4f1996e7bbc;p=jalview.git
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index f5913e6..778fc18 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -1,36 +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 .
+ * 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 testRnaSeqRetrieve() throws Exception
{
- List sps = new SequenceFetcher(false)
- .getSourceProxy("PDB");
+ List 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);
}
}