From 2bf5ab62374818b10dc4842137d02abb57e140aa Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 6 Oct 2014 12:38:24 +0100
Subject: [PATCH] JAL-654 updated pdb db fetcher test to verify the number of
 annotation rows retrieved for a single chain query

---
 test/jalview/ws/PDBSequenceFetcherTest.java |  129 +++++++++++++--------------
 1 file changed, 60 insertions(+), 69 deletions(-)

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 5a9e954..6f0bf26 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -1,69 +1,60 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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 java.util.List;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class PDBSequenceFetcherTest
-{
-
-  SequenceFetcher sf;
-
-  @Before
-  public void setUp() throws Exception
-  {
-    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");
-    AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
-    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);
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+  SequenceFetcher sf;
+
+  @Before
+  public void setUp() throws Exception
+  {
+    sf = new SequenceFetcher(false);
+  }
+
+  @Test
+  public void testRnaSeqRetrieve() throws Exception
+  {
+    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("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);
+    }
+  }
+
+}
-- 
1.7.10.2