JAL-654 updated pdb db fetcher test to verify the number of annotation

rows retrieved for a single chain query

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 5a9e954..6f0bf26 100644 (file)
--- 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);
-    }
-  }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ *  \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.ws;\r
+\r
+import static org.junit.Assert.*;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+\r
+import java.util.List;\r
+\r
+import org.junit.Before;\r
+import org.junit.Test;\r
+\r
+public class PDBSequenceFetcherTest\r
+{\r
+\r
+  SequenceFetcher sf;\r
+\r
+  @Before\r
+  public void setUp() throws Exception\r
+  {\r
+    sf = new SequenceFetcher(false);\r
+  }\r
+\r
+  @Test\r
+  public void testRnaSeqRetrieve() throws Exception\r
+  {\r
+    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");\r
+    AlignmentI response = sps.get(0).getSequenceRecords("2GIS");\r
+    assertTrue(response != null);\r
+    assertTrue(response.getHeight() == 1);\r
+    for (SequenceI sq : response.getSequences())\r
+    {\r
+      assertTrue("No annotation transfered to sequence.",\r
+              sq.getAnnotation().length > 0);\r
+      assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);\r
+      assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);\r
+    }\r
+  }\r
+\r
+}\r