X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=4b9437ac12d3619a60e054020ab085a781945e29;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=f5913e6040c03491955ebc9d6da3049d05c8b798;hpb=3b94f01f4edf56896ae3b5f0ce6cb4f1996e7bbc;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index f5913e6..4b9437a 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -1,36 +1,118 @@
+/*
+ * 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 static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.List;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PDBSequenceFetcherTest
 {
 
-  @Before
+  SequenceFetcher sf;
+
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    // 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
+  /**
+   * Test that RNA structure can be added by a call to the RNAML service.
+   * 
+   * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
+   * not always reliable.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
-    List<DbSourceProxy> sps = new SequenceFetcher(false)
-    .getSourceProxy("PDB");
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "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.getAllPDBEntries().size() > 0);
+      assertTrue(
+              "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
+              sq.getRNA() != null);
+    }
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testPdbSeqRetrieve() throws Exception
+  {
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testmmCifSeqRetrieve() throws Exception
+  {
+    StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  private void testRetrieveProteinSeqFromPDB() throws Exception
+  {
+    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+    AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
+    assertTrue(response != null);
+    assertTrue(response.getHeight() == 4);
+    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.getAllPDBEntries().size() > 0);
+      org.testng.Assert
+              .assertEquals(sq.getEnd() - sq.getStart() + 1,
+                      sq.getLength(),
+                      "Sequence start/end doesn't match number of residues in sequence");
     }
   }