+/*
+ * 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");
}
}