-/*\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
+/*
+ * 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.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureViewSettings;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+ SequenceFetcher sf;
+
+ @BeforeMethod(alwaysRun = true)
+ 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 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
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_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("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
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ StructureViewSettings.setCurrentDefaultFormat("PDB");
+
+ testRetrieveProteinSeqFromPDB();
+ }
+
+ @Test(groups = { "Network" }, enabled = true)
+ public void testmmCifSeqRetrieve() throws Exception
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ StructureViewSettings.setCurrentDefaultFormat("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.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");
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff