-/*\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.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ 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.setPropertyNoSave("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.setPropertyNoSave("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+
+ sf = new SequenceFetcher();
+ }
+
+ /**
+ * 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.setPropertyNoSave("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("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 class TestRetrieveObject
+ {
+ String id;
+
+ int expectedHeight;
+
+ public TestRetrieveObject(String id, int expectedHeight)
+ {
+ super();
+ this.id = id;
+ this.expectedHeight = expectedHeight;
+ }
+
+ }
+
+ private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+ new TestRetrieveObject("1QIP", 4),
+ new TestRetrieveObject("4IM2", 1));
+
+ private void testRetrieveProteinSeqFromPDB() throws Exception
+ {
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+ StringBuilder errors = new StringBuilder();
+ for (TestRetrieveObject str : toRetrieve)
+ {
+ AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+ assertTrue("No aligment for " + str.id, response != null);
+ assertEquals(response.getHeight(), str.expectedHeight,
+ "Number of chains for " + str.id);
+ for (SequenceI sq : response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence " + sq.getName(),
+ sq.getAnnotation().length > 0);
+ assertTrue("No PDBEntry on sequence " + sq.getName(),
+ sq.getAllPDBEntries().size() > 0);
+ // FIXME: should test that all residues extracted as sequences from
+ // chains in structure have a mapping to data in the structure
+ List<SequenceFeature> prev = null;
+ int lastp = -1;
+ for (int col = 1; col <= sq.getLength(); col++)
+ {
+ List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
+ if (sf.size() != 1)
+ {
+ errors.append(
+ str.id + ": " +
+ "Expected one feature at column (position): "
+ + (col - 1)
+ + " (" + sq.findPosition(col - 1) + ")"
+ + ": saw "
+ + sf.size());
+ errors.append("\n");
+ if (prev != null)
+ {
+ errors.append("Last Feature was at position " + lastp + ": "
+ + prev.get(0).toString());
+ errors.append("\n");
+ }
+ }
+ else
+ {
+ prev = sf;
+ lastp = sq.findPosition(col - 1);
+ }
+ }
+ }
+ }
+ if (errors.length() > 0)
+ {
+ Assert.fail(errors.toString());
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff