/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws;
-import static org.junit.Assert.*;
+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.junit.Before;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class PDBSequenceFetcherTest
{
- SequenceFetcher sf;
- @Before
- public void setUp() throws Exception
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- sf = new SequenceFetcher(false);
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @Test
- public void testPdbPerChainRetrieve() throws Exception
+ SequenceFetcher sf;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp() throws Exception
{
- List<DbSourceProxy> sps = sf
- .getSourceProxy("PDB");
- AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
- assertTrue(response!=null);
- assertTrue(response.getHeight()==1);
+ 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();
}
- @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 = sf
- .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 class TestRetrieveObject
+ {
+ String id;
+
+ int expectedHeight;
+
+ public TestRetrieveObject(String id, int expectedHeight)
{
- 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);
+ 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