--- /dev/null
+package MCview;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.IOException;
+
+import org.junit.Ignore;
+import org.junit.Test;
+
+public class PDBfileTest
+{
+ @Test
+ public void testIsRna()
+ {
+ SequenceI seq = new Sequence("Seq1", "CGAU");
+ assertTrue(PDBfile.isRNA(seq));
+
+ seq.setSequence("CGAu");
+ assertFalse(PDBfile.isRNA(seq));
+
+ seq.setSequence("CGAT");
+ assertFalse(PDBfile.isRNA(seq));
+
+ seq.setSequence("GRSWYFLAVM");
+ assertFalse(PDBfile.isRNA(seq));
+ }
+
+ /**
+ * Test the 'high level' outputs of parsing. More detailed tests in
+ * PDBChainTest.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testParse() throws IOException
+ {
+ /*
+ * Constructor with file path performs parse()
+ */
+ PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
+ AppletFormatAdapter.FILE);
+
+ assertEquals("3W5V", pf.id);
+ // verify no alignment annotations created
+ assertNull(getAlignmentAnnotations(pf));
+
+ assertEquals(4, pf.chains.size());
+ assertEquals("A", pf.chains.get(0).id);
+ assertEquals("B", pf.chains.get(1).id);
+ assertEquals("C", pf.chains.get(2).id);
+ assertEquals("D", pf.chains.get(3).id);
+
+ PDBChain chainA = pf.chains.get(0);
+ assertEquals(0, chainA.seqstart); // not set
+ assertEquals(0, chainA.seqend); // not set
+ assertEquals(18, chainA.sequence.getStart());
+ assertEquals(314, chainA.sequence.getEnd());
+ assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
+ assertEquals("3W5V|A", chainA.sequence.getName());
+ assertNull(chainA.sequence.getAnnotation());
+ assertEquals(1, chainA.sequence.getPDBId().size());
+ PDBEntry pdb = chainA.sequence.getPDBId().get(0);
+ assertEquals("A", pdb.getChainCode());
+ assertEquals("PDB", pdb.getType());
+ assertEquals("3W5V", pdb.getId());
+
+ PDBChain chainB = pf.chains.get(1);
+ assertEquals(1, chainB.sequence.getStart());
+ assertEquals(96, chainB.sequence.getEnd());
+ assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
+ assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
+ assertEquals("3W5V|B", chainB.sequence.getName());
+
+ PDBChain chainC = pf.chains.get(2);
+ assertEquals(18, chainC.sequence.getStart());
+ assertEquals(314, chainC.sequence.getEnd());
+ assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
+ assertEquals("3W5V|C", chainC.sequence.getName());
+
+ PDBChain chainD = pf.chains.get(3);
+ assertEquals(1, chainD.sequence.getStart());
+ assertEquals(96, chainD.sequence.getEnd());
+ assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
+ assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
+ assertEquals("3W5V|D", chainD.sequence.getName());
+ }
+
+ /**
+ * Test parsing, with annotations added to the alignment but no secondary
+ * structure prediction
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testParse_withAnnotations_noSS() throws IOException
+ {
+ PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
+ AppletFormatAdapter.FILE);
+
+ AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
+ assertEquals(4, anns.length);
+
+ /*
+ * Inspect temp factor annotation for chain A
+ */
+ AlignmentAnnotation chainAnnotation = anns[0];
+ assertEquals("Temperature Factor", chainAnnotation.label);
+ // PDBChain constructor changes PDB id to lower case (why?)
+ assertEquals("Temperature Factor for 3w5vA",
+ chainAnnotation.description);
+ assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef);
+ assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph);
+ assertEquals(0f, chainAnnotation.graphMin, 0.001f);
+ assertEquals(40f, chainAnnotation.graphMax, 0.001f);
+ assertEquals(297, chainAnnotation.annotations.length);
+ assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f);
+
+ /*
+ * Chain B temp factor
+ */
+ chainAnnotation = anns[1];
+ assertEquals("Temperature Factor for 3w5vB",
+ chainAnnotation.description);
+ assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef);
+ assertEquals(96, chainAnnotation.annotations.length);
+
+ /*
+ * Chain C temp factor
+ */
+ chainAnnotation = anns[2];
+ assertEquals("Temperature Factor for 3w5vC",
+ chainAnnotation.description);
+ assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef);
+ assertEquals(297, chainAnnotation.annotations.length);
+
+ /*
+ * Chain D temp factor
+ */
+ chainAnnotation = anns[3];
+ assertEquals("Temperature Factor for 3w5vD",
+ chainAnnotation.description);
+ assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef);
+ assertEquals(96, chainAnnotation.annotations.length);
+ }
+
+ /**
+ * Test parsing including secondary structure annotation using JMol; this test
+ * for the case where flag to add annotations to alignment is set false
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testParse_withJmol_noAnnotations() throws IOException
+ {
+ PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
+ AppletFormatAdapter.FILE);
+
+ /*
+ * alignment annotations _are_ created anyway (in
+ * AlignSeq.replaceMatchingSeqsWith())
+ */
+ final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
+ assertEquals(4, anns.length);
+
+ /*
+ * no sequence annotations created - tempFactor annotation is not added
+ * unless the flag to 'addAlignmentAnnotations' is set true
+ */
+ for (PDBChain c : pf.chains)
+ {
+ assertNull(c.sequence.getAnnotation());
+ }
+ }
+
+ /**
+ * Test parsing including secondary structure prediction and annotation using
+ * JMol
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testParse_withJmolAddAlignmentAnnotations()
+ throws IOException
+ {
+ PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
+ AppletFormatAdapter.FILE);
+
+ /*
+ * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
+ */
+ AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
+ assertEquals(8, anns.length);
+
+ /*
+ * other tests have detailed assertions for Temp Factor annotations
+ */
+ assertEquals("Temperature Factor for 3w5vA", anns[1].description);
+ assertEquals("Temperature Factor for 3w5vB", anns[3].description);
+ assertEquals("Temperature Factor for 3w5vC", anns[5].description);
+ assertEquals("Temperature Factor for 3w5vD", anns[7].description);
+
+ /*
+ * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
+ */
+ assertEquals("Secondary Structure for 3W5VA", anns[0].description);
+ assertEquals("Secondary Structure for 3W5VB", anns[2].description);
+ assertEquals("Secondary Structure for 3W5VC", anns[4].description);
+ assertEquals("Secondary Structure for 3W5VD", anns[6].description);
+
+ /*
+ * Verify SS annotations are linked to respective sequences (chains)
+ */
+ assertSame(pf.getSeqs().get(0), anns[0].sequenceRef);
+ assertSame(pf.getSeqs().get(1), anns[2].sequenceRef);
+ assertSame(pf.getSeqs().get(2), anns[4].sequenceRef);
+ assertSame(pf.getSeqs().get(3), anns[6].sequenceRef);
+
+ /*
+ * Verify a sample of SS predictions
+ */
+ for (int i = 0; i < 20; i++)
+ {
+ assertNull(anns[0].annotations[i]);
+ assertEquals("E", anns[0].annotations[20].displayCharacter);
+ assertEquals('E', anns[0].annotations[20].secondaryStructure);
+ assertEquals("E", anns[2].annotations[18].displayCharacter);
+ assertEquals("H", anns[2].annotations[23].displayCharacter);
+ }
+ }
+
+ /**
+ * Placeholder for a test of parsing RNA structure with secondary structure
+ * prediction using the Annotate3D service
+ *
+ * @throws IOException
+ */
+ @Test
+ @Ignore
+ public void testParse_withAnnotate3D() throws IOException
+ {
+ // TODO requires a mock for Annotate3D processing
+ // and/or run as an integration test
+ PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
+ AppletFormatAdapter.FILE);
+ }
+ /**
+ * Helper method to extract parsed annotations from the PDBfile
+ *
+ * @param pf
+ * @return
+ */
+ private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
+ {
+ AlignmentI al = new Alignment(pf.getSeqsAsArray());
+ pf.addAnnotations((Alignment) al);
+ return al.getAlignmentAnnotation();
+ }
+ }
git://source.jalview.org / jalview.git / blobdiff