+++ /dev/null
-/*
- * 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 mc_view;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.bin.Cache;
-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.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.structure.StructureImportSettings;
-
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-public class PDBfileTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- 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(groups = { "Functional" })
- public void testParse() throws IOException
- {
- /*
- * Constructor with file path performs parse()
- */
- PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
- DataSourceType.FILE);
-
- assertEquals("3W5V", pf.getId());
- // verify no alignment annotations created
- assertNull(getAlignmentAnnotations(pf));
-
- assertEquals(4, pf.getChains().size());
- assertEquals("A", pf.getChains().get(0).id);
- assertEquals("B", pf.getChains().get(1).id);
- assertEquals("C", pf.getChains().get(2).id);
- assertEquals("D", pf.getChains().get(3).id);
-
- PDBChain chainA = pf.getChains().get(0);
- SequenceI seqA = pf.getSeqs().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, seqA.getAllPDBEntries().size());
- PDBEntry pdb = seqA.getAllPDBEntries().get(0);
- assertEquals("A", pdb.getChainCode());
- assertEquals("PDB", pdb.getType());
- assertEquals("3W5V", pdb.getId());
-
- PDBChain chainB = pf.getChains().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.getChains().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.getChains().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());
-
- /*
- * verify PDB-related data in parsed sequences
- */
- List<SequenceI> seqs = pf.getSeqs();
- assertEquals(4, seqs.size());
- assertEquals("3W5V|A", seqs.get(0).getName());
- assertEquals("3W5V|B", seqs.get(1).getName());
- assertEquals("3W5V|C", seqs.get(2).getName());
- assertEquals("3W5V|D", seqs.get(3).getName());
- assertEquals(1, seqs.get(0).getAllPDBEntries().size());
- PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
- assertEquals("A", pdbe.getChainCode());
- assertEquals("3W5V", pdbe.getId());
- assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
- }
-
- /**
- * Test parsing, with annotations added to the alignment but no secondary
- * structure prediction
- *
- * @throws IOException
- */
- @Test(groups = { "Functional" })
- public void testParse_withAnnotations_noSS() throws IOException
- {
- PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
- DataSourceType.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(groups = { "Functional" })
- public void testParse_withJmol_noAnnotations() throws IOException
- {
- PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
- DataSourceType.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.getChains())
- {
- assertNull(c.sequence.getAnnotation());
- }
- }
-
- /**
- * Test parsing including secondary structure prediction and annotation using
- * JMol
- *
- * @throws IOException
- */
- @Test(groups = { "Functional" })
- public void testParse_withJmolAddAlignmentAnnotations()
- throws IOException
- {
- PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
- DataSourceType.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(groups = { "Functional" }, enabled = false)
- 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",
- DataSourceType.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(al);
- return al.getAlignmentAnnotation();
- }
-
- @BeforeMethod(alwaysRun = true)
- public void setUp()
- {
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.setPropertyNoSave("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
- Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
- Boolean.TRUE.toString());
- Cache.setPropertyNoSave("ADD_SS_ANN",
- Boolean.TRUE.toString());
- StructureImportSettings.setDefaultStructureFileFormat("PDB");
- }
-}
git://source.jalview.org / jalview.git / blobdiff