public boolean accepts(Class<? extends IChemObject> classObject) { return chemObjectReader.accepts(classObject); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(ChemModel.class)); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); }
@Test public void testAccepts() { Assert.assertTrue(chemObjectIO.accepts(AtomContainer.class)); }
if (chemReader.accepts(Molecule.class)) {
private static IAtomContainer createMolecule(String molecule) throws IOException, CDKException { IAtomContainer structure = null; if (molecule != null) { ISimpleChemObjectReader reader = new MDLV2000Reader(new StringReader(molecule)); Assert.assertNotNull("Could not create reader", reader); if (reader.accepts(AtomContainer.class)) { structure = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class)); } } return structure; }
if (reader.accepts(Molecule.class)) {
@Test public void testRead_IChemObject() throws Exception { Assert.assertNotNull("No test file has been set!", testFile); boolean read = false; for (IChemObject object : acceptableChemObjects()) { if (chemObjectIO.accepts(object.getClass())) { InputStream ins = SimpleChemObjectReaderTest.class.getClassLoader().getResourceAsStream(testFile); chemObjectIO.setReader(ins); IChemObject readObject = chemObjectIO.read(object); chemObjectIO.close(); Assert.assertNotNull("Failed attempt to read the file as " + object.getClass().getName(), readObject); read = true; } } if (!read) { Assert.fail("Reading an IChemObject from the Reader did not work properly."); } }
@Test public void testRead_IChemObject() throws Exception { Assert.assertNotNull("No test file has been set!", testFile); boolean read = false; for (IChemObject object : acceptableChemObjects()) { if (chemObjectIO.accepts(object.getClass())) { InputStream ins = SimpleChemObjectReaderTest.class.getClassLoader().getResourceAsStream(testFile); chemObjectIO.setReader(ins); IChemObject readObject = chemObjectIO.read(object); chemObjectIO.close(); Assert.assertNotNull("Failed attempt to read the file as " + object.getClass().getName(), readObject); read = true; } } if (!read) { Assert.fail("Reading an IChemObject from the Reader did not work properly."); } }
ChemModel chemModel = null; IChemFile chemFile = null; if (cor.accepts(IChemFile.class) && chemModel==null) { chemModel = (ChemModel) chemFile.getChemSequence(0).getChemModel(0); if (cor.accepts(ChemModel.class) && chemModel==null) { if (cor.accepts(IAtomContainerSet.class) && chemModel==null) { if (cor.accepts(IAtomContainer.class) && chemModel==null) { if (cor.accepts(RGroupQuery.class) && chemModel==null) { IRGroupQuery rgroupQuery = (RGroupQuery) cor.read(new RGroupQuery(DefaultChemObjectBuilder.getInstance())); if(rgroupQuery!=null )
void expectReader(String filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount) throws Exception { InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); Assert.assertNotNull("Cannot find file: " + filename, ins); if (expectedFormat instanceof IChemFormatMatcher) { factory.registerFormat((IChemFormatMatcher) expectedFormat); } ISimpleChemObjectReader reader = factory.createReader(ins); Assert.assertNotNull(reader); Assert.assertEquals(((IChemFormat) expectedFormat).getReaderClassName(), reader.getClass().getName()); // now try reading something from it IChemObject[] objects = {new ChemFile(), new ChemModel(), new AtomContainer(), new Reaction()}; boolean read = false; for (int i = 0; (i < objects.length && !read); i++) { if (reader.accepts(objects[i].getClass())) { IChemObject chemObject = reader.read(objects[i]); Assert.assertNotNull("Reader accepted a " + objects[i].getClass().getName() + " but failed to read it", chemObject); assertAtomCount(expectedAtomCount, chemObject); assertBondCount(expectedBondCount, chemObject); read = true; } } if (read) { // ok, reseting worked } else { Assert.fail("Reading an IChemObject from the Reader did not work properly."); } }
reader.setReader(ins); IAtomContainer mol = null; if (reader.accepts(AtomContainer.class)) { mol = reader.read(new AtomContainer()); } else if (reader.accepts(ChemFile.class)) { IChemFile cf = reader.read(new ChemFile()); mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
chemModel.getBuilder().newInstance(IAtomContainer.class); try { if (reader.accepts(IAtomContainer.class)) { toPaste = (IAtomContainer) reader.read(readMolecule); } else if (reader.accepts(ChemFile.class)) { toPaste = readMolecule; IChemFile file = (IChemFile) reader.read(new ChemFile()); } else if (reader.accepts(RGroupQuery.class)) { rgrpQuery=true; IRGroupQuery rgroupQuery = (RGroupQuery) reader.read(new RGroupQuery(DefaultChemObjectBuilder.getInstance()));