From: <eg...@us...> - 2008-03-21 13:59:48
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Revision: 10461 http://cdk.svn.sourceforge.net/cdk/?rev=10461&view=rev Author: egonw Date: 2008-03-21 06:59:43 -0700 (Fri, 21 Mar 2008) Log Message: ----------- More JUnit3->JUnit4 transition Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java cdk/trunk/src/test/org/openscience/cdk/CloneAtomContainerTest.java cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java cdk/trunk/src/test/org/openscience/cdk/MappingTest.java cdk/trunk/src/test/org/openscience/cdk/applications/APIVersionTesterTest.java cdk/trunk/src/test/org/openscience/cdk/applications/swing/PeriodicTablePanelTest.java cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java cdk/trunk/src/test/org/openscience/cdk/dict/DictDBTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MexperimentalTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java Modified: cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,12 +24,9 @@ */ package org.openscience.cdk; -import junit.framework.Test; -import junit.framework.TestSuite; +import org.junit.Assert; +import org.junit.Test; -import org.openscience.cdk.Association; -import org.openscience.cdk.Atom; - /** * Checks the functionality of the Association class. * @@ -37,68 +34,58 @@ * * @see org.openscience.cdk.Association */ -public class AssociationTest extends CDKTestCase { +public class AssociationTest extends NewCDKTestCase { - public AssociationTest(String name) { - super(name); - } - - public void setUp() {} - - public static Test suite() { - return new TestSuite(AssociationTest.class); - } - - public void testAssociation() { + @Test public void testAssociation() { Association association = new Association(); - assertEquals(0, association.getElectronCount()); - assertEquals(0, association.getAtomCount()); + Assert.assertEquals(0, association.getElectronCount()); + Assert.assertEquals(0, association.getAtomCount()); } - public void testAssociation_IAtom_IAtom() { + @Test public void testAssociation_IAtom_IAtom() { Association association = new Association(new Atom("C"), new Atom("C")); - assertEquals(0, association.getElectronCount()); - assertEquals(2, association.getAtomCount()); + Assert.assertEquals(0, association.getElectronCount()); + Assert.assertEquals(2, association.getAtomCount()); } /** Test for RFC #9 */ - public void testToString() { + @Test public void testToString() { Association association = new Association(); String description = association.toString(); for (int i=0; i< description.length(); i++) { - assertTrue(description.charAt(i) != '\n'); - assertTrue(description.charAt(i) != '\r'); + Assert.assertTrue(description.charAt(i) != '\n'); + Assert.assertTrue(description.charAt(i) != '\r'); } } - public void testContains() { + @Test public void testContains() { Atom c = new Atom("C"); Atom o = new Atom("O"); Association association = new Association(c, o); - assertTrue(association.contains(c)); - assertTrue(association.contains(o)); + Assert.assertTrue(association.contains(c)); + Assert.assertTrue(association.contains(o)); } - public void testGetAtomCount() { + @Test public void testGetAtomCount() { Atom c = new Atom("C"); Atom o = new Atom("O"); Association association = new Association(c, o); - assertEquals(2, association.getAtomCount()); + Assert.assertEquals(2, association.getAtomCount()); } - public void testGetAtoms() { + @Test public void testGetAtoms() { Atom c = new Atom("C"); Atom o = new Atom("O"); Association association = new Association(c, o); Atom[] atoms = association.getAtoms(); - assertEquals(2, atoms.length); - assertNotNull(atoms[0]); - assertNotNull(atoms[1]); + Assert.assertEquals(2, atoms.length); + Assert.assertNotNull(atoms[0]); + Assert.assertNotNull(atoms[1]); } } Modified: cdk/trunk/src/test/org/openscience/cdk/CloneAtomContainerTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CloneAtomContainerTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/CloneAtomContainerTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -27,10 +27,8 @@ * */ package org.openscience.cdk; -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.Molecule; +import org.junit.Assert; +import org.junit.Test; import org.openscience.cdk.templates.MoleculeFactory; /** @@ -41,28 +39,20 @@ * @author Christoph Steinbeck * @cdk.created 2001-08-09 */ -public class CloneAtomContainerTest extends CDKTestCase { +public class CloneAtomContainerTest extends NewCDKTestCase { - public CloneAtomContainerTest(String name) { - super(name); - } - - public static Test suite() { - return new TestSuite(CloneAtomContainerTest.class); - } - - public void testClone() throws Exception + @Test public void testClone() throws Exception { Molecule molecule = MoleculeFactory.makeAlphaPinene(); Molecule clonedMol = (Molecule)molecule.clone(); - assertTrue(molecule.getAtomCount() == clonedMol.getAtomCount()); + Assert.assertTrue(molecule.getAtomCount() == clonedMol.getAtomCount()); for (int f = 0; f < molecule.getAtomCount(); f++) { for (int g = 0; g < clonedMol.getAtomCount(); g++) { - assertNotNull(molecule.getAtom(f)); - assertNotNull(clonedMol.getAtom(g)); - assertTrue(molecule.getAtom(f) != clonedMol.getAtom(g)); + Assert.assertNotNull(molecule.getAtom(f)); + Assert.assertNotNull(clonedMol.getAtom(g)); + Assert.assertTrue(molecule.getAtom(f) != clonedMol.getAtom(g)); } } } Modified: cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -20,10 +20,6 @@ */ package org.openscience.cdk; -import junit.framework.Test; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; - import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; @@ -34,13 +30,19 @@ import java.util.List; import java.util.Set; +import junit.framework.Test; +import junit.framework.TestCase; + +import org.openscience.cdk.annotations.TestClass; +import org.openscience.cdk.annotations.TestMethod; + /** * This test class is <b>not</b> intended to be tested directly, * but serve as helper class for actual coverage testers. * * @cdk.module test */ -abstract public class CoverageAnnotationTest extends CDKTestCase { +abstract public class CoverageAnnotationTest extends TestCase { private final String basePackageName = "org.openscience.cdk."; Modified: cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -31,6 +31,7 @@ import java.util.List; import junit.framework.Test; +import junit.framework.TestCase; /** * This test class is <b>not</b> intended to be tested directly, @@ -38,7 +39,7 @@ * * @cdk.module test */ -abstract public class CoverageTest extends CDKTestCase { +abstract public class CoverageTest extends TestCase { private final String basePackageName = "org.openscience.cdk."; Modified: cdk/trunk/src/test/org/openscience/cdk/MappingTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/MappingTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/MappingTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,13 +24,10 @@ */ package org.openscience.cdk; -import junit.framework.Test; -import junit.framework.TestSuite; +import java.util.Iterator; -import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; -import org.openscience.cdk.Mapping; -import org.openscience.cdk.PseudoAtom; +import org.junit.Assert; +import org.junit.Test; import org.openscience.cdk.interfaces.IChemObject; /** @@ -40,21 +37,11 @@ * * @see org.openscience.cdk.Mapping */ -public class MappingTest extends CDKTestCase { +public class MappingTest extends NewCDKTestCase { - public MappingTest(String name) { - super(name); - } - - public void setUp() {} - - public static Test suite() { - return new TestSuite(MappingTest.class); - } - - public void testMapping_IChemObject_IChemObject() { + @Test public void testMapping_IChemObject_IChemObject() { Mapping mapping = new Mapping(new Atom(), new Atom()); - assertNotNull(mapping); + Assert.assertNotNull(mapping); } /** @@ -64,23 +51,23 @@ Mapping mapping = new Mapping(new Atom(), new Atom()); String description = mapping.toString(); for (int i=0; i< description.length(); i++) { - assertTrue(description.charAt(i) != '\n'); - assertTrue(description.charAt(i) != '\r'); + Assert.assertTrue(description.charAt(i) != '\n'); + Assert.assertTrue(description.charAt(i) != '\r'); } } public void testClone() throws Exception { Mapping mapping = new Mapping(new Atom(), new Atom()); Object clone = mapping.clone(); - assertTrue(clone instanceof Mapping); + Assert.assertTrue(clone instanceof Mapping); } public void testGetChemObject_int() { Atom atom0 = new Atom(); Atom atom1 = new Atom(); Mapping mapping = new Mapping(atom0, atom1); - assertEquals(atom0, mapping.getChemObject(0)); - assertEquals(atom1, mapping.getChemObject(1)); + Assert.assertEquals(atom0, mapping.getChemObject(0)); + Assert.assertEquals(atom1, mapping.getChemObject(1)); } public void testRelatedChemObjects() { @@ -88,12 +75,12 @@ Atom atom1 = new Atom(); Mapping mapping = new Mapping(atom0, atom1); - java.util.Iterator iter = mapping.relatedChemObjects(); - assertTrue(iter.hasNext()); - assertEquals(atom0, (Atom)iter.next()); - assertTrue(iter.hasNext()); - assertEquals(atom1, (Atom)iter.next()); - assertFalse(iter.hasNext()); + Iterator<IChemObject> iter = mapping.relatedChemObjects(); + Assert.assertTrue(iter.hasNext()); + Assert.assertEquals(atom0, (Atom)iter.next()); + Assert.assertTrue(iter.hasNext()); + Assert.assertEquals(atom1, (Atom)iter.next()); + Assert.assertFalse(iter.hasNext()); } public void testClone_ChemObject() throws Exception { @@ -105,9 +92,9 @@ //assertEquals(map.length, mapClone.length); for (int f = 0; f < 2; f++) { for (int g = 0; g < 2; g++) { - assertNotNull(mapping.getChemObject(f)); - assertNotNull(clone.getChemObject(g)); - assertNotSame(mapping.getChemObject(f), clone.getChemObject(g)); + Assert.assertNotNull(mapping.getChemObject(f)); + Assert.assertNotNull(clone.getChemObject(g)); + Assert.assertNotSame(mapping.getChemObject(f), clone.getChemObject(g)); } } } Modified: cdk/trunk/src/test/org/openscience/cdk/applications/APIVersionTesterTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/applications/APIVersionTesterTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/applications/APIVersionTesterTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,39 +24,27 @@ */ package org.openscience.cdk.applications; -import junit.framework.Test; -import junit.framework.TestSuite; +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; -import org.openscience.cdk.applications.APIVersionTester; -import org.openscience.cdk.CDKTestCase; - /** * Checks the functionality of the APIVersionTester. * * @cdk.module test-extra */ -public class APIVersionTesterTest extends CDKTestCase { +public class APIVersionTesterTest extends NewCDKTestCase { - public APIVersionTesterTest(String name) { - super(name); + @Test public void testIsBiggerOrEqual() { + Assert.assertTrue(APIVersionTester.isBiggerOrEqual("1.6", "1.6")); + Assert.assertTrue(APIVersionTester.isBiggerOrEqual("1.6", "1.12")); + Assert.assertFalse(APIVersionTester.isBiggerOrEqual("1.12", "1.7")); } - public void setUp() {} - - public static Test suite() { - return new TestSuite(APIVersionTesterTest.class); + @Test public void testIsSmaller() { + Assert.assertFalse(APIVersionTester.isSmaller("1.6", "1.6")); + Assert.assertFalse(APIVersionTester.isSmaller("1.6", "1.12")); + Assert.assertTrue(APIVersionTester.isSmaller("1.12", "1.7")); } - public void testIsBiggerOrEqual() { - assertTrue(APIVersionTester.isBiggerOrEqual("1.6", "1.6")); - assertTrue(APIVersionTester.isBiggerOrEqual("1.6", "1.12")); - assertFalse(APIVersionTester.isBiggerOrEqual("1.12", "1.7")); - } - - public void testIsSmaller() { - assertFalse(APIVersionTester.isSmaller("1.6", "1.6")); - assertFalse(APIVersionTester.isSmaller("1.6", "1.12")); - assertTrue(APIVersionTester.isSmaller("1.12", "1.7")); - } - } Modified: cdk/trunk/src/test/org/openscience/cdk/applications/swing/PeriodicTablePanelTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/applications/swing/PeriodicTablePanelTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/applications/swing/PeriodicTablePanelTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,9 +24,8 @@ import javax.swing.JFrame; -import org.openscience.cdk.applications.swing.PeriodicTablePanel; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.config.AtomTypeFactory; -import org.openscience.cdk.CDKTestCase; /** * Checks the functionality of the PeriodicTablePanelTest @@ -35,29 +34,10 @@ *@cdk.created February 10, 2004 *@cdk.module test-extra */ -public class PeriodicTablePanelTest extends CDKTestCase { +public class PeriodicTablePanelTest extends NewCDKTestCase { AtomTypeFactory atf = null; - - /** - * Constructor for the AtomTypeFactoryTest object - * - *@param name Description of the Parameter - */ - public PeriodicTablePanelTest(String name) - { - super(name); - } - - - /** - * The JUnit setup method - */ - public void setUp() - { - } - public void runVisual() { PeriodicTablePanel ptp = new PeriodicTablePanel(); Modified: cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -20,35 +20,26 @@ */ package org.openscience.cdk.config; -import junit.framework.Test; -import junit.framework.TestSuite; +import org.junit.Assert; +import org.junit.Test; -import org.openscience.cdk.config.Symbols; -import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.NewCDKTestCase; /** * @cdk.module test-standard */ -public class SymbolsTest extends CDKTestCase { +public class SymbolsTest extends NewCDKTestCase { - public SymbolsTest(String name) { - super(name); - } - - public static Test suite() { - return new TestSuite(SymbolsTest.class); + @Test public void testCarbon() { + Assert.assertEquals("C", Symbols.byAtomicNumber[6]); } - public void testCarbon() { - assertEquals("C", Symbols.byAtomicNumber[6]); + @Test public void testDummy() { + Assert.assertEquals("Xx", Symbols.byAtomicNumber[0]); } - - public void testDummy() { - assertEquals("Xx", Symbols.byAtomicNumber[0]); - } - public void testLastEntry() { - assertEquals("Uuh", Symbols.byAtomicNumber[116]); + @Test public void testLastEntry() { + Assert.assertEquals("Uuh", Symbols.byAtomicNumber[116]); } } Modified: cdk/trunk/src/test/org/openscience/cdk/dict/DictDBTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/dict/DictDBTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/dict/DictDBTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,14 +24,10 @@ */ package org.openscience.cdk.dict; -import junit.framework.Test; -import junit.framework.TestSuite; +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; -import org.openscience.cdk.dict.Dictionary; -import org.openscience.cdk.dict.DictionaryDatabase; -import org.openscience.cdk.dict.Entry; -import org.openscience.cdk.CDKTestCase; - /** * Checks the functionality of the DictionaryDatabase class. * @@ -39,42 +35,32 @@ * * @see org.openscience.cdk.dict.DictionaryDatabase */ -public class DictDBTest extends CDKTestCase { +public class DictDBTest extends NewCDKTestCase { - public DictDBTest(String name) { - super(name); - } - - public void setUp() {} - - public static Test suite() { - return new TestSuite(DictDBTest.class); - } - - public void testDictionaryDatabase() { + @Test public void testDictionaryDatabase() { DictionaryDatabase db = new DictionaryDatabase(); - assertTrue(db.hasDictionary("chemical")); - assertTrue(db.hasDictionary("elements")); - assertTrue(db.hasDictionary("descriptor-algorithms")); - assertTrue(db.hasDictionary("reaction-processes")); + Assert.assertTrue(db.hasDictionary("chemical")); + Assert.assertTrue(db.hasDictionary("elements")); + Assert.assertTrue(db.hasDictionary("descriptor-algorithms")); + Assert.assertTrue(db.hasDictionary("reaction-processes")); } - public void testOWLDictionary() { + @Test public void testOWLDictionary() { DictionaryDatabase db = new DictionaryDatabase(); Dictionary dict = db.getDictionary("descriptor-algorithms"); - assertTrue(dict.size() > 0); - assertTrue(dict.getNS() != null); + Assert.assertTrue(dict.size() > 0); + Assert.assertTrue(dict.getNS() != null); } - public void testOWLEntry() { + @Test public void testOWLEntry() { DictionaryDatabase db = new DictionaryDatabase(); Dictionary dict = db.getDictionary("descriptor-algorithms"); Entry entry = dict.getEntry("apol"); - assertNotNull(entry); - assertEquals("Atomic Polarizabilities", entry.getLabel()); + Assert.assertNotNull(entry); + Assert.assertEquals("Atomic Polarizabilities", entry.getLabel()); String def = entry.getDefinition(); - assertNotNull(def); - assertTrue(def.length() > 0); + Assert.assertNotNull(def); + Assert.assertTrue(def.length() > 0); } } Modified: cdk/trunk/src/test/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -1,5 +1,4 @@ -/* - * $RCSfile$ +/* $RCSfile$ * $Author$ * $Date$ * $Revision$ @@ -25,37 +24,25 @@ * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - * */ - package org.openscience.cdk.fingerprint; -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.fingerprint.StandardSubstructureSets; +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IAtomContainerSet; -import org.openscience.cdk.CDKTestCase; /** * @cdk.module test-extra */ -public class StandardSubstructureSetsTest extends CDKTestCase { +public class StandardSubstructureSetsTest extends NewCDKTestCase { - public StandardSubstructureSetsTest(String name) { - super(name); - } - - public static Test suite() { - return new TestSuite(StandardSubstructureSetsTest.class); - } - - public void testGetFunctionalGroupSubstructureSet() throws Exception { + @Test public void testGetFunctionalGroupSubstructureSet() throws Exception { IAtomContainerSet set = null; set = StandardSubstructureSets.getFunctionalGroupSubstructureSet(); - assertNotNull(set); - assertEquals(8, set.getAtomContainerCount()); + Assert.assertNotNull(set); + Assert.assertEquals(8, set.getAtomContainerCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -29,35 +29,23 @@ import java.util.BitSet; -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.fingerprint.IFingerprinter; -import org.openscience.cdk.fingerprint.StandardSubstructureSets; -import org.openscience.cdk.fingerprint.SubstructureFingerprinter; +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IAminoAcid; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.templates.AminoAcids; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.manipulator.AminoAcidManipulator; /** * @cdk.module test-extra */ -public class SubstructureFingerprinterTest extends CDKTestCase { +public class SubstructureFingerprinterTest extends NewCDKTestCase { - public SubstructureFingerprinterTest(String name) { - super(name); - } - - public static Test suite() { - return new TestSuite(SubstructureFingerprinterTest.class); - } - - public void testFunctionalGroups() throws Exception { + @Test public void testFunctionalGroups() throws Exception { BitSet bitset = null; IAtomContainerSet set = null; set = StandardSubstructureSets.getFunctionalGroupSubstructureSet(); @@ -66,11 +54,11 @@ IMolecule pinene = MoleculeFactory.makeAlphaPinene(); bitset = printer.getFingerprint(pinene); - assertNotNull(set); - assertNotNull(bitset); - // none of the funtional groups is found in this molecule + Assert.assertNotNull(set); + Assert.assertNotNull(bitset); + // none of the functional groups is found in this molecule for (int i=0; i<set.getAtomContainerCount(); i++) { - assertFalse(bitset.get(i)); + Assert.assertFalse(bitset.get(i)); } } @@ -84,10 +72,10 @@ bitset = printer.getFingerprint(matchesAll); System.out.println("BitSet: " + bitset); - assertNotNull(set); - assertNotNull(bitset); + Assert.assertNotNull(set); + Assert.assertNotNull(bitset); // all funtional groups are found in this molecule - assertEquals(set.getAtomContainerCount(), bitset.cardinality()); + Assert.assertEquals(set.getAtomContainerCount(), bitset.cardinality()); } public void testAminoAcids() throws Exception { @@ -98,7 +86,7 @@ IAminoAcid[] aas = AminoAcids.createAAs(); IFingerprinter printer = new SubstructureFingerprinter(set); - assertNotNull(set); + Assert.assertNotNull(set); // test whether all molecules have an amine and carboxylic acid group for (int i=0; i<aas.length; i++) { @@ -106,14 +94,14 @@ IMolecule aminoAcid = aas[i].getBuilder().newMolecule(aas[i]); addExplicitHydrogens(aminoAcid); - assertNotNull(aminoAcid); + Assert.assertNotNull(aminoAcid); bitset = printer.getFingerprint(aminoAcid); - assertNotNull(bitset); + Assert.assertNotNull(bitset); System.out.println("AA: " + aas[i].getProperty(AminoAcids.RESIDUE_NAME)); System.out.println(" -> " + bitset); - assertTrue(bitset.get(0)); // carboxylic acid group + Assert.assertTrue(bitset.get(0)); // carboxylic acid group if (!aas[i].getProperty(AminoAcids.RESIDUE_NAME).equals("PRO")) - assertTrue(bitset.get(1)); // amine group + Assert.assertTrue(bitset.get(1)); // amine group } } } Modified: cdk/trunk/src/test/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -5,18 +5,16 @@ import javax.vecmath.Point3d; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.geometry.alignment.KabschAlignment; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.io.HINReader; import org.openscience.cdk.io.IChemObjectReader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -30,35 +28,22 @@ * * @see org.openscience.cdk.geometry.alignment.KabschAlignment */ -public class KabschAlignmentTest extends CDKTestCase { +public class KabschAlignmentTest extends NewCDKTestCase { - public KabschAlignmentTest(String name) - { - super(name); - } - /** - * Defines a set of tests that can be used in automatic regression testing - * with JUnit. - */ - public static Test suite() { - TestSuite suite = new TestSuite(KabschAlignmentTest.class); - return suite; - } - - public void testAlign() throws ClassNotFoundException, CDKException, java.lang.Exception{ + @Test public void testAlign() throws ClassNotFoundException, CDKException, java.lang.Exception{ IAtomContainer ac; String filename = "data/hin/gravindex.hin"; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); IChemObjectReader reader = new HINReader(ins); ChemFile content = (ChemFile)reader.read((ChemObject)new ChemFile()); - List cList = ChemFileManipulator.getAllAtomContainers(content); + List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); ac = (IAtomContainer) cList.get(0); KabschAlignment ka = new KabschAlignment(ac,ac); ka.align(); double rmsd = ka.getRMSD(); - assertTrue(1e-8 > rmsd); - assertNotNull(ka.getRotationMatrix()); + Assert.assertTrue(1e-8 > rmsd); + Assert.assertNotNull(ka.getRotationMatrix()); double[][] p1 = { {16.754 ,20.462 ,45.049 }, @@ -103,7 +88,7 @@ ka = new KabschAlignment(a1,a2); ka.align(); rmsd = ka.getRMSD(); - assertEquals(0.13479726, rmsd, 0.00000001); + Assert.assertEquals(0.13479726, rmsd, 0.00000001); } } Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MexperimentalTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MexperimentalTests.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MexperimentalTests.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -20,6 +20,7 @@ */ package org.openscience.cdk.modulesuites; +import junit.framework.JUnit4TestAdapter; import junit.framework.Test; import junit.framework.TestSuite; @@ -39,7 +40,7 @@ public static Test suite () { TestSuite suite= new TestSuite("The cdk.experimental Tests"); - suite.addTest(AssociationTest.suite()); + suite.addTest(new JUnit4TestAdapter(AssociationTest.class)); suite.addTest(VASPReaderTest.suite()); suite.addTest(GenerateFragmentsTest.suite()); Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -24,8 +24,9 @@ import junit.framework.Test; import junit.framework.TestSuite; +import org.openscience.cdk.VariousTests; +import org.openscience.cdk.applications.APIVersionTesterTest; import org.openscience.cdk.applications.swing.MoleculeListViewer; -import org.openscience.cdk.VariousTests; import org.openscience.cdk.applications.undoredo.AddAtomsAndBondsEditTest; import org.openscience.cdk.applications.undoredo.AddHydrogenEditTest; import org.openscience.cdk.applications.undoredo.AdjustBondOrdersEditTest; @@ -39,6 +40,8 @@ import org.openscience.cdk.applications.undoredo.RemoveAtomsAndBondsEditTest; import org.openscience.cdk.dict.DictDBTest; import org.openscience.cdk.fingerprint.ExtendedFingerprinterTest; +import org.openscience.cdk.fingerprint.StandardSubstructureSetsTest; +import org.openscience.cdk.fingerprint.SubstructureFingerprinterTest; import org.openscience.cdk.geometry.RDFCalculatorTest; import org.openscience.cdk.geometry.alignment.KabschAlignmentTest; import org.openscience.cdk.index.CASNumberTest; @@ -54,6 +57,8 @@ import org.openscience.cdk.tools.HOSECodeAnalyserTest; import org.openscience.cdk.tools.HOSECodeGeneratorTest; +import org.openscience.cdk.CloneAtomContainerTest; + /** * TestSuite that runs all the sample tests. * @@ -70,14 +75,16 @@ TestSuite suite= new TestSuite("All CDK Tests"); // Individual Tests + suite.addTest(new JUnit4TestAdapter(CloneAtomContainerTest.class)); // from cdk.test.applications + suite.addTest(new JUnit4TestAdapter(APIVersionTesterTest.class)); // from cdk.test.aromaticity // from cdk.test.dict - suite.addTest(DictDBTest.suite()); + suite.addTest(new JUnit4TestAdapter(DictDBTest.class)); // from cdk.test.geometry suite.addTest(RDFCalculatorTest.suite()); // from cdk.test.geometry.align - suite.addTest(KabschAlignmentTest.suite()); + suite.addTest(new JUnit4TestAdapter(KabschAlignmentTest.class)); // from cdk.test.index suite.addTest(CASNumberTest.suite()); // from cdk.test.isomorphism @@ -95,6 +102,8 @@ suite.addTest(HOSECodeGeneratorTest.suite()); suite.addTest(HOSECodeAnalyserTest.suite()); suite.addTest(new JUnit4TestAdapter(ExtendedFingerprinterTest.class)); + suite.addTest(new JUnit4TestAdapter(SubstructureFingerprinterTest.class)); + suite.addTest(new JUnit4TestAdapter(StandardSubstructureSetsTest.class)); suite.addTest(new JUnit4TestAdapter(DeAromatizationToolTest.class)); suite.addTest(ShelXWriterTest.suite()); Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java 2008-03-20 19:30:02 UTC (rev 10460) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java 2008-03-21 13:59:43 UTC (rev 10461) @@ -152,7 +152,7 @@ suite.addTest(new JUnit4TestAdapter(GraphOnlyFingerprinterTest.class)); suite.addTest(new JUnit4TestAdapter(FingerprinterToolTest.class)); suite.addTest(new JUnit4TestAdapter(ProblemMarkerTest.class)); - suite.addTest(SymbolsTest.suite()); + suite.addTest(new JUnit4TestAdapter(SymbolsTest.class)); suite.addTest(GeometryToolsInternalCoordinatesTest.suite()); suite.addTest(new JUnit4TestAdapter(BondToolsTest.class)); suite.addTest(new JUnit4TestAdapter(UnsupportedChemObjectExceptionTest.class)); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-03-22 07:22:44
|
Revision: 10486 http://cdk.svn.sourceforge.net/cdk/?rev=10486&view=rev Author: egonw Date: 2008-03-22 00:22:38 -0700 (Sat, 22 Mar 2008) Log Message: ----------- Added missing test classes... I wonder why the Coverage testing did not pick this up... :( Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java Added: cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java 2008-03-22 07:22:38 UTC (rev 10486) @@ -0,0 +1,41 @@ +/* $RCSfile$ + * $Author: egonw $ + * $Date: 2008-02-25 14:11:58 +0100 (Mon, 25 Feb 2008) $ + * $Revision: 10234 $ + * + * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * + */ +package org.openscience.cdk.debug; + +import org.junit.BeforeClass; +import org.openscience.cdk.FragmentAtomTest; + +/** + * Checks the functionality of the AtomContainer. + * + * @cdk.module test-datadebug + */ +public class DebugFragmentAtomTest extends FragmentAtomTest { + + @BeforeClass public static void setUp() { + FragmentAtomTest.builder = DebugChemObjectBuilder.getInstance(); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java 2008-03-22 07:09:23 UTC (rev 10485) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java 2008-03-22 07:22:38 UTC (rev 10486) @@ -44,6 +44,7 @@ import org.openscience.cdk.debug.DebugCrystalTest; import org.openscience.cdk.debug.DebugElectronContainerTest; import org.openscience.cdk.debug.DebugElementTest; +import org.openscience.cdk.debug.DebugFragmentAtomTest; import org.openscience.cdk.debug.DebugIsotopeTest; import org.openscience.cdk.debug.DebugLonePairTest; import org.openscience.cdk.debug.DebugMoleculeSetTest; @@ -90,6 +91,7 @@ suite.addTest(new JUnit4TestAdapter(DebugCrystalTest.class)); suite.addTest(new JUnit4TestAdapter(DebugElectronContainerTest.class)); suite.addTest(new JUnit4TestAdapter(DebugElementTest.class)); + suite.addTest(new JUnit4TestAdapter(DebugFragmentAtomTest.class)); suite.addTest(new JUnit4TestAdapter(DebugIsotopeTest.class)); suite.addTest(new JUnit4TestAdapter(DebugLonePairTest.class)); suite.addTest(new JUnit4TestAdapter(DebugMoleculeTest.class)); Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java 2008-03-22 07:09:23 UTC (rev 10485) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java 2008-03-22 07:22:38 UTC (rev 10486) @@ -44,6 +44,7 @@ import org.openscience.cdk.nonotify.NNCrystalTest; import org.openscience.cdk.nonotify.NNElectronContainerTest; import org.openscience.cdk.nonotify.NNElementTest; +import org.openscience.cdk.nonotify.NNFragmentAtomTest; import org.openscience.cdk.nonotify.NNIsotopeTest; import org.openscience.cdk.nonotify.NNLonePairTest; import org.openscience.cdk.nonotify.NNMoleculeSetTest; @@ -90,6 +91,7 @@ suite.addTest(new JUnit4TestAdapter(NNCrystalTest.class)); suite.addTest(new JUnit4TestAdapter(NNElectronContainerTest.class)); suite.addTest(new JUnit4TestAdapter(NNElementTest.class)); + suite.addTest(new JUnit4TestAdapter(NNFragmentAtomTest.class)); suite.addTest(new JUnit4TestAdapter(NNIsotopeTest.class)); suite.addTest(new JUnit4TestAdapter(NNLonePairTest.class)); suite.addTest(new JUnit4TestAdapter(NNMoleculeTest.class)); Added: cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java 2008-03-22 07:22:38 UTC (rev 10486) @@ -0,0 +1,41 @@ +/* $RCSfile$ + * $Author: egonw $ + * $Date: 2006-04-12 11:16:35 +0200 (Wed, 12 Apr 2006) $ + * $Revision: 5921 $ + * + * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * + */ +package org.openscience.cdk.nonotify; + +import org.junit.BeforeClass; +import org.openscience.cdk.FragmentAtomTest; + +/** + * Checks the functionality of the AtomContainer. + * + * @cdk.module test-nonotify + */ +public class NNFragmentAtomTest extends FragmentAtomTest { + + @BeforeClass public static void setUp() { + FragmentAtomTest.builder = NoNotificationChemObjectBuilder.getInstance(); + } + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-04-30 15:53:51
|
Revision: 10737 http://cdk.svn.sourceforge.net/cdk/?rev=10737&view=rev Author: egonw Date: 2008-04-30 08:53:47 -0700 (Wed, 30 Apr 2008) Log Message: ----------- Take advantage of src/main, src/test split up: protected methods should now be tested too Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java 2008-04-30 15:52:59 UTC (rev 10736) +++ cdk/trunk/src/test/org/openscience/cdk/CoverageAnnotationTest.java 2008-04-30 15:53:47 UTC (rev 10737) @@ -117,7 +117,7 @@ Method[] sourceMethods = coreClass.getDeclaredMethods(); for (Method method : sourceMethods) { int modifiers = method.getModifiers(); - if (Modifier.isPrivate(modifiers) || Modifier.isProtected(modifiers)) continue; + if (Modifier.isPrivate(modifiers)) continue; TestMethod testMethodAnnotation = method.getAnnotation(TestMethod.class); Modified: cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java 2008-04-30 15:52:59 UTC (rev 10736) +++ cdk/trunk/src/test/org/openscience/cdk/CoverageTest.java 2008-04-30 15:53:47 UTC (rev 10737) @@ -123,7 +123,7 @@ Method[] methods = coreClass.getDeclaredMethods(); for (int i=0; i<methods.length; i++) { int modifiers = methods[i].getModifiers(); - if (!Modifier.isPrivate(modifiers) && !Modifier.isProtected(modifiers) && + if (!Modifier.isPrivate(modifiers) && !removePackage(methods[i].getName()).startsWith("access")) { String testMethod = "test" + capitalizeName(removePackage(methods[i].getName())); Class[] paramTypes = methods[i].getParameterTypes(); @@ -159,7 +159,7 @@ Constructor[] constructors = coreClass.getDeclaredConstructors(); for (int i=0; i<constructors.length; i++) { int modifiers = constructors[i].getModifiers(); - if (!Modifier.isPrivate(modifiers) && !Modifier.isProtected(modifiers)) { + if (!Modifier.isPrivate(modifiers)) { String testMethod = "test" + capitalizeName(removePackage(constructors[i].getName())); Class[] paramTypes = constructors[i].getParameterTypes(); for (int j=0; j<paramTypes.length; j++) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-05-03 06:57:47
|
Revision: 10775 http://cdk.svn.sourceforge.net/cdk/?rev=10775&view=rev Author: egonw Date: 2008-05-02 23:57:44 -0700 (Fri, 02 May 2008) Log Message: ----------- Fixed svn:keywords for many test modules Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/VariousTests.java cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ReactionStructuresTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ResonanceStructuresTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ValencyMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/charges/AtomTypeChargesTest.java cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugAtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugMoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/exception/InvalidSmilesExceptionTest.java cdk/trunk/src/test/org/openscience/cdk/exception/UnsupportedChemObjectExceptionTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/ExtendedFingerprinterTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/GraphOnlyFingerprinterTest.java cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/formula/IsotopePatternGeneratorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaRangeManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaRangeTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaSetTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ChargeRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ElementRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/MMElementRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ToleranceRangeRuleTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/BondToolsTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/GeometryToolsInternalCoordinatesTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/ZMatrixToolsTest.java cdk/trunk/src/test/org/openscience/cdk/graph/BFSShortestPathTest.java cdk/trunk/src/test/org/openscience/cdk/graph/MoleculeGraphsTest.java cdk/trunk/src/test/org/openscience/cdk/graph/SpanningTreeTest.java cdk/trunk/src/test/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java cdk/trunk/src/test/org/openscience/cdk/graph/matrix/AdjacencyMatrixTest.java cdk/trunk/src/test/org/openscience/cdk/graph/matrix/ConnectionMatrixTest.java cdk/trunk/src/test/org/openscience/cdk/graph/rebond/BsptTest.java cdk/trunk/src/test/org/openscience/cdk/graph/rebond/PointTest.java cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOInstantionTests.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PCCompoundASNReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PDBWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/PMPReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ShelXWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/WriterFactoryTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/cml/CMLStackTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RGraphTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RMapTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RNodeTest.java cdk/trunk/src/test/org/openscience/cdk/libio/cml/ConvertorTest.java cdk/trunk/src/test/org/openscience/cdk/libio/md/MDMoleculeTest.java cdk/trunk/src/test/org/openscience/cdk/math/FortranFormatTest.java cdk/trunk/src/test/org/openscience/cdk/math/PrimesTest.java cdk/trunk/src/test/org/openscience/cdk/math/RandomNumbersToolTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MatomtypeTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MchargesTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/McoreTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdataTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MforcefieldTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MformulaTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MlibiocmlTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MlibiomdTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MpdbTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsaratomicTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarbondTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarproteinTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmartsTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmilesTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MvalencycheckTests.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAminoAcidTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomContainerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomParityTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomTypeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNBioPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNBondTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemFileTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemModelTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemObjectBuilderTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemObjectTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemSequenceTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNCrystalTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNElectronContainerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNElementTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNIsotopeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNLonePairTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMoleculeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPseudoAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNReactionTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNRingSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNRingTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNSingleElectronTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNStrandTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/ChiIndexUtilsTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorSpecificationTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorValueTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomicDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/MassNumberDifferenceDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/BooleanResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/BooleanResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleArrayResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleArrayResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerArrayResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerArrayResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionEngineTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionSpecificationTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactSBEReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/PathTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/QueueTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/SSSRFinderTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/ParserTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/RecursiveTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java cdk/trunk/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java cdk/trunk/src/test/org/openscience/cdk/tools/CDKValencyCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/tools/DataFeaturesTest.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogens.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensAndCharges.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromHybridization.java cdk/trunk/src/test/org/openscience/cdk/tools/ElementComparatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/HOSECodeAnalyserTest.java cdk/trunk/src/test/org/openscience/cdk/tools/LonePairElectronCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AminoAcidManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomTypeManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/BondManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemFileManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemModelManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemSequenceManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/MoleculeSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ReactionSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingSizeComparatorTest.java cdk/trunk/src/test/org/openscience/cdk/validate/Geometry3DValidatorTest.java cdk/trunk/src/test/org/openscience/cdk/validate/ProblemMarkerTest.java Property Changed: ---------------- cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ConformerContainerTest.java cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/VariousTests.java cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ReactionStructuresTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ResonanceStructuresTest.java cdk/trunk/src/test/org/openscience/cdk/atomtype/ValencyMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/charges/AtomTypeChargesTest.java cdk/trunk/src/test/org/openscience/cdk/config/SymbolsTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugAtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugFragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugMoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugPDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/debug/DebugReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/exception/InvalidSmilesExceptionTest.java cdk/trunk/src/test/org/openscience/cdk/exception/UnsupportedChemObjectExceptionTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/ExtendedFingerprinterTest.java cdk/trunk/src/test/org/openscience/cdk/fingerprint/GraphOnlyFingerprinterTest.java cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/formula/IsotopePatternGeneratorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaRangeManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaRangeTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaSetTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ChargeRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ElementRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/MMElementRuleTest.java cdk/trunk/src/test/org/openscience/cdk/formula/rules/ToleranceRangeRuleTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/BondToolsTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/GeometryToolsInternalCoordinatesTest.java cdk/trunk/src/test/org/openscience/cdk/geometry/ZMatrixToolsTest.java cdk/trunk/src/test/org/openscience/cdk/graph/BFSShortestPathTest.java cdk/trunk/src/test/org/openscience/cdk/graph/MoleculeGraphsTest.java cdk/trunk/src/test/org/openscience/cdk/graph/SpanningTreeTest.java cdk/trunk/src/test/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java cdk/trunk/src/test/org/openscience/cdk/graph/matrix/AdjacencyMatrixTest.java cdk/trunk/src/test/org/openscience/cdk/graph/matrix/ConnectionMatrixTest.java cdk/trunk/src/test/org/openscience/cdk/graph/matrix/TopologicalMatrixTest.java cdk/trunk/src/test/org/openscience/cdk/graph/rebond/BsptTest.java cdk/trunk/src/test/org/openscience/cdk/graph/rebond/PointTest.java cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOInstantionTests.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PCCompoundASNReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PDBWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/PMPReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ShelXWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/WriterFactoryTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/cml/CMLStackTest.java cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RGraphTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RMapTest.java cdk/trunk/src/test/org/openscience/cdk/isomorphism/mcss/RNodeTest.java cdk/trunk/src/test/org/openscience/cdk/libio/cml/ConvertorTest.java cdk/trunk/src/test/org/openscience/cdk/libio/md/MDMoleculeTest.java cdk/trunk/src/test/org/openscience/cdk/math/FortranFormatTest.java cdk/trunk/src/test/org/openscience/cdk/math/PrimesTest.java cdk/trunk/src/test/org/openscience/cdk/math/RandomNumbersToolTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MatomtypeTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MchargesTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/McoreTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdataTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdatadebugTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MforcefieldTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MformulaTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MlibiocmlTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MlibiomdTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MpcoreTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MpdbTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsaratomicTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarbondTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarproteinTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmartsTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmilesTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MvalencycheckTests.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAminoAcidTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomContainerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomParityTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNAtomTypeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNBioPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNBondTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemFileTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemModelTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemObjectBuilderTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemObjectTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNChemSequenceTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNCrystalTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNElectronContainerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNElementTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNFragmentAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNIsotopeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNLonePairTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMoleculeSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMoleculeTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNPseudoAtomTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNReactionSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNReactionTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNRingSetTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNRingTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNSingleElectronTest.java cdk/trunk/src/test/org/openscience/cdk/nonotify/NNStrandTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreAtomTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreBondTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryAtomTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryBondTest.java cdk/trunk/src/test/org/openscience/cdk/pharmacophore/PharmacophoreUtilityTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBMonomerTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBPolymerTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/ChiIndexUtilsTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorSpecificationTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorValueTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomicDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3RTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDRTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHRTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topolTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSRTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/MassNumberDifferenceDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorChargeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizabilityTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/model/R2/CNNRegressionModelTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/model/R2/LinearRegressionModelTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/model/R2/QSARRModelTests.java cdk/trunk/src/test/org/openscience/cdk/qsar/model/R2/RJavaEnvironmentTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/BooleanResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/BooleanResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleArrayResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleArrayResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/DoubleResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerArrayResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerArrayResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerResultTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/result/IntegerResultTypeTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionEngineTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionSpecificationTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactSBEReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/PiBondingMovemetReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/PathTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/QueueTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/SSSRFinderTest.java cdk/trunk/src/test/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleTest.java cdk/trunk/src/test/org/openscience/cdk/similarity/DistanceMomentTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/ParserTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/RecursiveTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/visitor/SmartsDumpVisitorTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/visitor/SmartsQueryVisitorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java cdk/trunk/src/test/org/openscience/cdk/tools/CDKValencyCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/tools/DataFeaturesTest.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogens.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensAndCharges.java cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromHybridization.java cdk/trunk/src/test/org/openscience/cdk/tools/ElementComparatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/HOSECodeAnalyserTest.java cdk/trunk/src/test/org/openscience/cdk/tools/LonePairElectronCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AminoAcidManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerComparatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomTypeManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/BondManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemFileManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemModelManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ChemSequenceManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/MoleculeSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/ReactionSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingSetManipulatorTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/RingSizeComparatorTest.java cdk/trunk/src/test/org/openscience/cdk/validate/Geometry3DValidatorTest.java cdk/trunk/src/test/org/openscience/cdk/validate/ProblemMarkerTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 6718 $ $Author: egonw $ $Date: 2006-08-01 21:13:42 +0200 (Tue, 01 Aug 2006) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * Property changes on: cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-09 00:35:55 +0100 (Fri, 09 Feb 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/AtomtypeCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/ChargesCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Property changes on: cdk/trunk/src/test/org/openscience/cdk/ConformerContainerTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-09 00:35:55 +0100 (Fri, 09 Feb 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/FormulaCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7037 $ $Author: egonw $ $Date: 2006-09-24 11:13:13 +0200 (Sun, 24 Sep 2006) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2002-2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/FragmentAtomTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,7 +1,7 @@ /* $RCSfile$ - * $Author: egonw $ - * $Date: 2006-08-01 21:13:42 +0200 (Tue, 01 Aug 2006) $ - * $Revision: 6718 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project * Property changes on: cdk/trunk/src/test/org/openscience/cdk/MoleculeSetTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/PcoreCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/QsaratomicCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/QsarbondCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-09 00:35:55 +0100 (Fri, 09 Feb 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/QsarmolecularCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-09 00:35:55 +0100 (Fri, 09 Feb 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/ReactionCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,7 +1,7 @@ /* $RCSfile$ - * $Author: egonw $ - * $Date: 2006-07-31 11:23:24 +0200 (Mon, 31 Jul 2006) $ - * $Revision: 6710 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * Property changes on: cdk/trunk/src/test/org/openscience/cdk/ReactionSetTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/StandardCoverageTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/VariousTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/VariousTests.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/VariousTests.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,7 +1,7 @@ /* $RCSfile$ - * $Author: egonw $ - * $Date: 2006-03-29 23:42:34 +0100 (Wed, 29 Mar 2006) $ - * $Revision: 5865 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright (C) 2002-2007 The Chemistry Development Kit (CDK) project * Property changes on: cdk/trunk/src/test/org/openscience/cdk/VariousTests.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,6 +1,6 @@ -/* $Revision: 8225 $ - * $Author: egonw $ - * $Date: 2007-04-21 02:23:13 +0200 (Sat, 21 Apr 2007) $ +/* $Revision$ + * $Author$ + * $Date$ * * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project * Property changes on: cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 5889 $ $Author: egonw $ $Date: 2006-04-06 15:24:58 +0200 (Thu, 06 Apr 2006) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 5889 $ $Author: egonw $ $Date: 2006-04-06 15:24:58 +0200 (Thu, 06 Apr 2006) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * 2007 Rajarshi Guha Property changes on: cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 5889 $ $Author: egonw $ $Date: 2006-04-06 15:24:58 +0200 (Thu, 06 Apr 2006) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java ___________________________________________________________________ Name: svn:keywords + Author Date Id Revision Modified: cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java 2008-05-03 06:50:01 UTC (rev 10774) +++ cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java 2008-05-03 06:57:44 UTC (rev 10775) @@ -1,4 +1,4 @@ -/* $Revision: 7691 $ $Author: egonw $ $Date: 2007-01-11 12:47:48 +0100 (Thu, 11 Jan 2007) $ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2007 Egon Willighagen <eg...@us...> * Property changes on: cdk/trunk/src/test/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java ___________________________... [truncated message content] |
From: <raj...@us...> - 2008-05-05 14:05:57
|
Revision: 10823 http://cdk.svn.sourceforge.net/cdk/?rev=10823&view=rev Author: rajarshi Date: 2008-05-05 07:05:55 -0700 (Mon, 05 May 2008) Log Message: ----------- Added bug id to the unit tests. Also replaced the molecule in the aromaticity with CDK source code rather than SMILES parsing. The aromaticity bug is fixed when CDK source format is used Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-05 13:05:04 UTC (rev 10822) +++ cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-05 14:05:55 UTC (rev 10823) @@ -605,9 +605,95 @@ return mol; } - @Test public void test3Amino2MethylPyridine() throws CDKException { - SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); - IAtomContainer mol = sp.parseSmiles("c1c(C)c(N)cnc1"); + /** + * cdk.bug 1957684 + */ + @Test + public void test3Amino2MethylPyridine() throws CDKException { + + IMolecule mol = new Molecule(); + IAtom a1 = mol.getBuilder().newAtom("N"); + a1.setPoint2d(new Point2d(3.7321, 1.345)); + mol.addAtom(a1); + IAtom a2 = mol.getBuilder().newAtom("N"); + a2.setPoint2d(new Point2d(4.5981, -1.155)); + mol.addAtom(a2); + IAtom a3 = mol.getBuilder().newAtom("C"); + a3.setPoint2d(new Point2d(2.866, -0.155)); + mol.addAtom(a3); + IAtom a4 = mol.getBuilder().newAtom("C"); + a4.setPoint2d(new Point2d(3.7321, 0.345)); + mol.addAtom(a4); + IAtom a5 = mol.getBuilder().newAtom("C"); + a5.setPoint2d(new Point2d(2.866, -1.155)); + mol.addAtom(a5); + IAtom a6 = mol.getBuilder().newAtom("C"); + a6.setPoint2d(new Point2d(2.0, 0.345)); + mol.addAtom(a6); + IAtom a7 = mol.getBuilder().newAtom("C"); + a7.setPoint2d(new Point2d(4.5981, -0.155)); + mol.addAtom(a7); + IAtom a8 = mol.getBuilder().newAtom("C"); + a8.setPoint2d(new Point2d(3.7321, -1.655)); + mol.addAtom(a8); + IAtom a9 = mol.getBuilder().newAtom("H"); + a9.setPoint2d(new Point2d(2.3291, -1.465)); + mol.addAtom(a9); + IAtom a10 = mol.getBuilder().newAtom("H"); + a10.setPoint2d(new Point2d(2.31, 0.8819)); + mol.addAtom(a10); + IAtom a11 = mol.getBuilder().newAtom("H"); + a11.setPoint2d(new Point2d(1.4631, 0.655)); + mol.addAtom(a11); + IAtom a12 = mol.getBuilder().newAtom("H"); + a12.setPoint2d(new Point2d(1.69, -0.1919)); + mol.addAtom(a12); + IAtom a13 = mol.getBuilder().newAtom("H"); + a13.setPoint2d(new Point2d(5.135, 0.155)); + mol.addAtom(a13); + IAtom a14 = mol.getBuilder().newAtom("H"); + a14.setPoint2d(new Point2d(3.7321, -2.275)); + mol.addAtom(a14); + IAtom a15 = mol.getBuilder().newAtom("H"); + a15.setPoint2d(new Point2d(4.269, 1.655)); + mol.addAtom(a15); + IAtom a16 = mol.getBuilder().newAtom("H"); + a16.setPoint2d(new Point2d(3.1951, 1.655)); + mol.addAtom(a16); + IBond b1 = mol.getBuilder().newBond(a1, a4, IBond.Order.SINGLE); + mol.addBond(b1); + IBond b2 = mol.getBuilder().newBond(a1, a15, IBond.Order.SINGLE); + mol.addBond(b2); + IBond b3 = mol.getBuilder().newBond(a1, a16, IBond.Order.SINGLE); + mol.addBond(b3); + IBond b4 = mol.getBuilder().newBond(a2, a7, IBond.Order.DOUBLE); + mol.addBond(b4); + IBond b5 = mol.getBuilder().newBond(a2, a8, IBond.Order.SINGLE); + mol.addBond(b5); + IBond b6 = mol.getBuilder().newBond(a3, a4, IBond.Order.DOUBLE); + mol.addBond(b6); + IBond b7 = mol.getBuilder().newBond(a3, a5, IBond.Order.SINGLE); + mol.addBond(b7); + IBond b8 = mol.getBuilder().newBond(a3, a6, IBond.Order.SINGLE); + mol.addBond(b8); + IBond b9 = mol.getBuilder().newBond(a4, a7, IBond.Order.SINGLE); + mol.addBond(b9); + IBond b10 = mol.getBuilder().newBond(a5, a8, IBond.Order.DOUBLE); + mol.addBond(b10); + IBond b11 = mol.getBuilder().newBond(a5, a9, IBond.Order.SINGLE); + mol.addBond(b11); + IBond b12 = mol.getBuilder().newBond(a6, a10, IBond.Order.SINGLE); + mol.addBond(b12); + IBond b13 = mol.getBuilder().newBond(a6, a11, IBond.Order.SINGLE); + mol.addBond(b13); + IBond b14 = mol.getBuilder().newBond(a6, a12, IBond.Order.SINGLE); + mol.addBond(b14); + IBond b15 = mol.getBuilder().newBond(a7, a13, IBond.Order.SINGLE); + mol.addBond(b15); + IBond b16 = mol.getBuilder().newBond(a8, a14, IBond.Order.SINGLE); + mol.addBond(b16); + + AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); boolean isAromatic = CDKHueckelAromaticityDetector.detectAromaticity(mol); Assert.assertTrue(isAromatic); Modified: cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java 2008-05-05 13:05:04 UTC (rev 10822) +++ cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java 2008-05-05 14:05:55 UTC (rev 10823) @@ -55,6 +55,10 @@ setDescriptor(MomentOfInertiaDescriptor.class); } + /** + * cdk.bug 1956139 + * @throws InvalidSmilesException + */ public void testMOIFromSmiles() throws InvalidSmilesException { SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("CCCC"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <raj...@us...> - 2008-05-05 14:23:27
|
Revision: 10828 http://cdk.svn.sourceforge.net/cdk/?rev=10828&view=rev Author: rajarshi Date: 2008-05-05 07:23:23 -0700 (Mon, 05 May 2008) Log Message: ----------- Fixed cdk.bug tags Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-05 14:22:30 UTC (rev 10827) +++ cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java 2008-05-05 14:23:23 UTC (rev 10828) @@ -606,7 +606,7 @@ } /** - * cdk.bug 1957684 + * @cdk.bug 1957684 */ @Test public void test3Amino2MethylPyridine() throws CDKException { Modified: cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java 2008-05-05 14:22:30 UTC (rev 10827) +++ cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java 2008-05-05 14:23:23 UTC (rev 10828) @@ -56,7 +56,7 @@ } /** - * cdk.bug 1956139 + * @cdk.bug 1956139 * @throws InvalidSmilesException */ public void testMOIFromSmiles() throws InvalidSmilesException { Modified: cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java 2008-05-05 14:22:30 UTC (rev 10827) +++ cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java 2008-05-05 14:23:23 UTC (rev 10828) @@ -1233,7 +1233,7 @@ /** - * cdk.bug 1957958 + * @cdk.bug 1957958 */ @Test public void test3amino4methylpyridine() throws Exception { IMolecule mol = sp.parseSmiles("c1c(C)c(N)cnc1"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-05-11 13:36:06
|
Revision: 10968 http://cdk.svn.sourceforge.net/cdk/?rev=10968&view=rev Author: egonw Date: 2008-05-11 06:36:00 -0700 (Sun, 11 May 2008) Log Message: ----------- Enabled unit test coverage testing for the io module Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/IoCoverageTest.java Added: cdk/trunk/src/test/org/openscience/cdk/IoCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/IoCoverageTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/IoCoverageTest.java 2008-05-11 13:36:00 UTC (rev 10968) @@ -0,0 +1,56 @@ +/* $Revision: 10234 $ $Author: egonw $ $Date: 2008-02-25 14:11:58 +0100 (Mon, 25 Feb 2008) $ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk; + +import junit.framework.Test; +import junit.framework.TestSuite; + +/** + * TestSuite that uses tests whether all public methods in the core + * module are tested. Unlike Emma, it does not test that all code is + * tested, just all methods. + * + * @cdk.module test-core + */ +public class IoCoverageTest extends CoverageAnnotationTest { + + private final static String CLASS_LIST = "io.javafiles"; + + public IoCoverageTest(String name) { + super(name); + } + + protected void setUp() throws Exception { + super.setUp(); + super.loadClassList(CLASS_LIST); + } + + public static Test suite() { + TestSuite suite = new TestSuite(); + suite.addTestSuite(IoCoverageTest.class); + return suite; + } + + public void testCoverage() { + assertTrue(super.runCoverageTest()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-05-11 07:36:00 UTC (rev 10967) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-05-11 13:36:00 UTC (rev 10968) @@ -26,6 +26,7 @@ import junit.framework.Test; import junit.framework.TestSuite; +import org.openscience.cdk.IoCoverageTest; import org.openscience.cdk.io.CDKSourceCodeWriterTest; import org.openscience.cdk.io.ChemObjectIOInstantionTests; import org.openscience.cdk.io.CrystClustReaderTest; @@ -70,6 +71,8 @@ public static Test suite() { TestSuite suite = new TestSuite("The cdk.io Tests"); + suite.addTest(IoCoverageTest.suite()); + suite.addTest(CMLIOTests.suite()); suite.addTest(CrystClustReaderTest.suite()); suite.addTest(CDKSourceCodeWriterTest.suite()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-05-11 16:54:19
|
Revision: 10974 http://cdk.svn.sourceforge.net/cdk/?rev=10974&view=rev Author: egonw Date: 2008-05-11 09:54:17 -0700 (Sun, 11 May 2008) Log Message: ----------- Typo: seUp -> setUp Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java 2008-05-11 15:04:57 UTC (rev 10973) +++ cdk/trunk/src/test/org/openscience/cdk/formula/rules/FormulaRuleTest.java 2008-05-11 16:54:17 UTC (rev 10974) @@ -62,7 +62,7 @@ * </pre> */ @Test public void testHasSetSuperDotRule() { - Assert.assertNotNull("The extending class must set the super.rule in its seUp() method.", rule); + Assert.assertNotNull("The extending class must set the super.rule in its setUp() method.", rule); } @Test public void testGetParameters() { Modified: cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java 2008-05-11 15:04:57 UTC (rev 10973) +++ cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java 2008-05-11 16:54:17 UTC (rev 10974) @@ -65,7 +65,7 @@ * </pre> */ public void testHasSetSuperDotDescriptor() { - assertNotNull("The extending class must set the super.descriptor in its seUp() method.", descriptor); + assertNotNull("The extending class must set the super.descriptor in its setUp() method.", descriptor); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java 2008-05-11 15:04:57 UTC (rev 10973) +++ cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java 2008-05-11 16:54:17 UTC (rev 10974) @@ -78,7 +78,7 @@ * </pre> */ @Test public void testHasSetSuperDotDescriptor() { - Assert.assertNotNull("The extending class must set the super.descriptor in its seUp() method.", reactionMechanism); + Assert.assertNotNull("The extending class must set the super.descriptor in its setUp() method.", reactionMechanism); } } Modified: cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java 2008-05-11 15:04:57 UTC (rev 10973) +++ cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java 2008-05-11 16:54:17 UTC (rev 10974) @@ -99,7 +99,7 @@ * </pre> */ @Test public void testHasSetSuperDotDescriptor() { - Assert.assertNotNull("The extending class must set the super.descriptor in its seUp() method.", reaction); + Assert.assertNotNull("The extending class must set the super.descriptor in its setUp() method.", reaction); } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-05-11 20:27:30
|
Revision: 10978 http://cdk.svn.sourceforge.net/cdk/?rev=10978&view=rev Author: egonw Date: 2008-05-11 13:27:23 -0700 (Sun, 11 May 2008) Log Message: ----------- Updated test method names to new API of data classes Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java cdk/trunk/src/test/org/openscience/cdk/ElementTest.java cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java cdk/trunk/src/test/org/openscience/cdk/PseudoAtomTest.java cdk/trunk/src/test/org/openscience/cdk/ReactionTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/AtomContainerSetTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -108,7 +108,7 @@ Assert.assertEquals(1.0, som.getMultiplier(0), 0.00001); } - @Test public void testSetMultiplier_int_double() { + @Test public void testSetMultiplier_int_Double() { IAtomContainerSet som = builder.newAtomContainerSet(); som.addAtomContainer(builder.newAtomContainer()); @@ -117,7 +117,7 @@ Assert.assertEquals(2.0, som.getMultiplier(0), 0.00001); } - @Test public void testSetMultipliers_arraydouble() { + @Test public void testSetMultipliers_arrayDouble() { IAtomContainerSet som = builder.newAtomContainerSet(); IAtomContainer container = builder.newAtomContainer(); som.addAtomContainer(container); @@ -134,7 +134,7 @@ Assert.assertEquals(3.0, som.getMultiplier(1), 0.00001); } - @Test public void testSetMultiplier_IAtomContainer_double() { + @Test public void testSetMultiplier_IAtomContainer_Double() { IAtomContainerSet som = builder.newAtomContainerSet(); IAtomContainer container = builder.newAtomContainer(); som.addAtomContainer(container); Modified: cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -178,14 +178,14 @@ Assert.assertEquals(spacegroup, crystal.getSpaceGroup()); } - @Test public void testSetZ_int() { + @Test public void testSetZ_Integer() { ICrystal crystal = builder.newCrystal(); int z = 2; crystal.setZ(z); Assert.assertEquals(z, crystal.getZ()); } @Test public void testGetZ() { - testSetZ_int(); + testSetZ_Integer(); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -53,13 +53,13 @@ Assert.assertEquals(0, ec.getElectronCount()); } - @Test public void testSetElectronCount_int() { + @Test public void testSetElectronCount_Integer() { IElectronContainer ec = builder.newElectronContainer(); ec.setElectronCount(3); Assert.assertEquals(3, ec.getElectronCount()); } @Test public void testGetElectronCount() { - testSetElectronCount_int(); + testSetElectronCount_Integer(); } @Test public void testClone() throws Exception { Modified: cdk/trunk/src/test/org/openscience/cdk/ElementTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -80,7 +80,7 @@ Assert.assertEquals("X", e.getSymbol()); } - @Test public void testSetAtomicNumber_int() { + @Test public void testSetAtomicNumber_Integer() { IElement e = builder.newElement("H"); e.setAtomicNumber(1); Assert.assertEquals(1, e.getAtomicNumber()); Modified: cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -77,31 +77,31 @@ Assert.assertEquals(80.0, i.getNaturalAbundance(), 0.001); } - @Test public void testSetNaturalAbundance_double() { + @Test public void testSetNaturalAbundance_Double() { IIsotope i = builder.newIsotope("C"); i.setNaturalAbundance(80.0); Assert.assertEquals(80.0, i.getNaturalAbundance(), 0.001); } @Test public void testGetNaturalAbundance() { - testSetNaturalAbundance_double(); + testSetNaturalAbundance_Double(); } - @Test public void testSetExactMass_double() { + @Test public void testSetExactMass_Double() { IIsotope i = builder.newIsotope("C"); i.setExactMass(12.03); Assert.assertEquals(12.03, i.getExactMass(), 0.001); } @Test public void testGetExactMass() { - testSetExactMass_double(); + testSetExactMass_Double(); } - @Test public void testSetMassNumber_int() { + @Test public void testSetMassNumber_Integer() { IIsotope i = builder.newIsotope("D"); i.setMassNumber(2); Assert.assertEquals(2, i.getMassNumber()); } @Test public void testGetMassNumber() { - testSetMassNumber_int(); + testSetMassNumber_Integer(); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/PseudoAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/PseudoAtomTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/PseudoAtomTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -117,31 +117,31 @@ Assert.assertEquals(0, atom.getFormalCharge().intValue()); } - @Test public void testSetFormalCharge_int() { + @Test public void testSetFormalCharge_Integer() { IPseudoAtom atom = builder.newPseudoAtom("Whatever"); atom.setFormalCharge(+5); Assert.assertEquals(0, atom.getFormalCharge().intValue()); } - @Test public void testSetHydrogenCount_int() { + @Test public void testSetHydrogenCount_Integer() { IPseudoAtom atom = builder.newPseudoAtom("Whatever"); atom.setHydrogenCount(+5); Assert.assertEquals(0, atom.getHydrogenCount().intValue()); } - @Test public void testSetCharge_double() { + @Test public void testSetCharge_Double() { IPseudoAtom atom = builder.newPseudoAtom("Whatever"); atom.setCharge(0.78); Assert.assertEquals(0.0, atom.getCharge(), 0.001); } - @Test public void testSetExactMass_double() { + @Test public void testSetExactMass_Double() { IPseudoAtom atom = builder.newPseudoAtom("Whatever"); atom.setExactMass(12.001); Assert.assertEquals(0.0, atom.getExactMass(), 0.001); } - @Test public void testSetStereoParity_int() { + @Test public void testSetStereoParity_Integer() { IPseudoAtom atom = builder.newPseudoAtom("Whatever"); atom.setStereoParity(-1); Assert.assertEquals(0, atom.getStereoParity().intValue()); Modified: cdk/trunk/src/test/org/openscience/cdk/ReactionTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ReactionTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/ReactionTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -105,7 +105,7 @@ Assert.assertEquals(1.0, reaction.getReactantCoefficient(aceticAcid), 0.00001); } - @Test public void testAddReactant_IMolecule_double() { + @Test public void testAddReactant_IMolecule_Double() { IReaction reaction = builder.newReaction(); IMolecule proton = builder.newMolecule(); IMolecule sulfate = builder.newMolecule(); @@ -148,7 +148,7 @@ Assert.assertEquals(1.0, reaction.getProductCoefficient(aceticAcid), 0.00001); } - @Test public void testAddProduct_IMolecule_double() { + @Test public void testAddProduct_IMolecule_Double() { IReaction reaction = builder.newReaction(); IMolecule proton = builder.newMolecule(); IMolecule sulfate = builder.newMolecule(); @@ -183,7 +183,7 @@ Assert.assertEquals(-1.0, reaction.getProductCoefficient(builder.newMolecule()), 0.00001); } - @Test public void testSetReactantCoefficient_IMolecule_double() { + @Test public void testSetReactantCoefficient_IMolecule_Double() { IReaction reaction = builder.newReaction(); IMolecule proton = builder.newMolecule(); reaction.addReactant(proton, 2.0); @@ -191,7 +191,7 @@ Assert.assertEquals(3.0, reaction.getReactantCoefficient(proton), 0.00001); } - @Test public void testSetProductCoefficient_IMolecule_double() { + @Test public void testSetProductCoefficient_IMolecule_Double() { IReaction reaction = builder.newReaction(); IMolecule proton = builder.newMolecule(); reaction.addProduct(proton, 2.0); @@ -223,7 +223,7 @@ Assert.assertEquals(2.0, pc[1], 0.00001); } - @Test public void testSetReactantCoefficients_arraydouble() { + @Test public void testSetReactantCoefficients_arrayDouble() { IReaction reaction = builder.newReaction(); IMolecule ed1 = builder.newMolecule(); IMolecule ed2 = builder.newMolecule(); @@ -238,7 +238,7 @@ Assert.assertFalse(reaction.setReactantCoefficients(ecFalse)); } - @Test public void testSetProductCoefficients_arraydouble() { + @Test public void testSetProductCoefficients_arrayDouble() { IReaction reaction = builder.newReaction(); IMolecule pr1 = builder.newMolecule(); reaction.addProduct(pr1, 1d); @@ -279,7 +279,7 @@ Assert.assertEquals(1, reaction.getAgents().getMoleculeCount()); } - @Test public void testSetDirection_int() { + @Test public void testSetDirection_IReaction_Direction() { IReaction reaction = builder.newReaction(); IReaction.Direction direction = IReaction.Direction.BIDIRECTIONAL; reaction.setDirection(direction); Modified: cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -193,7 +193,7 @@ Assert.assertEquals(atom.getTempFactor(),0.0, 001); } - @Test public void testSetTempFactor_double(){ + @Test public void testSetTempFactor_Double(){ testGetTempFactor(); } @@ -247,7 +247,7 @@ Assert.assertEquals("123", atom.getSegID()); } - @Test public void testSetSerial_int(){ + @Test public void testSetSerial_Integer(){ testGetSerial(); } @@ -267,7 +267,7 @@ Assert.assertEquals("123", atom.getResSeq()); } - @Test public void testSetOxt_boolean(){ + @Test public void testSetOxt_Boolean(){ testGetOxt(); } @@ -277,7 +277,7 @@ Assert.assertTrue(atom.getOxt()); } - @Test public void testSetHetAtom_boolean(){ + @Test public void testSetHetAtom_Boolean(){ testGetHetAtom(); } @@ -287,7 +287,7 @@ Assert.assertTrue(atom.getHetAtom()); } - @Test public void testSetOccupancy_double(){ + @Test public void testSetOccupancy_Double(){ testGetOccupancy(); } Modified: cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java 2008-05-11 19:39:13 UTC (rev 10977) +++ cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java 2008-05-11 20:27:23 UTC (rev 10978) @@ -58,7 +58,7 @@ Assert.assertNull(structure.getEndChainID()); } - @Test public void testSetEndChainID_char() { + @Test public void testSetEndChainID_Character() { IPDBStructure structure = builder.newPDBStructure(); char endChainID = 'x'; structure.setEndChainID(endChainID); @@ -70,7 +70,7 @@ Assert.assertNull(structure.getEndInsertionCode()); } - @Test public void testSetEndInsertionCode_char() { + @Test public void testSetEndInsertionCode_Character() { IPDBStructure structure = builder.newPDBStructure(); char endInsertionCode = 'x'; structure.setEndInsertionCode(endInsertionCode); @@ -82,7 +82,7 @@ Assert.assertNull(structure.getEndSequenceNumber()); } - @Test public void testSetEndSequenceNumber_int() { + @Test public void testSetEndSequenceNumber_Integer() { IPDBStructure structure = builder.newPDBStructure(); int endSequenceNumber = 5; structure.setEndSequenceNumber(endSequenceNumber); @@ -94,7 +94,7 @@ Assert.assertNull(structure.getStartChainID()); } - @Test public void testSetStartChainID_char() { + @Test public void testSetStartChainID_Character() { IPDBStructure structure = builder.newPDBStructure(); char startChainID = 'x'; structure.setStartChainID(startChainID); @@ -106,7 +106,7 @@ Assert.assertNull(structure.getStartInsertionCode()); } - @Test public void testSetStartInsertionCode_char() { + @Test public void testSetStartInsertionCode_Character() { IPDBStructure structure = builder.newPDBStructure(); char startInsertionCode = 'x'; structure.setStartInsertionCode(startInsertionCode); @@ -118,7 +118,7 @@ Assert.assertNull(structure.getStartSequenceNumber()); } - @Test public void testSetStartSequenceNumber_int() { + @Test public void testSetStartSequenceNumber_Integer() { IPDBStructure structure = builder.newPDBStructure(); int startSequenceNumber = 5; structure.setStartSequenceNumber(startSequenceNumber); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-05-19 20:54:25
|
Revision: 11063 http://cdk.svn.sourceforge.net/cdk/?rev=11063&view=rev Author: egonw Date: 2008-05-19 13:53:37 -0700 (Mon, 19 May 2008) Log Message: ----------- Java 1.5 seems to complain about assertEquals(Object, Object), which can be solved by forcing a assertEquals(native, native), e.g. assertEquals(int, int) Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java cdk/trunk/src/test/org/openscience/cdk/ElementTest.java cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java cdk/trunk/src/test/org/openscience/cdk/LonePairTest.java cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java cdk/trunk/src/test/org/openscience/cdk/SingleElectronTest.java cdk/trunk/src/test/org/openscience/cdk/config/AtomTypeFactoryTest.java cdk/trunk/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java cdk/trunk/src/test/org/openscience/cdk/config/atomtypes/AtomTypeReaderTest.java cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java cdk/trunk/src/test/org/openscience/cdk/io/PDBReaderTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -38,13 +38,13 @@ @Test public void testAssociation() { Association association = new Association(); - Assert.assertEquals(0, association.getElectronCount()); + Assert.assertEquals(0, association.getElectronCount().intValue()); Assert.assertEquals(0, association.getAtomCount()); } @Test public void testAssociation_IAtom_IAtom() { Association association = new Association(new Atom("C"), new Atom("C")); - Assert.assertEquals(0, association.getElectronCount()); + Assert.assertEquals(0, association.getElectronCount().intValue()); Assert.assertEquals(2, association.getAtomCount()); } Modified: cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/CrystalTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -182,7 +182,7 @@ ICrystal crystal = builder.newCrystal(); int z = 2; crystal.setZ(z); - Assert.assertEquals(z, crystal.getZ()); + Assert.assertEquals(z, crystal.getZ().intValue()); } @Test public void testGetZ() { testSetZ_Integer(); Modified: cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/ElectronContainerTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -50,13 +50,13 @@ @Test public void testElectronContainer() { IElectronContainer ec = builder.newElectronContainer(); Assert.assertNotNull(ec); - Assert.assertEquals(0, ec.getElectronCount()); + Assert.assertEquals(0, ec.getElectronCount().intValue()); } @Test public void testSetElectronCount_Integer() { IElectronContainer ec = builder.newElectronContainer(); ec.setElectronCount(3); - Assert.assertEquals(3, ec.getElectronCount()); + Assert.assertEquals(3, ec.getElectronCount().intValue()); } @Test public void testGetElectronCount() { testSetElectronCount_Integer(); Modified: cdk/trunk/src/test/org/openscience/cdk/ElementTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -64,7 +64,7 @@ @Test public void testElement_String_int() { IElement e = builder.newElement("H", 1); Assert.assertEquals("H", e.getSymbol()); - Assert.assertEquals(1, e.getAtomicNumber()); + Assert.assertEquals(1, e.getAtomicNumber().intValue()); } // test methods @@ -83,12 +83,12 @@ @Test public void testSetAtomicNumber_Integer() { IElement e = builder.newElement("H"); e.setAtomicNumber(1); - Assert.assertEquals(1, e.getAtomicNumber()); + Assert.assertEquals(1, e.getAtomicNumber().intValue()); } @Test public void testGetAtomicNumber() { IElement e = builder.newElement("D", 1); - Assert.assertEquals(1, e.getAtomicNumber()); + Assert.assertEquals(1, e.getAtomicNumber().intValue()); } @Test public void testClone() throws Exception { @@ -112,7 +112,7 @@ // test cloning of atomic number elem.setAtomicNumber(5); // don't care about symbol - Assert.assertEquals(6, clone.getAtomicNumber()); + Assert.assertEquals(6, clone.getAtomicNumber().intValue()); } /** Test for RFC #9 */ Modified: cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -56,23 +56,23 @@ @Test public void testIsotope_int_String_int_double_double() { IIsotope i = builder.newIsotope(6, "C", 12, 12.001, 80.0); - Assert.assertEquals(12, i.getMassNumber()); + Assert.assertEquals(12, i.getMassNumber().intValue()); Assert.assertEquals("C", i.getSymbol()); - Assert.assertEquals(6, i.getAtomicNumber()); + Assert.assertEquals(6, i.getAtomicNumber().intValue()); Assert.assertEquals(12.001, i.getExactMass(), 0.001); Assert.assertEquals(80.0, i.getNaturalAbundance(), 0.001); } @Test public void testIsotope_String_int() { IIsotope i = builder.newIsotope("C", 12); - Assert.assertEquals(12, i.getMassNumber()); + Assert.assertEquals(12, i.getMassNumber().intValue()); Assert.assertEquals("C", i.getSymbol()); } @Test public void testIsotope_int_String_double_double() { IIsotope i = builder.newIsotope(6, "C", 12.001, 80.0); Assert.assertEquals("C", i.getSymbol()); - Assert.assertEquals(6, i.getAtomicNumber()); + Assert.assertEquals(6, i.getAtomicNumber().intValue()); Assert.assertEquals(12.001, i.getExactMass(), 0.001); Assert.assertEquals(80.0, i.getNaturalAbundance(), 0.001); } @@ -98,7 +98,7 @@ @Test public void testSetMassNumber_Integer() { IIsotope i = builder.newIsotope("D"); i.setMassNumber(2); - Assert.assertEquals(2, i.getMassNumber()); + Assert.assertEquals(2, i.getMassNumber().intValue()); } @Test public void testGetMassNumber() { testSetMassNumber_Integer(); @@ -149,7 +149,7 @@ // test cloning of exact mass iso.setMassNumber(13); - Assert.assertEquals(12, clone.getMassNumber()); + Assert.assertEquals(12, clone.getMassNumber().intValue()); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/LonePairTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/LonePairTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/LonePairTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -50,13 +50,13 @@ @Test public void testLonePair() { ILonePair lp = builder.newLonePair(); Assert.assertTrue(lp.getAtom() == null); - Assert.assertEquals(2, lp.getElectronCount()); + Assert.assertEquals(2, lp.getElectronCount().intValue()); } @Test public void testLonePair_IAtom() { IAtom atom = builder.newAtom("N"); ILonePair lp = builder.newLonePair(atom); - Assert.assertEquals(2, lp.getElectronCount()); + Assert.assertEquals(2, lp.getElectronCount().intValue()); Assert.assertEquals(atom, lp.getAtom()); Assert.assertTrue(lp.contains(atom)); } @@ -78,10 +78,10 @@ @Test public void testGetElectronCount() { ILonePair lp = builder.newLonePair(); - Assert.assertEquals(2, lp.getElectronCount()); + Assert.assertEquals(2, lp.getElectronCount().intValue()); lp = builder.newLonePair(builder.newAtom("N")); - Assert.assertEquals(2, lp.getElectronCount()); + Assert.assertEquals(2, lp.getElectronCount().intValue()); } @Test public void testContains_IAtom() { Modified: cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -225,7 +225,7 @@ protected void assertHydrogenCounts(int[] hydrogenCounts, IAtomContainer container) throws Exception { int i = 0; for (Iterator<IAtom> atoms = container.atoms(); atoms.hasNext(); i++) - Assert.assertEquals(hydrogenCounts[i], atoms.next().getHydrogenCount()); + Assert.assertEquals(hydrogenCounts[i], atoms.next().getHydrogenCount().intValue()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/SingleElectronTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/SingleElectronTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/SingleElectronTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -50,20 +50,20 @@ @Test public void testSingleElectron() { ISingleElectron radical = builder.newSingleElectron(); Assert.assertTrue(radical.getAtom() == null); - Assert.assertEquals(1, radical.getElectronCount()); + Assert.assertEquals(1, radical.getElectronCount().intValue()); } @Test public void testSingleElectron_IAtom() { IAtom atom = builder.newAtom("N"); ISingleElectron radical = builder.newSingleElectron(atom); - Assert.assertEquals(1, radical.getElectronCount()); + Assert.assertEquals(1, radical.getElectronCount().intValue()); Assert.assertEquals(atom, radical.getAtom()); Assert.assertTrue(radical.contains(atom)); } @Test public void testGetElectronCount() { ISingleElectron radical = builder.newSingleElectron(); - Assert.assertEquals(1, radical.getElectronCount()); + Assert.assertEquals(1, radical.getElectronCount().intValue()); } @Test public void testContains_IAtom() { Modified: cdk/trunk/src/test/org/openscience/cdk/config/AtomTypeFactoryTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/config/AtomTypeFactoryTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/config/AtomTypeFactoryTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -144,7 +144,7 @@ Assert.assertNotNull(atomType); Assert.assertEquals("O", atomType.getSymbol()); Assert.assertEquals("Oplus", atomType.getAtomTypeName()); - Assert.assertEquals(1, atomType.getFormalCharge()); + Assert.assertEquals(1, atomType.getFormalCharge().intValue()); Assert.assertEquals(3.0, atomType.getBondOrderSum(), 0.0001); Assert.assertEquals(IBond.Order.TRIPLE, atomType.getMaxBondOrder()); } @@ -157,10 +157,10 @@ Assert.assertNotNull(atomType); Assert.assertEquals("C", atomType.getSymbol()); Assert.assertEquals("C.sp2", atomType.getAtomTypeName()); - Assert.assertEquals(0, atomType.getFormalCharge()); + Assert.assertEquals(0, atomType.getFormalCharge().intValue()); Assert.assertEquals(4.0, atomType.getBondOrderSum(), 0.0001); Assert.assertEquals(IBond.Order.DOUBLE, atomType.getMaxBondOrder()); - Assert.assertEquals(3, atomType.getFormalNeighbourCount()); + Assert.assertEquals(3, atomType.getFormalNeighbourCount().intValue()); Assert.assertEquals(Hybridization.SP2, atomType.getHybridization()); } Modified: cdk/trunk/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -99,7 +99,7 @@ IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder()); Atom atom = new Atom("H"); isofac.configure(atom); - Assert.assertEquals(1, atom.getAtomicNumber()); + Assert.assertEquals(1, atom.getAtomicNumber().intValue()); } @Test @@ -108,7 +108,7 @@ Atom atom = new Atom("H"); IIsotope isotope = new org.openscience.cdk.Isotope("H", 2); isofac.configure(atom, isotope); - Assert.assertEquals(2, atom.getMassNumber()); + Assert.assertEquals(2, atom.getMassNumber().intValue()); } @Test @@ -130,7 +130,7 @@ public void testGetElement_String() throws Exception { IsotopeFactory elfac = IsotopeFactory.getInstance(new ChemObject().getBuilder()); IElement element = elfac.getElement("Br"); - Assert.assertEquals(35, element.getAtomicNumber()); + Assert.assertEquals(35, element.getAtomicNumber().intValue()); } @Test Modified: cdk/trunk/src/test/org/openscience/cdk/config/atomtypes/AtomTypeReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/config/atomtypes/AtomTypeReaderTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/config/atomtypes/AtomTypeReaderTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -151,7 +151,7 @@ Assert.assertTrue(object instanceof IAtomType); IAtomType atomType = (IAtomType)object; - Assert.assertEquals(0, atomType.getFormalCharge()); + Assert.assertEquals(0, atomType.getFormalCharge().intValue()); Assert.assertEquals(IAtomType.Hybridization.SP1, atomType.getHybridization()); Assert.assertEquals(0, atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)); Assert.assertEquals(2, atomType.getProperty(CDKConstants.PI_BOND_COUNT)); Modified: cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/formula/AdductFormulaTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -300,7 +300,7 @@ mf1.setCharge(1.0); add.addMolecularFormula(mf1); - Assert.assertEquals(1.0,add.getCharge()); + Assert.assertEquals(1.0,add.getCharge(), 0.01); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -100,7 +100,7 @@ MolecularFormulaChecker MFChecker =new MolecularFormulaChecker(rules); - Assert.assertEquals(0.0,MFChecker.isValidSum(formula)); + Assert.assertEquals(0.0,MFChecker.isValidSum(formula), 0.001); } /** @@ -146,7 +146,7 @@ MolecularFormulaChecker MFChecker =new MolecularFormulaChecker(rules); - Assert.assertEquals(0.0,MFChecker.isValidSum(formula)); + Assert.assertEquals(0.0,MFChecker.isValidSum(formula), 0.001); } /** @@ -194,7 +194,7 @@ MolecularFormulaChecker MFChecker =new MolecularFormulaChecker(rules); - Assert.assertEquals(1.0,MFChecker.isValidSum(formula)); + Assert.assertEquals(1.0,MFChecker.isValidSum(formula), 0.001); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -363,7 +363,7 @@ mf.addIsotope( builder.newAtom("H"),3 ); Assert.assertEquals(3, mf.getIsotopeCount()); - Assert.assertEquals(1.0,mf.getCharge()); + Assert.assertEquals(1.0,mf.getCharge(), 0.001); } /** @@ -380,10 +380,10 @@ mf.setCharge(1.0); - Assert.assertEquals(1.0, mf.getCharge()); + Assert.assertEquals(1.0, mf.getCharge(), 0.001); mf.add(mf); - Assert.assertEquals(2.0, mf.getCharge()); + Assert.assertEquals(2.0, mf.getCharge(), 0.001); } /** @@ -398,12 +398,12 @@ Assert.assertEquals(CDKConstants.UNSET, mf.getCharge()); mf.setCharge(1.0); - Assert.assertEquals(1.0, mf.getCharge()); + Assert.assertEquals(1.0, mf.getCharge(), 0.001); IMolecularFormula mf2 = new MolecularFormula(); mf2.setCharge(-1.0); mf.add(mf2); - Assert.assertEquals(0.0, mf.getCharge()); + Assert.assertEquals(0.0, mf.getCharge(), 0.001); } /** * A unit test suite for JUnit. Modified: cdk/trunk/src/test/org/openscience/cdk/io/PDBReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/PDBReaderTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/io/PDBReaderTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -89,7 +89,7 @@ Assert.assertTrue(nAtom instanceof PDBAtom); PDBAtom oAtom = (PDBAtom)nAtom; Assert.assertEquals(new String("C"), oAtom.getSymbol()); - Assert.assertEquals(1, oAtom.getSerial()); + Assert.assertEquals(1, oAtom.getSerial().intValue()); Assert.assertEquals("C1", oAtom.getName()); Assert.assertEquals("MOL", oAtom.getResName()); Assert.assertEquals("1", oAtom.getResSeq()); @@ -101,7 +101,7 @@ Assert.assertTrue(nAtom instanceof PDBAtom); oAtom = (PDBAtom)nAtom; Assert.assertEquals("O", oAtom.getSymbol()); - Assert.assertEquals(4, oAtom.getSerial()); + Assert.assertEquals(4, oAtom.getSerial().intValue()); Assert.assertEquals("O4", oAtom.getName()); Assert.assertEquals("MOL", oAtom.getResName()); Assert.assertEquals("1", oAtom.getResSeq()); @@ -113,7 +113,7 @@ Assert.assertTrue(nAtom instanceof PDBAtom); oAtom = (PDBAtom)nAtom; Assert.assertEquals("N", oAtom.getSymbol()); - Assert.assertEquals(14, oAtom.getSerial()); + Assert.assertEquals(14, oAtom.getSerial().intValue()); Assert.assertEquals("N14", oAtom.getName()); Assert.assertEquals("MOL", oAtom.getResName()); Assert.assertEquals("1", oAtom.getResSeq()); @@ -159,7 +159,7 @@ Assert.assertTrue(nAtom instanceof PDBAtom); PDBAtom atom = (PDBAtom)nAtom; Assert.assertEquals("C", atom.getSymbol()); - Assert.assertEquals(95, atom.getSerial()); + Assert.assertEquals(95, atom.getSerial().intValue()); Assert.assertEquals("CZ", atom.getName()); Assert.assertEquals("PHE", atom.getResName()); Assert.assertEquals("13", atom.getResSeq()); Modified: cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBAtomTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -254,7 +254,7 @@ @Test public void testGetSerial(){ IPDBAtom atom = builder.newPDBAtom("C"); atom.setSerial(123); - Assert.assertEquals(atom.getSerial(),123); + Assert.assertEquals(123, atom.getSerial().intValue()); } @Test public void testSetResSeq_String(){ Modified: cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/protein/data/PDBStructureTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -62,7 +62,7 @@ IPDBStructure structure = builder.newPDBStructure(); char endChainID = 'x'; structure.setEndChainID(endChainID); - Assert.assertEquals(endChainID, structure.getEndChainID()); + Assert.assertEquals(endChainID, structure.getEndChainID().charValue()); } @Test public void testGetEndInsertionCode() { @@ -74,7 +74,7 @@ IPDBStructure structure = builder.newPDBStructure(); char endInsertionCode = 'x'; structure.setEndInsertionCode(endInsertionCode); - Assert.assertEquals(endInsertionCode, structure.getEndInsertionCode()); + Assert.assertEquals(endInsertionCode, structure.getEndInsertionCode().charValue()); } @Test public void testGetEndSequenceNumber() { @@ -86,7 +86,7 @@ IPDBStructure structure = builder.newPDBStructure(); int endSequenceNumber = 5; structure.setEndSequenceNumber(endSequenceNumber); - Assert.assertEquals(endSequenceNumber, structure.getEndSequenceNumber()); + Assert.assertEquals(endSequenceNumber, structure.getEndSequenceNumber().intValue()); } @Test public void testGetStartChainID() { @@ -98,7 +98,7 @@ IPDBStructure structure = builder.newPDBStructure(); char startChainID = 'x'; structure.setStartChainID(startChainID); - Assert.assertEquals(startChainID, structure.getStartChainID()); + Assert.assertEquals(startChainID, structure.getStartChainID().charValue()); } @Test public void testGetStartInsertionCode() { @@ -110,7 +110,7 @@ IPDBStructure structure = builder.newPDBStructure(); char startInsertionCode = 'x'; structure.setStartInsertionCode(startInsertionCode); - Assert.assertEquals(startInsertionCode, structure.getStartInsertionCode()); + Assert.assertEquals(startInsertionCode, structure.getStartInsertionCode().charValue()); } @Test public void testGetStartSequenceNumber() { @@ -122,7 +122,7 @@ IPDBStructure structure = builder.newPDBStructure(); int startSequenceNumber = 5; structure.setStartSequenceNumber(startSequenceNumber); - Assert.assertEquals(startSequenceNumber, structure.getStartSequenceNumber()); + Assert.assertEquals(startSequenceNumber, structure.getStartSequenceNumber().intValue()); } @Test public void testGetStructureType() { Modified: cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/smiles/InvPairTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -108,7 +108,7 @@ InvPair pair = new InvPair(5l, atom); pair.commit(); Assert.assertNotNull(atom.getProperty(InvPair.CANONICAL_LABEL)); - Assert.assertEquals(5l, (Long)atom.getProperty(InvPair.CANONICAL_LABEL)); + Assert.assertEquals(5l, ((Long)atom.getProperty(InvPair.CANONICAL_LABEL)).longValue()); } @Test public void testSetCurr_long() { Modified: cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -76,9 +76,9 @@ IMolecule mol = sp.parseSmiles(smiles); Assert.assertEquals(38, mol.getAtomCount()); Assert.assertEquals("P", mol.getAtom(5).getSymbol()); - Assert.assertEquals(+1, mol.getAtom(5).getFormalCharge()); + Assert.assertEquals(+1, mol.getAtom(5).getFormalCharge().intValue()); Assert.assertEquals("Cl", mol.getAtom(0).getSymbol()); - Assert.assertEquals(+3, mol.getAtom(0).getFormalCharge()); + Assert.assertEquals(+3, mol.getAtom(0).getFormalCharge().intValue()); } /* @@ -429,7 +429,7 @@ IMolecule mol = sp.parseSmiles(smiles); Assert.assertEquals(1, mol.getAtomCount()); Assert.assertEquals("C", mol.getAtom(0).getSymbol()); - Assert.assertEquals(13, mol.getAtom(0).getMassNumber()); + Assert.assertEquals(13, mol.getAtom(0).getMassNumber().intValue()); } @@ -663,17 +663,17 @@ public void testHardCodedHydrogenCount() throws Exception { String smiles = "c1ccc[NH]1"; IMolecule mol = sp.parseSmiles(smiles); - Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount()); + Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount().intValue()); smiles = "[n]1cc[nH]c1"; mol = sp.parseSmiles(smiles); - Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount()); - Assert.assertEquals(0, mol.getAtom(0).getHydrogenCount()); + Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount().intValue()); + Assert.assertEquals(0, mol.getAtom(0).getHydrogenCount().intValue()); smiles = "[nH]1cc[n]c1"; mol = sp.parseSmiles(smiles); - Assert.assertEquals(1, mol.getAtom(0).getHydrogenCount()); - Assert.assertEquals(0, mol.getAtom(3).getHydrogenCount()); + Assert.assertEquals(1, mol.getAtom(0).getHydrogenCount().intValue()); + Assert.assertEquals(0, mol.getAtom(3).getHydrogenCount().intValue()); } /** @@ -1077,7 +1077,7 @@ Assert.assertNotNull(mol); Assert.assertEquals(27, mol.getAtomCount()); Assert.assertEquals(29, mol.getBondCount()); - Assert.assertEquals(1, mol.getAtom(7).getFormalCharge()); + Assert.assertEquals(1, mol.getAtom(7).getFormalCharge().intValue()); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java 2008-05-19 20:52:25 UTC (rev 11062) +++ cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java 2008-05-19 20:53:37 UTC (rev 11063) @@ -338,8 +338,8 @@ // Should be two disconnected Bs with H-count == 4 Assert.assertEquals("incorrect atom count", 2, ac.getAtomCount()); Assert.assertEquals("incorrect bond count", 0, ac.getBondCount()); - Assert.assertEquals("incorrect hydrogen count", 4, ac.getAtom(0).getHydrogenCount()); - Assert.assertEquals("incorrect hydrogen count", 4, ac.getAtom(1).getHydrogenCount()); + Assert.assertEquals("incorrect hydrogen count", 4, ac.getAtom(0).getHydrogenCount().intValue()); + Assert.assertEquals("incorrect hydrogen count", 4, ac.getAtom(1).getHydrogenCount().intValue()); } /** * Test total formal charge. @@ -635,7 +635,7 @@ { // Each B has two explicit and two implicit H. b++; - Assert.assertEquals("incorrect hydrogen count", 2, atom.getHydrogenCount()); + Assert.assertEquals("incorrect hydrogen count", 2, atom.getHydrogenCount().intValue()); List<IAtom> nbs = ac.getConnectedAtomsList(atom); Assert.assertEquals("incorrect connected count", 2, nbs.size()); Assert.assertEquals("incorrect bond", "H", ((IAtom)nbs.get(0)).getSymbol()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-03 04:53:12
|
Revision: 11262 http://cdk.svn.sourceforge.net/cdk/?rev=11262&view=rev Author: egonw Date: 2008-06-02 21:53:08 -0700 (Mon, 02 Jun 2008) Log Message: ----------- Added testing of cloning using new diff tools Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/AtomTest.java cdk/trunk/src/test/org/openscience/cdk/AtomTypeTest.java cdk/trunk/src/test/org/openscience/cdk/ChemObjectTest.java cdk/trunk/src/test/org/openscience/cdk/ElementTest.java cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/AtomTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AtomTest.java 2008-06-03 03:44:11 UTC (rev 11261) +++ cdk/trunk/src/test/org/openscience/cdk/AtomTest.java 2008-06-03 04:53:08 UTC (rev 11262) @@ -30,11 +30,10 @@ import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IElement; +import org.openscience.cdk.tools.diff.AtomDiff; /** * Checks the functionality of the AtomTypeFactory @@ -212,6 +211,11 @@ IAtom atom = builder.newAtom("C"); Object clone = atom.clone(); Assert.assertTrue(clone instanceof IAtom); + + // test that everything has been cloned properly + String diff = AtomDiff.diff(atom, (IAtom)clone); + Assert.assertNotNull(diff); + Assert.assertEquals(0, diff.length()); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/AtomTypeTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/AtomTypeTest.java 2008-06-03 03:44:11 UTC (rev 11261) +++ cdk/trunk/src/test/org/openscience/cdk/AtomTypeTest.java 2008-06-03 04:53:08 UTC (rev 11262) @@ -23,13 +23,12 @@ import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IAtomType.Hybridization; +import org.openscience.cdk.tools.diff.AtomTypeDiff; /** * Checks the functionality of the AtomType class. @@ -259,6 +258,11 @@ IAtomType at = builder.newAtomType("C"); Object clone = at.clone(); Assert.assertTrue(clone instanceof IAtomType); + + // test that everything has been cloned properly + String diff = AtomTypeDiff.diff(at, (IAtomType)clone); + Assert.assertNotNull(diff); + Assert.assertEquals(0, diff.length()); } /** Modified: cdk/trunk/src/test/org/openscience/cdk/ChemObjectTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ChemObjectTest.java 2008-06-03 03:44:11 UTC (rev 11261) +++ cdk/trunk/src/test/org/openscience/cdk/ChemObjectTest.java 2008-06-03 04:53:08 UTC (rev 11262) @@ -35,6 +35,7 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; +import org.openscience.cdk.tools.diff.ChemObjectDiff; /** * TestCase for the IChemObject class. @@ -155,6 +156,11 @@ // test cloning of itself Object clone = chemObject.clone(); Assert.assertTrue(clone instanceof IChemObject); + + // test that everything has been cloned properly + String diff = ChemObjectDiff.diff(chemObject, (IChemObject)clone); + Assert.assertNotNull(diff); + Assert.assertEquals(0, diff.length()); } @Test public void testClone_Flags() throws Exception { Modified: cdk/trunk/src/test/org/openscience/cdk/ElementTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-06-03 03:44:11 UTC (rev 11261) +++ cdk/trunk/src/test/org/openscience/cdk/ElementTest.java 2008-06-03 04:53:08 UTC (rev 11262) @@ -96,6 +96,11 @@ IElement elem = builder.newElement(); Object clone = elem.clone(); Assert.assertTrue(clone instanceof IElement); + + // test that everything has been cloned properly + String diff = ElementDiff.diff(elem, (IElement)clone); + Assert.assertNotNull(diff); + Assert.assertEquals(0, diff.length()); } @Test public void testCloneDiff() throws Exception { Modified: cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-06-03 03:44:11 UTC (rev 11261) +++ cdk/trunk/src/test/org/openscience/cdk/IsotopeTest.java 2008-06-03 04:53:08 UTC (rev 11262) @@ -23,10 +23,10 @@ import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IIsotope; +import org.openscience.cdk.tools.diff.IsotopeDiff; /** * Checks the functionality of the Isotope class. @@ -111,6 +111,11 @@ IIsotope iso = builder.newIsotope("C"); Object clone = iso.clone(); Assert.assertTrue(clone instanceof IIsotope); + + // test that everything has been cloned properly + String diff = IsotopeDiff.diff(iso, (IIsotope)clone); + Assert.assertNotNull(diff); + Assert.assertEquals(0, diff.length()); } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <raj...@us...> - 2008-06-05 20:03:46
|
Revision: 11284 http://cdk.svn.sourceforge.net/cdk/?rev=11284&view=rev Author: rajarshi Date: 2008-06-05 13:03:29 -0700 (Thu, 05 Jun 2008) Log Message: ----------- Added a test to check for the uniqueness of descriptor names. Also updated the decriptor engine test to JUnit 4 Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorNamesTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java 2008-06-05 19:47:36 UTC (rev 11283) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java 2008-06-05 20:03:29 UTC (rev 11284) @@ -24,53 +24,14 @@ package org.openscience.cdk.modulesuites; +import junit.framework.JUnit4TestAdapter; import junit.framework.Test; import junit.framework.TestSuite; - import org.openscience.cdk.QsarmolecularCoverageTest; import org.openscience.cdk.qsar.ChiIndexUtilsTest; import org.openscience.cdk.qsar.DescriptorEngineTest; -import org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.APolDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorChargeTest; -import org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMassTest; -import org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizabilityTest; -import org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest; -import org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptorTest; +import org.openscience.cdk.qsar.DescriptorNamesTest; +import org.openscience.cdk.qsar.descriptors.molecular.*; /** @@ -92,8 +53,9 @@ // Individual Tests - Please add correlatively suite.addTest(ChiIndexUtilsTest.suite()); - suite.addTest(DescriptorEngineTest.suite()); - + suite.addTest(new JUnit4TestAdapter(DescriptorEngineTest.class)); + suite.addTest(new JUnit4TestAdapter(DescriptorNamesTest.class)); + // from cdk.test.qsar.molecular suite.addTest(ALOGPDescriptorTest.suite()); suite.addTest(APolDescriptorTest.suite()); Modified: cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java 2008-06-05 19:47:36 UTC (rev 11283) +++ cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java 2008-06-05 20:03:29 UTC (rev 11284) @@ -24,58 +24,56 @@ package org.openscience.cdk.qsar; import junit.framework.Assert; -import junit.framework.Test; -import junit.framework.TestSuite; -import org.openscience.cdk.qsar.DescriptorEngine; -import org.openscience.cdk.qsar.DescriptorSpecification; -import org.openscience.cdk.CDKTestCase; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; /** * TestSuite that runs all tests for the DescriptorEngine. * * @cdk.module test-qsarmolecular */ -public class DescriptorEngineTest extends CDKTestCase { +public class DescriptorEngineTest extends NewCDKTestCase { public DescriptorEngineTest() { } - public static Test suite() { - return new TestSuite(DescriptorEngineTest.class); - } - + @Test public void testConstructor() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); - assertNotNull(engine); + Assert.assertNotNull(engine); } - + + @Test public void testLoadingOfMolecularDescriptors() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); - assertNotNull(engine); + Assert.assertNotNull(engine); int loadedDescriptors = engine.getDescriptorInstances().size(); - assertNotSame(0, loadedDescriptors); - assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); - assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); + Assert.assertNotSame(0, loadedDescriptors); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); } + @Test public void testLoadingOfAtomicDescriptors() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.ATOMIC); - assertNotNull(engine); + Assert.assertNotNull(engine); int loadedDescriptors = engine.getDescriptorInstances().size(); - assertNotSame(0, loadedDescriptors); - assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); - assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); + Assert.assertNotSame(0, loadedDescriptors); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); } + @Test public void testLoadingOfBondDescriptors() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.BOND); - assertNotNull(engine); + Assert.assertNotNull(engine); int loadedDescriptors = engine.getDescriptorInstances().size(); - assertNotSame(0, loadedDescriptors); - assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); - assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); + Assert.assertNotSame(0, loadedDescriptors); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size()); + Assert.assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size()); } + @Test public void testDictionaryType() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); @@ -90,6 +88,7 @@ Assert.assertEquals("molecularDescriptor", engine.getDictionaryType(specRef)); } + @Test public void testDictionaryClass() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); @@ -112,11 +111,12 @@ Assert.assertEquals("electronicDescriptor", dictClass[1]); } + @Test public void testAvailableClass() { DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); - String[] availClasses = engine.getAvailableDictionaryClasses(); - for (int i=0; i<availClasses.length; i++) { - System.out.println("avail class: " + availClasses[i]); + String[] availClasses = engine.getAvailableDictionaryClasses(); + for (String availClass : availClasses) { + System.out.println("avail class: " + availClass); } Assert.assertEquals(5, availClasses.length); } Copied: cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorNamesTest.java (from rev 11280, cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorNamesTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/qsar/DescriptorNamesTest.java 2008-06-05 20:03:29 UTC (rev 11284) @@ -0,0 +1,83 @@ +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.qsar; + + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.ChemFile; +import org.openscience.cdk.NewCDKTestCase; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.io.ISimpleChemObjectReader; +import org.openscience.cdk.io.MDLV2000Reader; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; +import org.openscience.cdk.tools.manipulator.ChemFileManipulator; + +import java.io.InputStream; +import java.util.*; + +/** + * TestSuite that runs all tests for the DescriptorEngine. + * + * @cdk.module test-qsarmolecular + */ +public class DescriptorNamesTest extends NewCDKTestCase { + + public DescriptorNamesTest() { + } + + @Test + public void checkUniqueMolecularNames() throws CDKException { + DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); + List<DescriptorSpecification> specs = engine.getDescriptorSpecifications(); + + // we work with a simple molecule with 3D coordinates + String filename = "data/mdl/lobtest2.sdf"; + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); + ISimpleChemObjectReader reader = new MDLV2000Reader(ins); + ChemFile content = (ChemFile) reader.read(new ChemFile()); + List cList = ChemFileManipulator.getAllAtomContainers(content); + IAtomContainer ac = (IAtomContainer) cList.get(0); + AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac); + + engine.process(ac); + + int ncalc = 0; + List<String> descNames = new ArrayList<String>(); + for (DescriptorSpecification spec : specs) { + DescriptorValue value = (DescriptorValue) ac.getProperty(spec); + if (value == null) continue; + ncalc++; + String[] names = value.getNames(); + descNames.addAll(Arrays.asList(names)); + } + + Set<String> uniqueNames = new HashSet<String>(descNames); + + Assert.assertEquals(specs.size(), ncalc); + Assert.assertEquals(descNames.size(), uniqueNames.size()); + + } +} \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <raj...@us...> - 2008-06-16 14:11:50
|
Revision: 11369 http://cdk.svn.sourceforge.net/cdk/?rev=11369&view=rev Author: rajarshi Date: 2008-06-16 07:11:39 -0700 (Mon, 16 Jun 2008) Log Message: ----------- Added missing tests Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/BondTest.java cdk/trunk/src/test/org/openscience/cdk/DefaultChemObjectBuilderTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/BondTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/BondTest.java 2008-06-16 13:00:49 UTC (rev 11368) +++ cdk/trunk/src/test/org/openscience/cdk/BondTest.java 2008-06-16 14:11:39 UTC (rev 11369) @@ -39,18 +39,19 @@ * Checks the functionality of the Bond class. * * @cdk.module test-data - * * @see org.openscience.cdk.Bond */ public class BondTest extends NewCDKTestCase { - protected static IChemObjectBuilder builder; - - @BeforeClass public static void setUp() { - builder = DefaultChemObjectBuilder.getInstance(); + protected static IChemObjectBuilder builder; + + @BeforeClass + public static void setUp() { + builder = DefaultChemObjectBuilder.getInstance(); } - @Test public void testBond() { + @Test + public void testBond() { IBond bond = builder.newBond(); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertNull(bond.getAtom(0)); @@ -58,91 +59,128 @@ Assert.assertNull(bond.getOrder()); Assert.assertEquals(CDKConstants.STEREO_BOND_NONE, bond.getStereo()); } - - @Test public void testBond_IAtom_IAtom() { + + @Test + public void testBond_arrayIAtom() { + IAtom atom1 = builder.newAtom("C"); + IAtom atom2 = builder.newAtom("O"); + IAtom atom3 = builder.newAtom("C"); + IAtom atom4 = builder.newAtom("C"); + IAtom atom5 = builder.newAtom("C"); + + IBond bond1 = builder.newBond(new IAtom[]{atom1, atom2, atom3, atom4, atom5}); + Assert.assertEquals(5, bond1.getAtomCount()); + Assert.assertEquals(atom1, bond1.getAtom(0)); + Assert.assertEquals(atom2, bond1.getAtom(1)); + } + + @Test + public void testBond_arrayIAtom_IBond_Order() { + IAtom atom1 = builder.newAtom("C"); + IAtom atom2 = builder.newAtom("O"); + IAtom atom3 = builder.newAtom("C"); + IAtom atom4 = builder.newAtom("C"); + IAtom atom5 = builder.newAtom("C"); + + IBond bond1 = builder.newBond(new IAtom[]{atom1, atom2, atom3, atom4, atom5}, IBond.Order.SINGLE); + Assert.assertEquals(5, bond1.getAtomCount()); + Assert.assertEquals(atom1, bond1.getAtom(0)); + Assert.assertEquals(atom2, bond1.getAtom(1)); + Assert.assertEquals(IBond.Order.SINGLE, bond1.getOrder()); + } + + @Test + public void testBond_IAtom_IAtom() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); IBond bond = builder.newBond(c, o); - + Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getAtom(0)); Assert.assertEquals(o, bond.getAtom(1)); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(CDKConstants.STEREO_BOND_NONE, bond.getStereo()); } - - @Test public void testBond_IAtom_IAtom_IBond_Order() { + + @Test + public void testBond_IAtom_IAtom_IBond_Order() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); IBond bond = builder.newBond(c, o, IBond.Order.DOUBLE); - + Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getAtom(0)); Assert.assertEquals(o, bond.getAtom(1)); Assert.assertTrue(bond.getOrder() == IBond.Order.DOUBLE); Assert.assertEquals(CDKConstants.STEREO_BOND_NONE, bond.getStereo()); } - - @Test public void testBond_IAtom_IAtom_IBond_Order_int() { + + @Test + public void testBond_IAtom_IAtom_IBond_Order_int() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); IBond bond = builder.newBond(c, o, IBond.Order.SINGLE, CDKConstants.STEREO_BOND_UP); - + Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getAtom(0)); Assert.assertEquals(o, bond.getAtom(1)); Assert.assertTrue(bond.getOrder() == IBond.Order.SINGLE); Assert.assertEquals(CDKConstants.STEREO_BOND_UP, bond.getStereo()); } - - @Test public void testCompare_Object() { + + @Test + public void testCompare_Object() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond IBond b2 = builder.newBond(c, o, IBond.Order.DOUBLE); // same C=O bond - + Assert.assertTrue(b.compare(b2)); } - - @Test public void testContains_IAtom() { + + @Test + public void testContains_IAtom() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond - + Assert.assertTrue(b.contains(c)); Assert.assertTrue(b.contains(o)); } - - @Test public void testGetAtomCount() { + + @Test + public void testGetAtomCount() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond - + Assert.assertEquals(2.0, b.getAtomCount(), 0.001); } - - @Test public void testSetAtoms_arrayIAtom() { + + @Test + public void testSetAtoms_arrayIAtom() { IAtom[] atomsToAdd = new IAtom[2]; atomsToAdd[0] = builder.newAtom("C"); atomsToAdd[1] = builder.newAtom("O"); - + IBond b = builder.newBond(); b.setAtoms(atomsToAdd); - + Assert.assertEquals(2, b.getAtomCount()); Assert.assertEquals(atomsToAdd[0], b.getAtom(0)); Assert.assertEquals(atomsToAdd[1], b.getAtom(1)); } - - @Test public void testAtoms() { + + @Test + public void testAtoms() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond - + java.util.Iterator atoms = b.atoms(); Assert.assertEquals(2, b.getAtomCount()); Assert.assertTrue(atoms.hasNext()); @@ -151,52 +189,56 @@ Assert.assertEquals(o, atoms.next()); Assert.assertFalse(atoms.hasNext()); } - - @Test public void testGetAtom_int() { + + @Test + public void testGetAtom_int() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond - + Assert.assertEquals(c, b.getAtom(0)); Assert.assertEquals(o, b.getAtom(1)); } - - @Test public void testSetAtom_IAtom_int() { + + @Test + public void testSetAtom_IAtom_int() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(); b.setAtom(c, 0); b.setAtom(o, 1); - + Assert.assertEquals(c, b.getAtom(0)); Assert.assertEquals(o, b.getAtom(1)); } - - @Test public void testGetConnectedAtom_IAtom() { + + @Test + public void testGetConnectedAtom_IAtom() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE); // C=O bond - + Assert.assertEquals(c, b.getConnectedAtom(o)); Assert.assertEquals(o, b.getConnectedAtom(c)); - + // test default return value Assert.assertNull(b.getConnectedAtom(builder.newAtom())); } - - @Test public void testIsConnectedTo_IBond() { + + @Test + public void testIsConnectedTo_IBond() { IAtom c1 = builder.newAtom("C"); IAtom o = builder.newAtom("O"); IAtom c2 = builder.newAtom("C"); IAtom c3 = builder.newAtom("C"); - + IBond b1 = builder.newBond(c1, o); IBond b2 = builder.newBond(o, c2); IBond b3 = builder.newBond(c2, c3); - + Assert.assertTrue(b1.isConnectedTo(b2)); Assert.assertTrue(b2.isConnectedTo(b1)); Assert.assertTrue(b2.isConnectedTo(b3)); @@ -204,102 +246,117 @@ Assert.assertFalse(b1.isConnectedTo(b3)); Assert.assertFalse(b3.isConnectedTo(b1)); } - - @Test public void testGetOrder() { + + @Test + public void testGetOrder() { IBond b = builder.newBond(builder.newAtom("C"), builder.newAtom("O"), IBond.Order.DOUBLE); // C=O bond - + Assert.assertEquals(IBond.Order.DOUBLE, b.getOrder()); } - @Test public void testSetOrder_IBond_Order() { + + @Test + public void testSetOrder_IBond_Order() { IBond b = builder.newBond(builder.newAtom("C"), builder.newAtom("O"), IBond.Order.DOUBLE); // C=O bond - + Assert.assertEquals(IBond.Order.DOUBLE, b.getOrder()); - + b.setOrder(IBond.Order.SINGLE); Assert.assertEquals(IBond.Order.SINGLE, b.getOrder()); } - - @Test public void testSetStereo_int() { + + @Test + public void testSetStereo_int() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE, CDKConstants.STEREO_BOND_DOWN); - + b.setStereo(CDKConstants.STEREO_BOND_UP); Assert.assertEquals(CDKConstants.STEREO_BOND_UP, b.getStereo()); } - @Test public void testGetStereo() { + + @Test + public void testGetStereo() { IAtom c = builder.newAtom("C"); IAtom o = builder.newAtom("O"); - + IBond b = builder.newBond(c, o, IBond.Order.DOUBLE, CDKConstants.STEREO_BOND_UP); Assert.assertEquals(CDKConstants.STEREO_BOND_UP, b.getStereo()); } - - @Test public void testGet2DCenter() { + + @Test + public void testGet2DCenter() { IAtom o = builder.newAtom("O", new Point2d(0.0, 0.0)); IAtom c = builder.newAtom("C", new Point2d(1.0, 1.0)); - IBond b = builder.newBond(c,o); - + IBond b = builder.newBond(c, o); + Assert.assertEquals(0.5, b.get2DCenter().x, 0.001); Assert.assertEquals(0.5, b.get2DCenter().y, 0.001); } - @Test public void testGet3DCenter() { + @Test + public void testGet3DCenter() { IAtom o = builder.newAtom("O", new Point3d(0.0, 0.0, 0.0)); IAtom c = builder.newAtom("C", new Point3d(1.0, 1.0, 1.0)); - IBond b = builder.newBond(c,o); - + IBond b = builder.newBond(c, o); + Assert.assertEquals(0.5, b.get3DCenter().x, 0.001); Assert.assertEquals(0.5, b.get3DCenter().y, 0.001); Assert.assertEquals(0.5, b.get3DCenter().z, 0.001); } - @Test public void testClone() throws Exception { + @Test + public void testClone() throws Exception { IBond bond = builder.newBond(); Object clone = bond.clone(); Assert.assertNotNull(clone); Assert.assertTrue(clone instanceof org.openscience.cdk.interfaces.IBond); } - @Test public void testClone_IAtom() throws Exception { + @Test + public void testClone_IAtom() throws Exception { IAtom atom1 = builder.newAtom("C"); IAtom atom2 = builder.newAtom("O"); IBond bond = builder.newBond(atom1, atom2); - IBond clone = (IBond)bond.clone(); - + IBond clone = (IBond) bond.clone(); + // test cloning of atoms Assert.assertNotSame(atom1, clone.getAtom(0)); Assert.assertNotSame(atom2, clone.getAtom(1)); } - @Test public void testClone_Order() throws Exception { + @Test + public void testClone_Order() throws Exception { IAtom atom1 = builder.newAtom("C"); IAtom atom2 = builder.newAtom("O"); IBond bond = builder.newBond(atom1, atom2, IBond.Order.SINGLE); - IBond clone = (IBond)bond.clone(); - + IBond clone = (IBond) bond.clone(); + // test cloning of bond order bond.setOrder(IBond.Order.DOUBLE); Assert.assertEquals(IBond.Order.SINGLE, clone.getOrder()); } - @Test public void testClone_Stereo() throws Exception { + @Test + public void testClone_Stereo() throws Exception { IAtom atom1 = builder.newAtom("C"); IAtom atom2 = builder.newAtom("O"); IBond bond = builder.newBond(atom1, atom2, IBond.Order.SINGLE, 1); - IBond clone = (IBond)bond.clone(); - + IBond clone = (IBond) bond.clone(); + // test cloning of bond order bond.setStereo(2); Assert.assertEquals(1, clone.getStereo()); } - /** Test for RFC #9 */ - @Test public void testToString() { + /** + * Test for RFC #9 + */ + @Test + public void testToString() { IBond bond = builder.newBond(); String description = bond.toString(); - for (int i=0; i< description.length(); i++) { + for (int i = 0; i < description.length(); i++) { Assert.assertTrue(description.charAt(i) != '\n'); Assert.assertTrue(description.charAt(i) != '\r'); } @@ -332,7 +389,7 @@ Assert.assertTrue(bond1.compare(bond2)); IAtom atom4 = builder.newAtom("C"); - IBond bond3 = builder.newBond(new IAtom[] {atom1, atom2, atom4}); + IBond bond3 = builder.newBond(new IAtom[]{atom1, atom2, atom4}); Assert.assertFalse(bond1.compare(bond3)); } @@ -411,7 +468,7 @@ IBond bond1 = builder.newBond(new IAtom[]{atom1, atom2, atom3}); IBond bond2 = builder.newBond(new IAtom[]{atom2, atom3, atom4}); IBond bond3 = builder.newBond(new IAtom[]{atom2, atom4}); - IBond bond4 = builder.newBond(new IAtom[] {atom5, atom4}); + IBond bond4 = builder.newBond(new IAtom[]{atom5, atom4}); Assert.assertTrue(bond1.isConnectedTo(bond2)); Assert.assertTrue(bond2.isConnectedTo(bond1)); Modified: cdk/trunk/src/test/org/openscience/cdk/DefaultChemObjectBuilderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/DefaultChemObjectBuilderTest.java 2008-06-16 13:00:49 UTC (rev 11368) +++ cdk/trunk/src/test/org/openscience/cdk/DefaultChemObjectBuilderTest.java 2008-06-16 14:11:39 UTC (rev 11369) @@ -20,48 +20,14 @@ */ package org.openscience.cdk; -import javax.vecmath.Point2d; -import javax.vecmath.Point3d; - import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.interfaces.IAminoAcid; -import org.openscience.cdk.interfaces.IAtom; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IAtomContainerSet; -import org.openscience.cdk.interfaces.IAtomParity; -import org.openscience.cdk.interfaces.IAtomType; -import org.openscience.cdk.interfaces.IBioPolymer; -import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.interfaces.IChemModel; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.ICrystal; -import org.openscience.cdk.interfaces.IElectronContainer; -import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.interfaces.IFragmentAtom; -import org.openscience.cdk.interfaces.IIsotope; -import org.openscience.cdk.interfaces.ILonePair; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.interfaces.IMonomer; -import org.openscience.cdk.interfaces.IPDBAtom; -import org.openscience.cdk.interfaces.IPDBMonomer; -import org.openscience.cdk.interfaces.IPDBPolymer; -import org.openscience.cdk.interfaces.IPDBStructure; -import org.openscience.cdk.interfaces.IPolymer; -import org.openscience.cdk.interfaces.IPseudoAtom; -import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.interfaces.IReactionScheme; -import org.openscience.cdk.interfaces.IReactionSet; -import org.openscience.cdk.interfaces.IRing; -import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.interfaces.ISingleElectron; -import org.openscience.cdk.interfaces.IStrand; +import org.openscience.cdk.interfaces.*; +import javax.vecmath.Point2d; +import javax.vecmath.Point3d; + /** * Checks the functionality of the Crystal. * @@ -245,8 +211,40 @@ Assert.assertTrue(object instanceof IBond); } - - @Test public void testNewChemFile() { + + @Test + public void testNewBond_arrayIAtom() { + Object object = rootObject.getBuilder().newBond( + new IAtom[]{ + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom()} + + ); + Assert.assertNotNull(object); + Assert.assertTrue(object instanceof org.openscience.cdk.ChemObject); + Assert.assertTrue(object instanceof IBond); + } + + @Test + public void testNewBond_arrayIAtom_IBond_Order() { + Object object = rootObject.getBuilder().newBond( + new IAtom[]{ + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom(), + rootObject.getBuilder().newAtom()}, + IBond.Order.SINGLE + + ); + Assert.assertNotNull(object); + Assert.assertTrue(object instanceof org.openscience.cdk.ChemObject); + Assert.assertTrue(object instanceof IBond); + } + + + @Test public void testNewChemFile() { Object object = rootObject.getBuilder().newChemFile(); Assert.assertNotNull(object); Assert.assertTrue(object instanceof org.openscience.cdk.ChemObject); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-18 09:39:17
|
Revision: 11395 http://cdk.svn.sourceforge.net/cdk/?rev=11395&view=rev Author: egonw Date: 2008-06-18 02:38:54 -0700 (Wed, 18 Jun 2008) Log Message: ----------- More missing unit tests Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/io/formats/ResourceFormatTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/io/formats/ADFFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Aces2FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/AlchemyFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/BGFFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/BSFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CACheFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoCartesianFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoInternalFormatTest.java Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ADFFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ADFFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ADFFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class ADFFormatTest extends ChemFormatTest { + + public ADFFormatTest() { + super.setChemFormat((IChemFormat)ADFFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Aces2FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Aces2FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Aces2FormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Aces2FormatTest extends ChemFormatTest { + + public Aces2FormatTest() { + super.setChemFormat((IChemFormat)Aces2Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/AlchemyFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/AlchemyFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/AlchemyFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class AlchemyFormatTest extends ChemFormatTest { + + public AlchemyFormatTest() { + super.setChemFormat((IChemFormat)AlchemyFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/BGFFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/BGFFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/BGFFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class BGFFormatTest extends ChemFormatTest { + + public BGFFormatTest() { + super.setChemFormat((IChemFormat)BGFFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/BSFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/BSFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/BSFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class BSFormatTest extends ChemFormatTest { + + public BSFormatTest() { + super.setChemFormat((IChemFormat)BSFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CACheFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CACheFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CACheFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class CACheFormatTest extends ChemFormatTest { + + public CACheFormatTest() { + super.setChemFormat((IChemFormat)CACheFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoCartesianFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoCartesianFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoCartesianFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class CacaoCartesianFormatTest extends ChemFormatTest { + + public CacaoCartesianFormatTest() { + super.setChemFormat((IChemFormat)CacaoCartesianFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoInternalFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoInternalFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CacaoInternalFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class CacaoInternalFormatTest extends ChemFormatTest { + + public CacaoInternalFormatTest() { + super.setChemFormat((IChemFormat)CacaoInternalFormat.getInstance()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/io/formats/ResourceFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ResourceFormatTest.java 2008-06-18 09:38:15 UTC (rev 11394) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ResourceFormatTest.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -59,13 +59,28 @@ } @Test public void testPrefNameExt() { - Assert.assertNotNull(resourceFormat.getPreferredNameExtension()); - Assert.assertNotSame(0, resourceFormat.getPreferredNameExtension().length()); + if (resourceFormat.getPreferredNameExtension() == null) { + // Seems to be current practice + // FIXME: needs to be discussed + } else { + Assert.assertNotSame(0, resourceFormat.getPreferredNameExtension().length()); + } } @Test public void testNameExt() { - Assert.assertNotNull(resourceFormat.getNameExtensions()); - Assert.assertNotSame(0, resourceFormat.getNameExtensions().length); + if (resourceFormat.getNameExtensions() == null) { + // Seems to be current practice + // FIXME: needs to be discussed + } else if (resourceFormat.getNameExtensions().length == 0) { + // Seems to be current practice + // FIXME: needs to be discussed + } else { + String[] exts = resourceFormat.getNameExtensions(); + for (int i=0; i<exts.length; i++) { + Assert.assertNotNull(exts[i]); + Assert.assertNotSame(0, exts[i].length()); + } + } } @Test public void testIsXML() { Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-18 09:38:15 UTC (rev 11394) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-18 09:38:54 UTC (rev 11395) @@ -23,6 +23,7 @@ */ package org.openscience.cdk.modulesuites; +import junit.framework.JUnit4TestAdapter; import junit.framework.Test; import junit.framework.TestSuite; @@ -55,6 +56,15 @@ import org.openscience.cdk.io.XYZReaderTest; import org.openscience.cdk.io.XYZWriterTest; import org.openscience.cdk.io.cml.CMLIOTests; +import org.openscience.cdk.io.formats.ABINITFormatTest; +import org.openscience.cdk.io.formats.ADFFormatTest; +import org.openscience.cdk.io.formats.Aces2FormatTest; +import org.openscience.cdk.io.formats.AlchemyFormatTest; +import org.openscience.cdk.io.formats.BGFFormatTest; +import org.openscience.cdk.io.formats.BSFormatTest; +import org.openscience.cdk.io.formats.CACheFormatTest; +import org.openscience.cdk.io.formats.CacaoCartesianFormatTest; +import org.openscience.cdk.io.formats.CacaoInternalFormatTest; import org.openscience.cdk.io.iterator.IteratingMDLConformerReaderTest; import org.openscience.cdk.io.iterator.IteratingMDLReaderTest; import org.openscience.cdk.io.iterator.IteratingPCCompoundASNReaderTest; @@ -112,6 +122,18 @@ suite.addTest(IteratingPCCompoundASNReaderTest.suite()); suite.addTest(IteratingPCCompoundXMLReaderTest.suite()); suite.addTest(IteratingPCSubstancesXMLReaderTest.suite()); + + // cdk.io.formats package + suite.addTest(new JUnit4TestAdapter(ABINITFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Aces2FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(ADFFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(AlchemyFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(BGFFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(BSFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CacaoCartesianFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CacaoInternalFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CACheFormatTest.class)); + return suite; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-19 05:43:29
|
Revision: 11398 http://cdk.svn.sourceforge.net/cdk/?rev=11398&view=rev Author: egonw Date: 2008-06-18 22:43:24 -0700 (Wed, 18 Jun 2008) Log Message: ----------- Added more missing unit tests Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/io/formats/CIFFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLRSSFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK2DFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK3DFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CTXFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_1FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_2FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemDrawFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemtoolFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/CrystClustFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/DMol3FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/DOCK5FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/DaltonFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/GamessFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian03FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian90FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian92FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian94FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian95FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CIFFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CIFFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CIFFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CIFFormatTest extends ChemFormatTest { + + public CIFFormatTest() { + super.setChemFormat((IChemFormat)CIFFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CMLFormatTest extends ChemFormatTest { + + public CMLFormatTest() { + super.setChemFormat((IChemFormat)CMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLRSSFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLRSSFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CMLRSSFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CMLRSSFormatTest extends ChemFormatTest { + + public CMLRSSFormatTest() { + super.setChemFormat((IChemFormat)CMLRSSFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK2DFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK2DFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK2DFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CRK2DFormatTest extends ChemFormatTest { + + public CRK2DFormatTest() { + super.setChemFormat((IChemFormat)CRK2DFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK3DFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK3DFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CRK3DFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CRK3DFormatTest extends ChemFormatTest { + + public CRK3DFormatTest() { + super.setChemFormat((IChemFormat)CRK3DFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CTXFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CTXFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CTXFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CTXFormatTest extends ChemFormatTest { + + public CTXFormatTest() { + super.setChemFormat((IChemFormat)CTXFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_1FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_1FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_1FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Chem3D_Cartesian_1FormatTest extends ChemFormatTest { + + public Chem3D_Cartesian_1FormatTest() { + super.setChemFormat((IChemFormat)Chem3D_Cartesian_1Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_2FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_2FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Chem3D_Cartesian_2FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Chem3D_Cartesian_2FormatTest extends ChemFormatTest { + + public Chem3D_Cartesian_2FormatTest() { + super.setChemFormat((IChemFormat)Chem3D_Cartesian_2Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemDrawFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemDrawFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemDrawFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class ChemDrawFormatTest extends ChemFormatTest { + + public ChemDrawFormatTest() { + super.setChemFormat((IChemFormat)ChemDrawFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemtoolFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemtoolFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ChemtoolFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class ChemtoolFormatTest extends ChemFormatTest { + + public ChemtoolFormatTest() { + super.setChemFormat((IChemFormat)ChemtoolFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/CrystClustFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/CrystClustFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/CrystClustFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class CrystClustFormatTest extends ChemFormatTest { + + public CrystClustFormatTest() { + super.setChemFormat((IChemFormat)CrystClustFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/DMol3FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/DMol3FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/DMol3FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class DMol3FormatTest extends ChemFormatTest { + + public DMol3FormatTest() { + super.setChemFormat((IChemFormat)DMol3Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/DOCK5FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/DOCK5FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/DOCK5FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class DOCK5FormatTest extends ChemFormatTest { + + public DOCK5FormatTest() { + super.setChemFormat((IChemFormat)DOCK5Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/DaltonFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/DaltonFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/DaltonFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class DaltonFormatTest extends ChemFormatTest { + + public DaltonFormatTest() { + super.setChemFormat((IChemFormat)DaltonFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class FenskeHall_ZMatrixFormatTest extends ChemFormatTest { + + public FenskeHall_ZMatrixFormatTest() { + super.setChemFormat((IChemFormat)FenskeHall_ZMatrixFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/GamessFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/GamessFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/GamessFormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class GamessFormatTest extends ChemFormatTest { + + public GamessFormatTest() { + super.setChemFormat((IChemFormat)GamessFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian03FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian03FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian03FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian03FormatTest extends ChemFormatTest { + + public Gaussian03FormatTest() { + super.setChemFormat((IChemFormat)Gaussian03Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian90FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian90FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian90FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian90FormatTest extends ChemFormatTest { + + public Gaussian90FormatTest() { + super.setChemFormat((IChemFormat)Gaussian90Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian92FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian92FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian92FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian92FormatTest extends ChemFormatTest { + + public Gaussian92FormatTest() { + super.setChemFormat((IChemFormat)Gaussian92Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian94FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian94FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian94FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian94FormatTest extends ChemFormatTest { + + public Gaussian94FormatTest() { + super.setChemFormat((IChemFormat)Gaussian94Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian95FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian95FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian95FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian95FormatTest extends ChemFormatTest { + + public Gaussian95FormatTest() { + super.setChemFormat((IChemFormat)Gaussian95Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -0,0 +1,37 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + + +/** + * @cdk.module test-io + */ +public class Gaussian98FormatTest extends ChemFormatTest { + + public Gaussian98FormatTest() { + super.setChemFormat((IChemFormat)Gaussian98Format.getInstance()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-18 15:20:53 UTC (rev 11397) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-19 05:43:24 UTC (rev 11398) @@ -63,14 +63,37 @@ import org.openscience.cdk.io.formats.BGFFormatTest; import org.openscience.cdk.io.formats.BSFormatTest; import org.openscience.cdk.io.formats.CACheFormatTest; +import org.openscience.cdk.io.formats.CIFFormatTest; +import org.openscience.cdk.io.formats.CMLFormatTest; +import org.openscience.cdk.io.formats.CMLRSSFormatTest; +import org.openscience.cdk.io.formats.CRK2DFormatTest; +import org.openscience.cdk.io.formats.CRK3DFormatTest; +import org.openscience.cdk.io.formats.CTXFormatTest; import org.openscience.cdk.io.formats.CacaoCartesianFormatTest; import org.openscience.cdk.io.formats.CacaoInternalFormatTest; +import org.openscience.cdk.io.formats.Chem3D_Cartesian_1FormatTest; +import org.openscience.cdk.io.formats.Chem3D_Cartesian_2FormatTest; +import org.openscience.cdk.io.formats.ChemDrawFormatTest; +import org.openscience.cdk.io.formats.ChemtoolFormatTest; +import org.openscience.cdk.io.formats.CrystClustFormatTest; +import org.openscience.cdk.io.formats.DMol3FormatTest; +import org.openscience.cdk.io.formats.DOCK5FormatTest; +import org.openscience.cdk.io.formats.DaltonFormatTest; +import org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormatTest; import org.openscience.cdk.io.iterator.IteratingMDLConformerReaderTest; import org.openscience.cdk.io.iterator.IteratingMDLReaderTest; import org.openscience.cdk.io.iterator.IteratingPCCompoundASNReaderTest; import org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReaderTest; import org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReaderTest; +import org.openscience.cdk.io.formats.GamessFormatTest; +import org.openscience.cdk.io.formats.Gaussian03FormatTest; +import org.openscience.cdk.io.formats.Gaussian90FormatTest; +import org.openscience.cdk.io.formats.Gaussian92FormatTest; +import org.openscience.cdk.io.formats.Gaussian94FormatTest; +import org.openscience.cdk.io.formats.Gaussian95FormatTest; +import org.openscience.cdk.io.formats.Gaussian98FormatTest; + /** * TestSuite that runs all the sample tests for the cdk.io package. * @@ -133,6 +156,28 @@ suite.addTest(new JUnit4TestAdapter(CacaoCartesianFormatTest.class)); suite.addTest(new JUnit4TestAdapter(CacaoInternalFormatTest.class)); suite.addTest(new JUnit4TestAdapter(CACheFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Chem3D_Cartesian_1FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Chem3D_Cartesian_2FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(ChemDrawFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(ChemtoolFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CIFFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CMLFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CMLRSSFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CRK2DFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CRK3DFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CrystClustFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(CTXFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(DaltonFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(DMol3FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(DOCK5FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(FenskeHall_ZMatrixFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(GamessFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian03FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian90FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian92FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian94FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian95FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Gaussian98FormatTest.class)); return suite; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-19 09:37:12
|
Revision: 11399 http://cdk.svn.sourceforge.net/cdk/?rev=11399&view=rev Author: egonw Date: 2008-06-19 02:37:05 -0700 (Thu, 19 Jun 2008) Log Message: ----------- Added more test classes Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/io/formats/GROMOS96FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalMMFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalSPMFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/HINFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIPlainTextFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/JMEFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/JaguarFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MACiEFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNV3000FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV2000FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV3000FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MMODFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC2002FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC7FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC93FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC97FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MPQCFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/MacroModelFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/Mol2FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/NWChemFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PCModelFormatTest.java Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/GROMOS96FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/GROMOS96FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/GROMOS96FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class GROMOS96FormatTest extends ChemFormatTest { + + public GROMOS96FormatTest() { + super.setChemFormat((IChemFormat)GROMOS96Format.getInstance()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java 2008-06-19 05:43:24 UTC (rev 11398) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -24,7 +24,6 @@ */ package org.openscience.cdk.io.formats; - /** * @cdk.module test-io */ Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalMMFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalMMFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalMMFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class GhemicalMMFormatTest extends ChemFormatTest { + + public GhemicalMMFormatTest() { + super.setChemFormat((IChemFormat)GhemicalMMFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalSPMFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalSPMFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/GhemicalSPMFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class GhemicalSPMFormatTest extends ChemFormatTest { + + public GhemicalSPMFormatTest() { + super.setChemFormat((IChemFormat)GhemicalSPMFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/HINFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/HINFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/HINFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class HINFormatTest extends ChemFormatTest { + + public HINFormatTest() { + super.setChemFormat((IChemFormat)HINFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class INChIFormatTest extends ChemFormatTest { + + public INChIFormatTest() { + super.setChemFormat((IChemFormat)INChIFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIPlainTextFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIPlainTextFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/INChIPlainTextFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class INChIPlainTextFormatTest extends ChemFormatTest { + + public INChIPlainTextFormatTest() { + super.setChemFormat((IChemFormat)INChIPlainTextFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/JMEFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/JMEFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/JMEFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class JMEFormatTest extends ChemFormatTest { + + public JMEFormatTest() { + super.setChemFormat((IChemFormat)JMEFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/JaguarFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/JaguarFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/JaguarFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class JaguarFormatTest extends ChemFormatTest { + + public JaguarFormatTest() { + super.setChemFormat((IChemFormat)JaguarFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MACiEFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MACiEFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MACiEFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MACiEFormatTest extends ChemFormatTest { + + public MACiEFormatTest() { + super.setChemFormat((IChemFormat)MACiEFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MDLFormatTest extends ChemFormatTest { + + public MDLFormatTest() { + super.setChemFormat((IChemFormat)MDLFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MDLRXNFormatTest extends ChemFormatTest { + + public MDLRXNFormatTest() { + super.setChemFormat((IChemFormat)MDLRXNFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNV3000FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNV3000FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLRXNV3000FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MDLRXNV3000FormatTest extends ChemFormatTest { + + public MDLRXNV3000FormatTest() { + super.setChemFormat((IChemFormat)MDLRXNV3000Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV2000FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV2000FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV2000FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MDLV2000FormatTest extends ChemFormatTest { + + public MDLV2000FormatTest() { + super.setChemFormat((IChemFormat)MDLV2000Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV3000FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV3000FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MDLV3000FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MDLV3000FormatTest extends ChemFormatTest { + + public MDLV3000FormatTest() { + super.setChemFormat((IChemFormat)MDLV3000Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MMODFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MMODFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MMODFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MMODFormatTest extends ChemFormatTest { + + public MMODFormatTest() { + super.setChemFormat((IChemFormat)MMODFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC2002FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC2002FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC2002FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MOPAC2002FormatTest extends ChemFormatTest { + + public MOPAC2002FormatTest() { + super.setChemFormat((IChemFormat)MOPAC2002Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC7FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC7FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC7FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MOPAC7FormatTest extends ChemFormatTest { + + public MOPAC7FormatTest() { + super.setChemFormat((IChemFormat)MOPAC7Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC93FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC93FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC93FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MOPAC93FormatTest extends ChemFormatTest { + + public MOPAC93FormatTest() { + super.setChemFormat((IChemFormat)MOPAC93Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC97FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC97FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MOPAC97FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MOPAC97FormatTest extends ChemFormatTest { + + public MOPAC97FormatTest() { + super.setChemFormat((IChemFormat)MOPAC97Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MPQCFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MPQCFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MPQCFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MPQCFormatTest extends ChemFormatTest { + + public MPQCFormatTest() { + super.setChemFormat((IChemFormat)MPQCFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/MacroModelFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/MacroModelFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/MacroModelFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class MacroModelFormatTest extends ChemFormatTest { + + public MacroModelFormatTest() { + super.setChemFormat((IChemFormat)MacroModelFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/Mol2FormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/Mol2FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/Mol2FormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class Mol2FormatTest extends ChemFormatTest { + + public Mol2FormatTest() { + super.setChemFormat((IChemFormat)Mol2Format.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/NWChemFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/NWChemFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/NWChemFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class NWChemFormatTest extends ChemFormatTest { + + public NWChemFormatTest() { + super.setChemFormat((IChemFormat)NWChemFormat.getInstance()); + } + +} Copied: cdk/trunk/src/test/org/openscience/cdk/io/formats/PCModelFormatTest.java (from rev 11398, cdk/trunk/src/test/org/openscience/cdk/io/formats/Gaussian98FormatTest.java) =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PCModelFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PCModelFormatTest.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PCModelFormatTest extends ChemFormatTest { + + public PCModelFormatTest() { + super.setChemFormat((IChemFormat)PCModelFormat.getInstance()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-19 05:43:24 UTC (rev 11398) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-19 09:37:05 UTC (rev 11399) @@ -80,12 +80,7 @@ import org.openscience.cdk.io.formats.DOCK5FormatTest; import org.openscience.cdk.io.formats.DaltonFormatTest; import org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormatTest; -import org.openscience.cdk.io.iterator.IteratingMDLConformerReaderTest; -import org.openscience.cdk.io.iterator.IteratingMDLReaderTest; -import org.openscience.cdk.io.iterator.IteratingPCCompoundASNReaderTest; -import org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReaderTest; -import org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReaderTest; - +import org.openscience.cdk.io.formats.GROMOS96FormatTest; import org.openscience.cdk.io.formats.GamessFormatTest; import org.openscience.cdk.io.formats.Gaussian03FormatTest; import org.openscience.cdk.io.formats.Gaussian90FormatTest; @@ -93,6 +88,34 @@ import org.openscience.cdk.io.formats.Gaussian94FormatTest; import org.openscience.cdk.io.formats.Gaussian95FormatTest; import org.openscience.cdk.io.formats.Gaussian98FormatTest; +import org.openscience.cdk.io.formats.GhemicalMMFormatTest; +import org.openscience.cdk.io.formats.GhemicalSPMFormatTest; +import org.openscience.cdk.io.formats.HINFormatTest; +import org.openscience.cdk.io.formats.INChIFormatTest; +import org.openscience.cdk.io.formats.INChIPlainTextFormatTest; +import org.openscience.cdk.io.formats.JMEFormatTest; +import org.openscience.cdk.io.formats.JaguarFormatTest; +import org.openscience.cdk.io.formats.MACiEFormatTest; +import org.openscience.cdk.io.formats.MDLFormatTest; +import org.openscience.cdk.io.formats.MDLRXNFormatTest; +import org.openscience.cdk.io.formats.MDLRXNV3000FormatTest; +import org.openscience.cdk.io.formats.MDLV2000FormatTest; +import org.openscience.cdk.io.formats.MDLV3000FormatTest; +import org.openscience.cdk.io.formats.MMODFormatTest; +import org.openscience.cdk.io.formats.MOPAC2002FormatTest; +import org.openscience.cdk.io.formats.MOPAC7FormatTest; +import org.openscience.cdk.io.formats.MOPAC93FormatTest; +import org.openscience.cdk.io.formats.MOPAC97FormatTest; +import org.openscience.cdk.io.formats.MPQCFormatTest; +import org.openscience.cdk.io.formats.MacroModelFormatTest; +import org.openscience.cdk.io.formats.Mol2FormatTest; +import org.openscience.cdk.io.formats.NWChemFormatTest; +import org.openscience.cdk.io.formats.PCModelFormatTest; +import org.openscience.cdk.io.iterator.IteratingMDLConformerReaderTest; +import org.openscience.cdk.io.iterator.IteratingMDLReaderTest; +import org.openscience.cdk.io.iterator.IteratingPCCompoundASNReaderTest; +import org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReaderTest; +import org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReaderTest; /** * TestSuite that runs all the sample tests for the cdk.io package. @@ -178,6 +201,30 @@ suite.addTest(new JUnit4TestAdapter(Gaussian94FormatTest.class)); suite.addTest(new JUnit4TestAdapter(Gaussian95FormatTest.class)); suite.addTest(new JUnit4TestAdapter(Gaussian98FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(GhemicalMMFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(GhemicalSPMFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(GROMOS96FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(HINFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(INChIFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(INChIPlainTextFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(JaguarFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(JMEFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MACiEFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MacroModelFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLRXNFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLRXNV3000FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLV2000FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLV3000FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MMODFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(Mol2FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MOPAC2002FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MOPAC7FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MOPAC93FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MOPAC97FormatTest.class)); + suite.addTest(new JUnit4TestAdapter(MPQCFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(NWChemFormatTest.class)); + suite.addTest(new JUnit4TestAdapter(PCModelFormatTest.class)); return suite; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-19 15:31:36
|
Revision: 11401 http://cdk.svn.sourceforge.net/cdk/?rev=11401&view=rev Author: egonw Date: 2008-06-19 08:25:05 -0700 (Thu, 19 Jun 2008) Log Message: ----------- Added last few IO format test classes Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PMPFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PQSChemFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemASNFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundXMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesASNFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/QChemFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/RawCopyFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SDFFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SMARTSFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFIXFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ShelXFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SpartanFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/SybylDescriptorFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerMM2FormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerXYZFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/TurboMoleFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/UniChemXYZFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/VASPFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ViewmolFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/XEDFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/XYZFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/YasaraFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ZMatrixFormatTest.java cdk/trunk/src/test/org/openscience/cdk/io/formats/ZindoFormatTest.java Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PDBFormatTest extends ChemFormatTest { + + public PDBFormatTest() { + super.setChemFormat((IChemFormat)PDBFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PDBMLFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PDBMLFormatTest extends ChemFormatTest { + + public PDBMLFormatTest() { + super.setChemFormat((IChemFormat)PDBMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PMPFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PMPFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PMPFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PMPFormatTest extends ChemFormatTest { + + public PMPFormatTest() { + super.setChemFormat((IChemFormat)PMPFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PQSChemFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PQSChemFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PQSChemFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PQSChemFormatTest extends ChemFormatTest { + + public PQSChemFormatTest() { + super.setChemFormat((IChemFormat)PQSChemFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemASNFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemASNFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemASNFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemASNFormatTest extends ChemFormatTest { + + public PubChemASNFormatTest() { + super.setChemFormat((IChemFormat)PubChemASNFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundXMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundXMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundXMLFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemCompoundXMLFormatTest extends ChemFormatTest { + + public PubChemCompoundXMLFormatTest() { + super.setChemFormat((IChemFormat)PubChemCompoundXMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemCompoundsXMLFormatTest extends ChemFormatTest { + + public PubChemCompoundsXMLFormatTest() { + super.setChemFormat((IChemFormat)PubChemCompoundsXMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemFormatTest extends ChemFormatTest { + + public PubChemFormatTest() { + super.setChemFormat((IChemFormat)PubChemFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemSubstanceXMLFormatTest extends ChemFormatTest { + + public PubChemSubstanceXMLFormatTest() { + super.setChemFormat((IChemFormat)PubChemSubstanceXMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesASNFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesASNFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesASNFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemSubstancesASNFormatTest extends ChemFormatTest { + + public PubChemSubstancesASNFormatTest() { + super.setChemFormat((IChemFormat)PubChemSubstancesASNFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class PubChemSubstancesXMLFormatTest extends ChemFormatTest { + + public PubChemSubstancesXMLFormatTest() { + super.setChemFormat((IChemFormat)PubChemSubstancesXMLFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/QChemFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/QChemFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/QChemFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class QChemFormatTest extends ChemFormatTest { + + public QChemFormatTest() { + super.setChemFormat((IChemFormat)QChemFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/RawCopyFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/RawCopyFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/RawCopyFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class RawCopyFormatTest extends ChemFormatTest { + + public RawCopyFormatTest() { + super.setChemFormat((IChemFormat)RawCopyFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SDFFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SDFFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SDFFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SDFFormatTest extends ChemFormatTest { + + public SDFFormatTest() { + super.setChemFormat((IChemFormat)SDFFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SMARTSFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SMARTSFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SMARTSFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SMARTSFormatTest extends ChemFormatTest { + + public SMARTSFormatTest() { + super.setChemFormat((IChemFormat)SMARTSFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFIXFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFIXFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFIXFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SMILESFIXFormatTest extends ChemFormatTest { + + public SMILESFIXFormatTest() { + super.setChemFormat((IChemFormat)SMILESFIXFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SMILESFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SMILESFormatTest extends ChemFormatTest { + + public SMILESFormatTest() { + super.setChemFormat((IChemFormat)SMILESFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ShelXFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ShelXFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ShelXFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class ShelXFormatTest extends ChemFormatTest { + + public ShelXFormatTest() { + super.setChemFormat((IChemFormat)ShelXFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SpartanFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SpartanFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SpartanFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SpartanFormatTest extends ChemFormatTest { + + public SpartanFormatTest() { + super.setChemFormat((IChemFormat)SpartanFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/SybylDescriptorFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/SybylDescriptorFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/SybylDescriptorFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class SybylDescriptorFormatTest extends ChemFormatTest { + + public SybylDescriptorFormatTest() { + super.setChemFormat((IChemFormat)SybylDescriptorFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerMM2FormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerMM2FormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerMM2FormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class TinkerMM2FormatTest extends ChemFormatTest { + + public TinkerMM2FormatTest() { + super.setChemFormat((IChemFormat)TinkerMM2Format.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerXYZFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerXYZFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/TinkerXYZFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class TinkerXYZFormatTest extends ChemFormatTest { + + public TinkerXYZFormatTest() { + super.setChemFormat((IChemFormat)TinkerXYZFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/TurboMoleFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/TurboMoleFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/TurboMoleFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class TurboMoleFormatTest extends ChemFormatTest { + + public TurboMoleFormatTest() { + super.setChemFormat((IChemFormat)TurboMoleFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/UniChemXYZFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/UniChemXYZFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/UniChemXYZFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class UniChemXYZFormatTest extends ChemFormatTest { + + public UniChemXYZFormatTest() { + super.setChemFormat((IChemFormat)UniChemXYZFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/VASPFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/VASPFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/VASPFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class VASPFormatTest extends ChemFormatTest { + + public VASPFormatTest() { + super.setChemFormat((IChemFormat)VASPFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ViewmolFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ViewmolFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ViewmolFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class ViewmolFormatTest extends ChemFormatTest { + + public ViewmolFormatTest() { + super.setChemFormat((IChemFormat)ViewmolFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/XEDFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/XEDFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/XEDFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class XEDFormatTest extends ChemFormatTest { + + public XEDFormatTest() { + super.setChemFormat((IChemFormat)XEDFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/XYZFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/XYZFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/XYZFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class XYZFormatTest extends ChemFormatTest { + + public XYZFormatTest() { + super.setChemFormat((IChemFormat)XYZFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/YasaraFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/YasaraFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/YasaraFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class YasaraFormatTest extends ChemFormatTest { + + public YasaraFormatTest() { + super.setChemFormat((IChemFormat)YasaraFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ZMatrixFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ZMatrixFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ZMatrixFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class ZMatrixFormatTest extends ChemFormatTest { + + public ZMatrixFormatTest() { + super.setChemFormat((IChemFormat)ZMatrixFormat.getInstance()); + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/io/formats/ZindoFormatTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/formats/ZindoFormatTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/formats/ZindoFormatTest.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -0,0 +1,36 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io.formats; + +/** + * @cdk.module test-io + */ +public class ZindoFormatTest extends ChemFormatTest { + + public ZindoFormatTest() { + super.setChemFormat((IChemFormat)ZindoFormat.getInstance()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-19 14:25:02 UTC (rev 11400) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-06-19 15:25:05 UTC (rev 11401) @@ -111,6 +111,37 @@ import org.openscience.cdk.io.formats.Mol2FormatTest; import org.openscience.cdk.io.formats.NWChemFormatTest; import org.openscience.cdk.io.formats.PCModelFormatTest; +import org.openscience.cdk.io.formats.PDBFormatTest; +import org.openscience.cdk.io.formats.PDBMLFormatTest; +import org.openscience.cdk.io.formats.PMPFormatTest; +import org.openscience.cdk.io.formats.PQSChemFormatTest; +import org.openscience.cdk.io.formats.PubChemASNFormatTest; +import org.openscience... [truncated message content] |
From: <eg...@us...> - 2008-06-21 11:00:55
|
Revision: 11414 http://cdk.svn.sourceforge.net/cdk/?rev=11414&view=rev Author: egonw Date: 2008-06-21 03:09:51 -0700 (Sat, 21 Jun 2008) Log Message: ----------- Added a generic assertion for testing for zero-length String's, with some meaningful error message Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomTypeDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/BondDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/ChemObjectDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElectronContainerDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElementDiffTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/IsotopeDiffTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/NewCDKTestCase.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -228,4 +228,17 @@ Assert.assertEquals(hydrogenCounts[i], atoms.next().getHydrogenCount().intValue()); } + /** + * Asserts that the given String has zero length. + * + * @param String String to test the length of. + */ + public void assertZeroLength(String testString) { + Assert.assertNotNull("Expected a non-null String.", testString); + Assert.assertEquals( + "Expected a zero-length String, but found '" + testString + "'", + 0, testString.length() + ); + } + } Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -23,18 +23,18 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.Atom; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IAtom; /** * @cdk.module test-diff */ -public class AtomDiffTest { +public class AtomDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IAtom atom1 = new Atom(); String result = AtomDiff.diff(atom1, atom1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomTypeDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomTypeDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/AtomTypeDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -24,18 +24,18 @@ import org.junit.Test; import org.openscience.cdk.AtomType; import org.openscience.cdk.Element; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IAtomType; /** * @cdk.module test-diff */ -public class AtomTypeDiffTest { +public class AtomTypeDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IAtomType element1 = new AtomType(new Element()); String result = AtomTypeDiff.diff(element1, element1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/BondDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/BondDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/BondDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -24,19 +24,18 @@ import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.Bond; -import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IBond; /** * @cdk.module test-diff */ -public class BondDiffTest { +public class BondDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IBond bond1 = new Bond(); String result = BondDiff.diff(bond1, bond1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/ChemObjectDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/ChemObjectDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/ChemObjectDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -24,21 +24,18 @@ import org.junit.Test; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.ChemObject; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IChemObject; /** * @cdk.module test-diff */ -public class ChemObjectDiffTest { +public class ChemObjectDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IChemObject atom1 = new ChemObject(); String result = ChemObjectDiff.diff(atom1, atom1); - Assert.assertNotNull(result); - Assert.assertEquals( - "Expected a zero-length result string, but found '" + result + "'", - 0, result.length() - ); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElectronContainerDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElectronContainerDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElectronContainerDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -23,18 +23,18 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.ElectronContainer; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IElectronContainer; /** * @cdk.module test-diff */ -public class ElectronContainerDiffTest { +public class ElectronContainerDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IElectronContainer atom1 = new ElectronContainer(); String result = ElectronContainerDiff.diff(atom1, atom1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElementDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElementDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/ElementDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -23,18 +23,18 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.Element; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IElement; /** * @cdk.module test-diff */ -public class ElementDiffTest { +public class ElementDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IElement element1 = new Element(); String result = ElementDiff.diff(element1, element1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { Modified: cdk/trunk/src/test/org/openscience/cdk/tools/diff/IsotopeDiffTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/IsotopeDiffTest.java 2008-06-21 10:09:21 UTC (rev 11413) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/IsotopeDiffTest.java 2008-06-21 10:09:51 UTC (rev 11414) @@ -24,18 +24,18 @@ import org.junit.Test; import org.openscience.cdk.Element; import org.openscience.cdk.Isotope; +import org.openscience.cdk.NewCDKTestCase; import org.openscience.cdk.interfaces.IIsotope; /** * @cdk.module test-diff */ -public class IsotopeDiffTest { +public class IsotopeDiffTest extends NewCDKTestCase { @Test public void testMatchAgainstItself() { IIsotope element1 = new Isotope(new Element()); String result = IsotopeDiff.diff(element1, element1); - Assert.assertNotNull(result); - Assert.assertEquals(0, result.length()); + assertZeroLength(result); } @Test public void testDiff() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-22 11:04:38
|
Revision: 11417 http://cdk.svn.sourceforge.net/cdk/?rev=11417&view=rev Author: egonw Date: 2008-06-21 03:10:53 -0700 (Sat, 21 Jun 2008) Log Message: ----------- Added unit tests for the new classes Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdiffTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/ cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/BooleanDifferenceTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/IntegerDifferenceTest.java cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/StringDifferenceTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdiffTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdiffTests.java 2008-06-21 10:10:32 UTC (rev 11416) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MdiffTests.java 2008-06-21 10:10:53 UTC (rev 11417) @@ -32,6 +32,9 @@ import org.openscience.cdk.tools.diff.ElectronContainerDiffTest; import org.openscience.cdk.tools.diff.ElementDiffTest; import org.openscience.cdk.tools.diff.IsotopeDiffTest; +import org.openscience.cdk.tools.diff.tree.BooleanDifferenceTest; +import org.openscience.cdk.tools.diff.tree.IntegerDifferenceTest; +import org.openscience.cdk.tools.diff.tree.StringDifferenceTest; /** * TestSuite that runs all the JUnit tests for the diff module. @@ -53,6 +56,11 @@ suite.addTest(new JUnit4TestAdapter(ElectronContainerDiffTest.class)); suite.addTest(new JUnit4TestAdapter(ElementDiffTest.class)); suite.addTest(new JUnit4TestAdapter(IsotopeDiffTest.class)); + + // cdk.tools.diff.tree + suite.addTest(new JUnit4TestAdapter(BooleanDifferenceTest.class)); + suite.addTest(new JUnit4TestAdapter(IntegerDifferenceTest.class)); + suite.addTest(new JUnit4TestAdapter(StringDifferenceTest.class)); return suite; } Added: cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/BooleanDifferenceTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/BooleanDifferenceTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/BooleanDifferenceTest.java 2008-06-21 10:10:53 UTC (rev 11417) @@ -0,0 +1,54 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.tools.diff.tree; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; + +/** + * @cdk.module test-diff + */ +public class BooleanDifferenceTest extends NewCDKTestCase { + + @Test public void testDiff() { + IDifference result = BooleanDifference.construct("Foo", true, false); + Assert.assertNotNull(result); + } + + @Test public void testSame() { + IDifference result = BooleanDifference.construct("Foo", false, false); + Assert.assertNull(result); + } + + @Test public void testTwoNull() { + IDifference result = BooleanDifference.construct("Foo", null, null); + Assert.assertNull(result); + } + + @Test public void testOneNull() { + IDifference result = BooleanDifference.construct("Foo", null, false); + Assert.assertNotNull(result); + + result = BooleanDifference.construct("Foo", false, null); + Assert.assertNotNull(result); + } +} Added: cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/IntegerDifferenceTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/IntegerDifferenceTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/IntegerDifferenceTest.java 2008-06-21 10:10:53 UTC (rev 11417) @@ -0,0 +1,54 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.tools.diff.tree; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; + +/** + * @cdk.module test-diff + */ +public class IntegerDifferenceTest extends NewCDKTestCase { + + @Test public void testDiff() { + IDifference result = IntegerDifference.construct("Foo", 1, 2); + Assert.assertNotNull(result); + } + + @Test public void testSame() { + IDifference result = IntegerDifference.construct("Foo", 1, 1); + Assert.assertNull(result); + } + + @Test public void testTwoNull() { + IDifference result = IntegerDifference.construct("Foo", null, null); + Assert.assertNull(result); + } + + @Test public void testOneNull() { + IDifference result = IntegerDifference.construct("Foo", null, 1); + Assert.assertNotNull(result); + + result = IntegerDifference.construct("Foo", 2, null); + Assert.assertNotNull(result); + } +} Added: cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/StringDifferenceTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/StringDifferenceTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/tools/diff/tree/StringDifferenceTest.java 2008-06-21 10:10:53 UTC (rev 11417) @@ -0,0 +1,54 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.tools.diff.tree; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; + +/** + * @cdk.module test-diff + */ +public class StringDifferenceTest extends NewCDKTestCase { + + @Test public void testDiff() { + IDifference result = StringDifference.construct("Foo", "foo", "bar"); + Assert.assertNotNull(result); + } + + @Test public void testSame() { + IDifference result = StringDifference.construct("Foo", "foo", "foo"); + Assert.assertNull(result); + } + + @Test public void testTwoNull() { + IDifference result = StringDifference.construct("Foo", null, null); + Assert.assertNull(result); + } + + @Test public void testOneNull() { + IDifference result = StringDifference.construct("Foo", null, "bar"); + Assert.assertNotNull(result); + + result = StringDifference.construct("Foo", "bar", null); + Assert.assertNotNull(result); + } +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-06-30 13:21:51
|
Revision: 11463 http://cdk.svn.sourceforge.net/cdk/?rev=11463&view=rev Author: egonw Date: 2008-06-30 06:21:40 -0700 (Mon, 30 Jun 2008) Log Message: ----------- Added coverage testing for the qsar module Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/QsarCoverageTest.java Added: cdk/trunk/src/test/org/openscience/cdk/QsarCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/QsarCoverageTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/QsarCoverageTest.java 2008-06-30 13:21:40 UTC (rev 11463) @@ -0,0 +1,56 @@ +/* $Revision: 10775 $ $Author: egonw $ $Date: 2008-05-03 08:57:44 +0200 (Sat, 03 May 2008) $ + * + * Copyright (C) 2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk; + +import junit.framework.Test; +import junit.framework.TestSuite; + +/** + * TestSuite that uses tests whether all public methods in the qsar + * module are tested. Unlike Emma, it does not test that all code is + * tested, just all methods. + * + * @cdk.module test-qsar + */ +public class QsarCoverageTest extends CoverageAnnotationTest { + + private final static String CLASS_LIST = "qsar.javafiles"; + + public QsarCoverageTest(String name) { + super(name); + } + + protected void setUp() throws Exception { + super.setUp(); + super.loadClassList(CLASS_LIST); + } + + public static Test suite() { + TestSuite suite = new TestSuite(); + suite.addTestSuite(QsarCoverageTest.class); + return suite; + } + + public void testCoverage() { + assertTrue(super.runCoverageTest()); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java 2008-06-29 20:19:44 UTC (rev 11462) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java 2008-06-30 13:21:40 UTC (rev 11463) @@ -27,6 +27,7 @@ import junit.framework.Test; import junit.framework.TestSuite; +import org.openscience.cdk.QsarCoverageTest; import org.openscience.cdk.qsar.model.R2.RJavaEnvironmentTest; /** @@ -42,7 +43,11 @@ TestSuite suite = new TestSuite("All QSAR Tests"); - // Individual Tests - Please add correlatively + suite.addTest(QsarCoverageTest.suite()); + + // Individual Tests - Please add correlatively + + // Stuff for R packages String rhome = System.getenv("R_HOME"); String ldlibrarypath = System.getenv("LD_LIBRARY_PATH"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-07-03 19:52:46
|
Revision: 11495 http://cdk.svn.sourceforge.net/cdk/?rev=11495&view=rev Author: egonw Date: 2008-07-03 12:52:32 -0700 (Thu, 03 Jul 2008) Log Message: ----------- Started to convert IO tests to JUnit4 Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java Modified: cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-03 19:51:31 UTC (rev 11494) +++ cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-03 19:52:32 UTC (rev 11495) @@ -26,14 +26,11 @@ import java.io.StringWriter; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; -import org.openscience.cdk.io.CDKSourceCodeWriter; -import org.openscience.cdk.CDKTestCase; /** * TestCase for the writer CDK source code files using one test file. @@ -42,23 +39,15 @@ * * @see org.openscience.cdk.io.CDKSourceCodeWriterTest */ -public class CDKSourceCodeWriterTest extends CDKTestCase { +public class CDKSourceCodeWriterTest extends ChemObjectIOTest { - public CDKSourceCodeWriterTest(String name) { - super(name); - } - - public static Test suite() { - return new TestSuite(CDKSourceCodeWriterTest.class); - } - - public void testAccepts() throws Exception { + @Test public void testAccepts() throws Exception { CDKSourceCodeWriter reader = new CDKSourceCodeWriter(); - assertTrue(reader.accepts(Molecule.class)); - assertTrue(reader.accepts(AtomContainer.class)); + Assert.assertTrue(reader.accepts(Molecule.class)); + Assert.assertTrue(reader.accepts(AtomContainer.class)); } - public void testOutput() throws Exception { + @Test public void testOutput() throws Exception { StringWriter writer = new StringWriter(); Molecule molecule = new Molecule(); Atom atom = new Atom("C"); @@ -68,6 +57,6 @@ CDKSourceCodeWriter sourceWriter = new CDKSourceCodeWriter(writer); sourceWriter.write(molecule); String output = writer.toString(); - assertTrue(output.indexOf("IAtom a1 = mol.getBuilder().newAtom(\"C\")") != -1); + Assert.assertTrue(output.indexOf("IAtom a1 = mol.getBuilder().newAtom(\"C\")") != -1); } } Added: cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java 2008-07-03 19:52:32 UTC (rev 11495) @@ -0,0 +1,60 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@sl... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.NewCDKTestCase; +import org.openscience.cdk.io.formats.IResourceFormat; + +/** + * TestCase for CDK IO classes. + * + * @cdk.module test-io + */ +public abstract class ChemObjectIOTest extends NewCDKTestCase { + + private IChemObjectIO chemObjectIO; + + public void setChemFormat(IChemObjectIO chemObjectIO) { + this.chemObjectIO = chemObjectIO; + } + + @Test public void testChemObjectIOSet() { + Assert.assertNotNull( + "You must use setChemObjectIO() to set the IChemObjectIO object.", + chemObjectIO + ); + } + + @Test public void testGetFormat() { + IResourceFormat format = chemObjectIO.getFormat(); + Assert.assertNotNull( + "The IChemObjectIO.getFormat method returned null.", + format + ); + } + +} Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-03 19:51:31 UTC (rev 11494) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-03 19:52:32 UTC (rev 11495) @@ -162,7 +162,7 @@ suite.addTest(CMLIOTests.suite()); suite.addTest(CrystClustReaderTest.suite()); - suite.addTest(CDKSourceCodeWriterTest.suite()); + suite.addTest(new JUnit4TestAdapter(CDKSourceCodeWriterTest.class)); suite.addTest(GamessReaderTest.suite()); suite.addTest(Gaussian98ReaderTest.suite()); suite.addTest(GhemicalReaderTest.suite()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-07-04 08:23:17
|
Revision: 11498 http://cdk.svn.sourceforge.net/cdk/?rev=11498&view=rev Author: egonw Date: 2008-07-04 01:22:58 -0700 (Fri, 04 Jul 2008) Log Message: ----------- More conversion to JUnit4 Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java Modified: cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -27,6 +27,7 @@ import java.io.StringWriter; import org.junit.Assert; +import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; @@ -41,10 +42,13 @@ */ public class CDKSourceCodeWriterTest extends ChemObjectIOTest { + @BeforeClass public static void setup() { + setChemObjectIO(new CDKSourceCodeWriter()); + } + @Test public void testAccepts() throws Exception { - CDKSourceCodeWriter reader = new CDKSourceCodeWriter(); - Assert.assertTrue(reader.accepts(Molecule.class)); - Assert.assertTrue(reader.accepts(AtomContainer.class)); + Assert.assertTrue(chemObjectIO.accepts(Molecule.class)); + Assert.assertTrue(chemObjectIO.accepts(AtomContainer.class)); } @Test public void testOutput() throws Exception { Modified: cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,9 +29,9 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; @@ -40,8 +40,6 @@ import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.io.CTXReader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -51,51 +49,47 @@ * * @see org.openscience.cdk.io.CrystClustReader */ -public class CTXReaderTest extends CDKTestCase { +public class CTXReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public CTXReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(CTXReaderTest.class); + setChemObjectIO(new CTXReader()); } - public static Test suite() { - return new TestSuite(CTXReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { CTXReader reader = new CTXReader(); - assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); } - public void testMethanol() throws Exception { + @Test public void testMethanol() throws Exception { String filename = "data/ctx/methanol_with_descriptors.ctx"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); CTXReader reader = new CTXReader(ins); IChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); IMoleculeSet moleculeSet = model.getMoleculeSet(); - assertNotNull(moleculeSet); - assertEquals(1, moleculeSet.getAtomContainerCount()); + Assert.assertNotNull(moleculeSet); + Assert.assertEquals(1, moleculeSet.getAtomContainerCount()); IAtomContainer container = moleculeSet.getAtomContainer(0); - assertNotNull(container); - assertEquals("Incorrect atom count.", 6, container.getAtomCount()); - assertEquals(5, container.getBondCount()); + Assert.assertNotNull(container); + Assert.assertEquals("Incorrect atom count.", 6, container.getAtomCount()); + Assert.assertEquals(5, container.getBondCount()); - assertEquals("Petra", container.getID()); + Assert.assertEquals("Petra", container.getID()); - assertNotNull(container.getProperty(CDKConstants.TITLE)); - assertEquals("CH4O", container.getProperty(CDKConstants.TITLE)); + Assert.assertNotNull(container.getProperty(CDKConstants.TITLE)); + Assert.assertEquals("CH4O", container.getProperty(CDKConstants.TITLE)); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -36,10 +36,10 @@ */ public abstract class ChemObjectIOTest extends NewCDKTestCase { - private IChemObjectIO chemObjectIO; + protected static IChemObjectIO chemObjectIO; - public void setChemFormat(IChemObjectIO chemObjectIO) { - this.chemObjectIO = chemObjectIO; + public static void setChemObjectIO(IChemObjectIO aChemObjectIO) { + chemObjectIO = aChemObjectIO; } @Test public void testChemObjectIOSet() { Modified: cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -31,13 +31,12 @@ import javax.vecmath.Vector3d; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.io.CrystClustReader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -47,62 +46,58 @@ * * @see org.openscience.cdk.io.CrystClustReader */ -public class CrystClustReaderTest extends CDKTestCase { +public class CrystClustReaderTest extends ChemObjectIOTest { - private org.openscience.cdk.tools.LoggingTool logger; - - public CrystClustReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + private static LoggingTool logger; + + @BeforeClass public static void setup() { + logger = new LoggingTool(CrystClustReaderTest.class); + setChemObjectIO(new CrystClustReader()); } - public static Test suite() { - return new TestSuite(CrystClustReaderTest.class); + @Test public void testAccepts() { + Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); + Assert.assertFalse(chemObjectIO.accepts(AtomContainer.class)); } - - public void testAccepts() { - CrystClustReader reader = new CrystClustReader(); - assertTrue(reader.accepts(ChemFile.class)); - } - public void testEstrone() throws Exception { + @Test public void testEstrone() throws Exception { String filename = "data/crystclust/estron.crystclust"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); CrystClustReader reader = new CrystClustReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(2, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(2, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.ICrystal crystal = model.getCrystal(); - assertNotNull(crystal); - assertEquals(42, crystal.getAtomCount()); - assertEquals(1, crystal.getZ().intValue()); + Assert.assertNotNull(crystal); + Assert.assertEquals(42, crystal.getAtomCount()); + Assert.assertEquals(1, crystal.getZ().intValue()); // test reading of partial charges org.openscience.cdk.interfaces.IAtom atom = crystal.getAtom(0); - assertNotNull(atom); - assertEquals("O", atom.getSymbol()); - assertEquals(-0.68264902, atom.getCharge(), 0.00000001); + Assert.assertNotNull(atom); + Assert.assertEquals("O", atom.getSymbol()); + Assert.assertEquals(-0.68264902, atom.getCharge(), 0.00000001); // test unit cell axes Vector3d a = crystal.getA(); - assertEquals(7.971030, a.x, 0.000001); - assertEquals(0.0, a.y, 0.000001); - assertEquals(0.0, a.z, 0.000001); + Assert.assertEquals(7.971030, a.x, 0.000001); + Assert.assertEquals(0.0, a.y, 0.000001); + Assert.assertEquals(0.0, a.z, 0.000001); Vector3d b = crystal.getB(); - assertEquals(0.0, b.x, 0.000001); - assertEquals(18.772200, b.y, 0.000001); - assertEquals(0.0, b.z, 0.000001); + Assert.assertEquals(0.0, b.x, 0.000001); + Assert.assertEquals(18.772200, b.y, 0.000001); + Assert.assertEquals(0.0, b.z, 0.000001); Vector3d c = crystal.getC(); - assertEquals(0.0, c.x, 0.000001); - assertEquals(0.0, c.y, 0.000001); - assertEquals(10.262220, c.z, 0.000001); + Assert.assertEquals(0.0, c.x, 0.000001); + Assert.assertEquals(0.0, c.y, 0.000001); + Assert.assertEquals(10.262220, c.z, 0.000001); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -6,14 +6,12 @@ import java.util.Iterator; import java.util.List; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.io.Gaussian98Reader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -23,40 +21,17 @@ * * @author Christoph Steinbeck */ +public class Gaussian98ReaderTest extends ChemObjectIOTest { -public class Gaussian98ReaderTest extends CDKTestCase { - - static boolean standAlone = false; - /** - * Test suite. - * - * <p><b>Performed tests</b>: - * <ul> - * <li>Gaussian98Reader general tests.</li> - * </ul> - * - * @return A test suite for Gaussian98Reader class. - */ - public static Test suite() { - return new TestSuite(Gaussian98ReaderTest.class); - } - - /** - * Constructs a new "Gaussian98ReaderTest" object given the test case's name. - * - * @param name The test case name. - */ - public Gaussian98ReaderTest(String name) { - super(name); - } - - - public void testAccepts() { - Gaussian98Reader reader = new Gaussian98Reader(); - assertTrue(reader.accepts(ChemFile.class)); + @BeforeClass public static void setup() { + setChemObjectIO(new Gaussian98Reader()); } - public void testNMRReading() throws Exception + @Test public void testAccepts() { + Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); + } + + @Test public void testNMRReading() throws Exception { IAtomContainer atomContainer = null; //boolean foundOneShieldingEntry = false; @@ -69,8 +44,8 @@ Gaussian98Reader g98Reader = new Gaussian98Reader(inputReader); ChemFile chemFile = (ChemFile)g98Reader.read(new ChemFile()); List atomContainersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertNotNull(atomContainersList); - assertTrue(atomContainersList.size() == 54); + Assert.assertNotNull(atomContainersList); + Assert.assertTrue(atomContainersList.size() == 54); //logger.debug("Found " + atomContainers.length + " atomContainers"); Iterator iterator = atomContainersList.iterator(); int counter = 0; @@ -88,8 +63,8 @@ shieldingCounter ++; } } - if (counter < 53) assertTrue(shieldingCounter == 0); - else assertTrue(shieldingCounter == ac.getAtomCount()); + if (counter < 53) Assert.assertTrue(shieldingCounter == 0); + else Assert.assertTrue(shieldingCounter == ac.getAtomCount()); //logger.debug("AtomContainer " + (f + 1) + " has " + atomContainers[f].getAtomCount() + " atoms and " + shieldingCounter + " shielding entries"); counter++; } Modified: cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,13 +29,11 @@ import java.io.StringReader; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemModel; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.io.GhemicalMMReader; -import org.openscience.cdk.CDKTestCase; /** * TestCase for the reading Ghemical molecular dynamics files using one test file. @@ -44,22 +42,17 @@ * * @see org.openscience.cdk.io.GhemicalReader */ -public class GhemicalReaderTest extends CDKTestCase { +public class GhemicalReaderTest extends ChemObjectIOTest { - public GhemicalReaderTest(String name) { - super(name); + @BeforeClass public static void setup() { + setChemObjectIO(new GhemicalMMReader()); } - public static Test suite() { - return new TestSuite(GhemicalReaderTest.class); + @Test public void testAccepts() { + Assert.assertTrue(chemObjectIO.accepts(ChemModel.class)); } - public void testAccepts() { - GhemicalMMReader reader = new GhemicalMMReader(); - assertTrue(reader.accepts(ChemModel.class)); - } - - public void testExample() throws Exception { + @Test public void testExample() throws Exception { String testfile = "!Header mm1gp 100\n" + "!Info 1\n" + @@ -95,22 +88,22 @@ GhemicalMMReader reader = new GhemicalMMReader(stringReader); ChemModel model = (ChemModel)reader.read((ChemObject)new ChemModel()); - assertNotNull(model); - assertNotNull(model.getMoleculeSet()); + Assert.assertNotNull(model); + Assert.assertNotNull(model.getMoleculeSet()); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(6, m.getAtomCount()); - assertEquals(5, m.getBondCount()); + Assert.assertNotNull(m); + Assert.assertEquals(6, m.getAtomCount()); + Assert.assertEquals(5, m.getBondCount()); // test reading of formal charges org.openscience.cdk.interfaces.IAtom a = m.getAtom(0); - assertNotNull(a); - assertEquals(6, a.getAtomicNumber().intValue()); - assertEquals(-0.2, a.getCharge(), 0.01); - assertEquals(0.06677, a.getPoint3d().x, 0.01); + Assert.assertNotNull(a); + Assert.assertEquals(6, a.getAtomicNumber().intValue()); + Assert.assertEquals(-0.2, a.getCharge(), 0.01); + Assert.assertEquals(0.06677, a.getPoint3d().x, 0.01); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,13 +29,12 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.io.HINReader; -import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.tools.LoggingTool; /** * TestCase for the reading HIN mol files using one test file. @@ -44,90 +43,85 @@ * * @see org.openscience.cdk.io.HINReader */ -public class HINReaderTest extends CDKTestCase { +public class HINReaderTest extends ChemObjectIOTest { - private org.openscience.cdk.tools.LoggingTool logger; - - public HINReaderTest(String name) { - super(name); - logger = new org.openscience.cdk.tools.LoggingTool(this); + private static LoggingTool logger; + + @BeforeClass public static void setup() { + logger = new LoggingTool(HINReaderTest.class); + setChemObjectIO(new HINReader()); } - public static Test suite() { - return new TestSuite(HINReaderTest.class); + @Test public void testAccepts() { + Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); } - public void testAccepts() { - HINReader reader = new HINReader(); - assertTrue(reader.accepts(ChemFile.class)); - } - - public void testBenzene() throws Exception { + @Test public void testBenzene() throws Exception { String filename = "data/hin/benzene.hin"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); HINReader reader = new HINReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(12, m.getAtomCount()); + Assert.assertNotNull(m); + Assert.assertEquals(12, m.getAtomCount()); // assertEquals(?, m.getBondCount()); } - public void testMoleculeTwo() throws Exception { + @Test public void testMoleculeTwo() throws Exception { String filename = "data/hin/molecule2.hin"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); HINReader reader = new HINReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(37, m.getAtomCount()); + Assert.assertNotNull(m); + Assert.assertEquals(37, m.getAtomCount()); // assertEquals(?, m.getBondCount()); } - public void testMultiple() throws Exception { + @Test public void testMultiple() throws Exception { String filename = "data/hin/multiple.hin"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); HINReader reader = new HINReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(3, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(3, som.getMoleculeCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,13 +29,11 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.io.INChIPlainTextReader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -46,49 +44,45 @@ * @see org.openscience.cdk.io.INChIReader * @cdk.require java1.4+ */ -public class INChIPlainTextReaderTest extends CDKTestCase { +public class INChIPlainTextReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public INChIPlainTextReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(INChIPlainTextReaderTest.class); + setChemObjectIO(new INChIPlainTextReader()); } - public static Test suite() { - return new TestSuite(INChIPlainTextReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { INChIPlainTextReader reader = new INChIPlainTextReader(); - assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); } /** * Test a INChI 1.12Beta file containing the two tautomers * of guanine. */ - public void testGuanine() throws Exception { + @Test public void testGuanine() throws Exception { String filename = "data/inchi/guanine.inchi"; logger.info("Testing: ", filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); INChIPlainTextReader reader = new INChIPlainTextReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet(); - assertNotNull(moleculeSet); + Assert.assertNotNull(moleculeSet); org.openscience.cdk.interfaces.IMolecule molecule = moleculeSet.getMolecule(0); - assertNotNull(molecule); + Assert.assertNotNull(molecule); - assertEquals(11, molecule.getAtomCount()); - assertEquals(12, molecule.getBondCount()); + Assert.assertEquals(11, molecule.getAtomCount()); + Assert.assertEquals(12, molecule.getBondCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,13 +29,11 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.io.INChIReader; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -46,49 +44,44 @@ * @see org.openscience.cdk.io.INChIReader * @cdk.require java1.4+ */ -public class INChIReaderTest extends CDKTestCase { +public class INChIReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public INChIReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(INChIReaderTest.class); + setChemObjectIO(new INChIReader()); } - - public static Test suite() { - return new TestSuite(INChIReaderTest.class); + + @Test public void testAccepts() { + Assert.assertTrue(chemObjectIO.accepts(ChemFile.class)); } - public void testAccepts() { - INChIReader reader = new INChIReader(); - assertTrue(reader.accepts(ChemFile.class)); - } - /** * Test a INChI 1.1Beta file containing the two tautomers * of guanine. */ - public void testGuanine() throws Exception { + @Test public void testGuanine() throws Exception { String filename = "data/inchi/guanine.inchi.xml"; logger.info("Testing: ", filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); INChIReader reader = new INChIReader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet(); - assertNotNull(moleculeSet); + Assert.assertNotNull(moleculeSet); org.openscience.cdk.interfaces.IMolecule molecule = moleculeSet.getMolecule(0); - assertNotNull(molecule); + Assert.assertNotNull(molecule); - assertEquals(11, molecule.getAtomCount()); - assertEquals(12, molecule.getBondCount()); + Assert.assertEquals(11, molecule.getAtomCount()); + Assert.assertEquals(12, molecule.getBondCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -28,10 +28,9 @@ import java.io.StringReader; import java.util.List; -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.CDKTestCase; +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemModel; import org.openscience.cdk.ChemObject; @@ -41,6 +40,7 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.nonotify.NNMolecule; +import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -52,28 +52,24 @@ * @see org.openscience.cdk.io.MDLReader * @see org.openscience.cdk.io.SDFReaderTest */ -public class MDLReaderTest extends CDKTestCase { +public class MDLReaderTest extends ChemObjectIOTest { - private org.openscience.cdk.tools.LoggingTool logger; + private static LoggingTool logger; - public MDLReaderTest(String name) { - super(name); - logger = new org.openscience.cdk.tools.LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(MDLReaderTest.class); + setChemObjectIO(new MDLReader()); } - public static Test suite() { - return new TestSuite(MDLReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { MDLReader reader = new MDLReader(); reader.setReaderMode(Mode.STRICT); - assertTrue(reader.accepts(ChemFile.class)); - assertTrue(reader.accepts(ChemModel.class)); - assertTrue(reader.accepts(Molecule.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemModel.class)); + Assert.assertTrue(reader.accepts(Molecule.class)); } - public void testReadFromStringReader() throws Exception { + @Test public void testReadFromStringReader() throws Exception { String mdl = "cyclopropane.mol\n" + "\n" + @@ -99,40 +95,40 @@ " 3 9 1 0 0 0\n"; MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT); ChemFile chemFile = (ChemFile) reader.read(new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(9, m.getAtomCount()); - assertEquals(9, m.getBondCount()); + Assert.assertNotNull(m); + Assert.assertEquals(9, m.getAtomCount()); + Assert.assertEquals(9, m.getBondCount()); } /** * @cdk.bug 1542467 */ - public void testBug1542467() throws Exception { + @Test public void testBug1542467() throws Exception { String filename = "data/mdl/Strychnine_nichtOK.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLReader reader = new MDLReader(ins, Mode.STRICT); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue((containersList.get(0)).getAtomCount() > 0); - assertTrue((containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue((containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue((containersList.get(0)).getBondCount() > 0); } - public void testReadProton() throws Exception { + @Test public void testReadProton() throws Exception { String mdl = "proton.mol\n" + "\n" + @@ -141,36 +137,36 @@ " -0.0073 -0.5272 0.9655 H 0 3 0 0 0\n"; MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT); Molecule mol = (Molecule)reader.read(new Molecule()); - assertNotNull(mol); - assertEquals(1, mol.getAtomCount()); - assertEquals(0, mol.getBondCount()); + Assert.assertNotNull(mol); + Assert.assertEquals(1, mol.getAtomCount()); + Assert.assertEquals(0, mol.getBondCount()); IAtom atom = mol.getAtom(0); - assertEquals(1, atom.getFormalCharge().intValue()); + Assert.assertEquals(1, atom.getFormalCharge().intValue()); } /** * The corrupt file is really ok; it is just not V2000 material. */ - public void testSDF() throws Exception { + @Test public void testSDF() throws Exception { String filename = "data/mdl/prev2000.sd"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLReader reader = new MDLReader(ins, Mode.STRICT); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(2, containersList.size()); - assertEquals(39, (containersList.get(0)).getAtomCount()); - assertEquals(41, (containersList.get(0)).getBondCount()); - assertEquals(29, (containersList.get(1)).getAtomCount()); - assertEquals(28, (containersList.get(1)).getBondCount()); + Assert.assertEquals(2, containersList.size()); + Assert.assertEquals(39, (containersList.get(0)).getAtomCount()); + Assert.assertEquals(41, (containersList.get(0)).getBondCount()); + Assert.assertEquals(29, (containersList.get(1)).getAtomCount()); + Assert.assertEquals(28, (containersList.get(1)).getBondCount()); } - public void testEmptyString() throws Exception { + @Test public void testEmptyString() throws Exception { String emptyString = ""; MDLReader reader = new MDLReader(new StringReader(emptyString), Mode.STRICT); IMolecule mol = (IMolecule)reader.read(new NNMolecule()); - assertNull(mol); + Assert.assertNull(mol); } } Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-04 06:55:28 UTC (rev 11497) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-04 08:22:58 UTC (rev 11498) @@ -29,6 +29,7 @@ import org.openscience.cdk.IoCoverageTest; import org.openscience.cdk.io.CDKSourceCodeWriterTest; +import org.openscience.cdk.io.CTXReaderTest; import org.openscience.cdk.io.ChemObjectIOInstantionTests; import org.openscience.cdk.io.CrystClustReaderTest; import org.openscience.cdk.io.GamessReaderTest; @@ -161,16 +162,16 @@ suite.addTest(IoCoverageTest.suite()); suite.addTest(CMLIOTests.suite()); - suite.addTest(CrystClustReaderTest.suite()); + suite.addTest(new JUnit4TestAdapter(CrystClustReaderTest.class)); suite.addTest(new JUnit4TestAdapter(CDKSourceCodeWriterTest.class)); + suite.addTest(new JUnit4TestAdapter(CTXReaderTest.class)); suite.addTest(GamessReaderTest.suite()); - suite.addTest(Gaussian98ReaderTest.suite()); - suite.addTest(GhemicalReaderTest.suite()); - suite.addTest(HINReaderTest.suite()); - //suite.addTest(IChIReaderTest.suite()); - suite.addTest(INChIReaderTest.suite()); - suite.addTest(INChIPlainTextReaderTest.suite()); - suite.addTest(MDLReaderTest.suite()); + suite.addTest(new JUnit4TestAdapter(Gaussian98ReaderTest.class)); + suite.addTest(new JUnit4TestAdapter(GhemicalReaderTest.class)); + suite.addTest(new JUnit4TestAdapter(HINReaderTest.class)); + suite.addTest(new JUnit4TestAdapter(INChIReaderTest.class)); + suite.addTest(new JUnit4TestAdapter(INChIPlainTextReaderTest.class)); + suite.addTest(new JUnit4TestAdapter(MDLReaderTest.class)); suite.addTest(MDLV2000ReaderTest.suite()); suite.addTest(MDLV3000ReaderTest.suite()); suite.addTest(SDFReaderTest.suite()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-07-04 12:01:16
|
Revision: 11499 http://cdk.svn.sourceforge.net/cdk/?rev=11499&view=rev Author: egonw Date: 2008-07-04 05:01:02 -0700 (Fri, 04 Jul 2008) Log Message: ----------- More JUnit4 conversion Modified Paths: -------------- cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/MDLWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/Mol2ReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PCCompoundASNReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PCCompoundXMLReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PDBReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/PDBWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/SDFReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/SMILESReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/ShelXReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/VASPReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZReaderTest.java cdk/trunk/src/test/org/openscience/cdk/io/XYZWriterTest.java cdk/trunk/src/test/org/openscience/cdk/io/ZMatrixReaderTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MexperimentalTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmilesTests.java Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNReaderTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -30,10 +30,9 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.CDKTestCase; +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemModel; import org.openscience.cdk.Molecule; @@ -58,30 +57,26 @@ * * @see org.openscience.cdk.io.MDLRXNReader */ -public class MDLRXNReaderTest extends CDKTestCase { +public class MDLRXNReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public MDLRXNReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(MDLV2000ReaderTest.class); + setChemObjectIO(new MDLV2000Reader()); } - public static Test suite() { - return new TestSuite(MDLRXNReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { MDLRXNReader reader = new MDLRXNReader(); - assertTrue(reader.accepts(ChemFile.class)); - assertTrue(reader.accepts(ChemModel.class)); - assertTrue(reader.accepts(Reaction.class)); - assertTrue(reader.accepts(ReactionSet.class)); - assertFalse(reader.accepts(MoleculeSet.class)); - assertFalse(reader.accepts(Molecule.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemModel.class)); + Assert.assertTrue(reader.accepts(Reaction.class)); + Assert.assertTrue(reader.accepts(ReactionSet.class)); + Assert.assertFalse(reader.accepts(MoleculeSet.class)); + Assert.assertFalse(reader.accepts(Molecule.class)); } - public void testReadReactions1() throws Exception { + @Test public void testReadReactions1() throws Exception { String filename1 = "data/mdl/reaction-1.rxn"; logger.info("Testing: " + filename1); InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename1); @@ -90,20 +85,20 @@ reaction1 = (IReaction)reader1.read(reaction1); reader1.close(); - assertNotNull(reaction1); - assertEquals(2, reaction1.getReactantCount()); - assertEquals(1, reaction1.getProductCount()); + Assert.assertNotNull(reaction1); + Assert.assertEquals(2, reaction1.getReactantCount()); + Assert.assertEquals(1, reaction1.getProductCount()); IMoleculeSet educts = reaction1.getReactants(); // Check Atom symbols of first educt String[] atomSymbolsOfEduct1 = { "C", "C", "O", "Cl"}; for (int i = 0; i < educts.getMolecule(0).getAtomCount(); i++) { - assertEquals(atomSymbolsOfEduct1[i], educts.getMolecule(0).getAtom(i).getSymbol()); + Assert.assertEquals(atomSymbolsOfEduct1[i], educts.getMolecule(0).getAtom(i).getSymbol()); } // Check Atom symbols of second educt for (int i = 0; i < educts.getMolecule(1).getAtomCount(); i++) { - assertEquals("C", educts.getMolecule(1).getAtom(i).getSymbol()); + Assert.assertEquals("C", educts.getMolecule(1).getAtom(i).getSymbol()); } // Check Atom symbols of first product @@ -120,11 +115,11 @@ "C" }; for (int i = 0; i < products.getMolecule(0).getAtomCount(); i++) { - assertEquals(atomSymbolsOfProduct1[i], products.getMolecule(0).getAtom(i).getSymbol()); + Assert.assertEquals(atomSymbolsOfProduct1[i], products.getMolecule(0).getAtom(i).getSymbol()); } } - public void testReadReactions2() throws Exception { + @Test public void testReadReactions2() throws Exception { String filename2 = "data/mdl/reaction-2.rxn"; logger.info("Testing: " + filename2); InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(filename2); @@ -133,12 +128,12 @@ reaction2 = (IReaction)reader2.read(reaction2); reader2.close(); - assertNotNull(reaction2); - assertEquals(2, reaction2.getReactantCount()); - assertEquals(2, reaction2.getProductCount()); + Assert.assertNotNull(reaction2); + Assert.assertEquals(2, reaction2.getReactantCount()); + Assert.assertEquals(2, reaction2.getProductCount()); } - public void testReadMapping() throws Exception { + @Test public void testReadMapping() throws Exception { String filename2 = "data/mdl/mappingTest.rxn"; logger.info("Testing: " + filename2); InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(filename2); @@ -147,91 +142,91 @@ reaction2 = (IReaction)reader2.read(reaction2); reader2.close(); - assertNotNull(reaction2); + Assert.assertNotNull(reaction2); java.util.Iterator maps = reaction2.mappings(); maps.next(); - assertTrue(maps.hasNext()); + Assert.assertTrue(maps.hasNext()); } /** * */ - public void testRDFChemFile() throws Exception { + @Test public void testRDFChemFile() throws Exception { String filename = "data/mdl/qsar-reaction-test.rdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLRXNReader reader = new MDLRXNReader(ins); IChemFile chemFile = (IChemFile)reader.read(new NNChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReactionCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactantCount()); - assertEquals(3, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactants().getMolecule(0).getAtomCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactants().getMolecule(1).getAtomCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProductCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProducts().getMolecule(0).getAtomCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProducts().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReactionCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactantCount()); + Assert.assertEquals(3, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getReactants().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProductCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(0).getProducts().getMolecule(1).getAtomCount()); - assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getReactantCount()); - assertEquals(3, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getReactants().getMolecule(0).getAtomCount()); - assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getProductCount()); - assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getReactantCount()); + Assert.assertEquals(3, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getProductCount()); + Assert.assertEquals(2, chemFile.getChemSequence(0).getChemModel(0).getReactionSet().getReaction(1).getProducts().getMolecule(0).getAtomCount()); } /** * */ - public void testRDFModel() throws Exception { + @Test public void testRDFModel() throws Exception { String filename = "data/mdl/qsar-reaction-test.rdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLRXNReader reader = new MDLRXNReader(ins); IChemModel chemModel = (IChemModel)reader.read(new NNChemModel()); - assertNotNull(chemModel); + Assert.assertNotNull(chemModel); - assertEquals(2, chemModel.getReactionSet().getReactionCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(0).getReactantCount()); - assertEquals(3, chemModel.getReactionSet().getReaction(0).getReactants().getMolecule(0).getAtomCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(0).getReactants().getMolecule(1).getAtomCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(0).getProductCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(0).getProducts().getMolecule(0).getAtomCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(0).getProducts().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReactionCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(0).getReactantCount()); + Assert.assertEquals(3, chemModel.getReactionSet().getReaction(0).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(0).getReactants().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(0).getProductCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(0).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(0).getProducts().getMolecule(1).getAtomCount()); - assertEquals(1, chemModel.getReactionSet().getReaction(1).getReactantCount()); - assertEquals(3, chemModel.getReactionSet().getReaction(1).getReactants().getMolecule(0).getAtomCount()); - assertEquals(1, chemModel.getReactionSet().getReaction(1).getProductCount()); - assertEquals(2, chemModel.getReactionSet().getReaction(1).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, chemModel.getReactionSet().getReaction(1).getReactantCount()); + Assert.assertEquals(3, chemModel.getReactionSet().getReaction(1).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, chemModel.getReactionSet().getReaction(1).getProductCount()); + Assert.assertEquals(2, chemModel.getReactionSet().getReaction(1).getProducts().getMolecule(0).getAtomCount()); } /** * */ - public void testRDFReactioniSet() throws Exception { + @Test public void testRDFReactioniSet() throws Exception { String filename = "data/mdl/qsar-reaction-test.rdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLRXNReader reader = new MDLRXNReader(ins); IReactionSet reactionSet = (IReactionSet)reader.read(new NNReactionSet()); - assertNotNull(reactionSet); + Assert.assertNotNull(reactionSet); - assertEquals(2, reactionSet.getReactionCount()); - assertEquals(2, reactionSet.getReaction(0).getReactantCount()); - assertEquals(3, reactionSet.getReaction(0).getReactants().getMolecule(0).getAtomCount()); - assertEquals(2, reactionSet.getReaction(0).getReactants().getMolecule(1).getAtomCount()); - assertEquals(2, reactionSet.getReaction(0).getProductCount()); - assertEquals(2, reactionSet.getReaction(0).getProducts().getMolecule(0).getAtomCount()); - assertEquals(2, reactionSet.getReaction(0).getProducts().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, reactionSet.getReactionCount()); + Assert.assertEquals(2, reactionSet.getReaction(0).getReactantCount()); + Assert.assertEquals(3, reactionSet.getReaction(0).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, reactionSet.getReaction(0).getReactants().getMolecule(1).getAtomCount()); + Assert.assertEquals(2, reactionSet.getReaction(0).getProductCount()); + Assert.assertEquals(2, reactionSet.getReaction(0).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, reactionSet.getReaction(0).getProducts().getMolecule(1).getAtomCount()); - assertEquals(1, reactionSet.getReaction(1).getReactantCount()); - assertEquals(3, reactionSet.getReaction(1).getReactants().getMolecule(0).getAtomCount()); - assertEquals(1, reactionSet.getReaction(1).getProductCount()); - assertEquals(2, reactionSet.getReaction(1).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, reactionSet.getReaction(1).getReactantCount()); + Assert.assertEquals(3, reactionSet.getReaction(1).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, reactionSet.getReaction(1).getProductCount()); + Assert.assertEquals(2, reactionSet.getReaction(1).getProducts().getMolecule(0).getAtomCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -26,17 +26,15 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemModel; import org.openscience.cdk.Reaction; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.io.MDLRXNV2000Reader; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -46,30 +44,26 @@ * * @see org.openscience.cdk.io.MDLRXNReader */ -public class MDLRXNV2000ReaderTest extends CDKTestCase { +public class MDLRXNV2000ReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public MDLRXNV2000ReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() throws Exception { + logger = new LoggingTool(MDLRXNV2000ReaderTest.class); + setChemObjectIO(new MDLRXNV2000Reader()); } - public static Test suite() { - return new TestSuite(MDLRXNV2000ReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { MDLRXNV2000Reader reader = new MDLRXNV2000Reader(); - assertTrue(reader.accepts(ChemFile.class)); - assertTrue(reader.accepts(ChemModel.class)); - assertTrue(reader.accepts(Reaction.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemModel.class)); + Assert.assertTrue(reader.accepts(Reaction.class)); } /** * @cdk.bug 1849923 */ - public void testReadReactions1() throws Exception { + @Test public void testReadReactions1() throws Exception { String filename1 = "data/mdl/0024.stg02.rxn"; logger.info("Testing: " + filename1); InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename1); @@ -78,24 +72,24 @@ reaction1 = (IReaction)reader1.read(reaction1); reader1.close(); - assertNotNull(reaction1); - assertEquals(1, reaction1.getReactantCount()); - assertEquals(1, reaction1.getProductCount()); + Assert.assertNotNull(reaction1); + Assert.assertEquals(1, reaction1.getReactantCount()); + Assert.assertEquals(1, reaction1.getProductCount()); IAtomContainer reactant = reaction1.getReactants().getAtomContainer(0); - assertNotNull(reactant); - assertEquals(46, reactant.getAtomCount()); - assertEquals(44, reactant.getBondCount()); + Assert.assertNotNull(reactant); + Assert.assertEquals(46, reactant.getAtomCount()); + Assert.assertEquals(44, reactant.getBondCount()); IAtomContainer product = reaction1.getProducts().getAtomContainer(0); - assertNotNull(product); - assertEquals(46, product.getAtomCount()); - assertEquals(43, product.getBondCount()); + Assert.assertNotNull(product); + Assert.assertEquals(46, product.getAtomCount()); + Assert.assertEquals(43, product.getBondCount()); } /** * @cdk.bug 1851202 */ - public void testBug1851202() throws Exception { + @Test public void testBug1851202() throws Exception { String filename1 = "data/mdl/0002.stg01.rxn"; logger.info("Testing: " + filename1); InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename1); @@ -104,17 +98,17 @@ reaction1 = (IReaction)reader1.read(reaction1); reader1.close(); - assertNotNull(reaction1); - assertEquals(1, reaction1.getReactantCount()); - assertEquals(1, reaction1.getProductCount()); + Assert.assertNotNull(reaction1); + Assert.assertEquals(1, reaction1.getReactantCount()); + Assert.assertEquals(1, reaction1.getProductCount()); IAtomContainer reactant = reaction1.getReactants().getAtomContainer(0); - assertNotNull(reactant); - assertEquals(30, reactant.getAtomCount()); - assertEquals(25, reactant.getBondCount()); + Assert.assertNotNull(reactant); + Assert.assertEquals(30, reactant.getAtomCount()); + Assert.assertEquals(25, reactant.getBondCount()); IAtomContainer product = reaction1.getProducts().getAtomContainer(0); - assertNotNull(product); - assertEquals(30, product.getAtomCount()); - assertEquals(26, product.getBondCount()); + Assert.assertNotNull(product); + Assert.assertEquals(30, product.getAtomCount()); + Assert.assertEquals(26, product.getBondCount()); } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -30,16 +30,14 @@ import java.io.InputStream; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.ChemModel; import org.openscience.cdk.Reaction; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.io.MDLRXNV3000Reader; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -49,29 +47,25 @@ * * @see org.openscience.cdk.io.MDLRXNReader */ -public class MDLRXNV3000ReaderTest extends CDKTestCase { +public class MDLRXNV3000ReaderTest extends ChemObjectIOTest { - private LoggingTool logger; + private static LoggingTool logger; - public MDLRXNV3000ReaderTest(String name) { - super(name); - logger = new LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(MDLRXNV3000ReaderTest.class); + setChemObjectIO(new MDLRXNV3000Reader()); } - public static Test suite() { - return new TestSuite(MDLRXNV3000ReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { MDLRXNV3000Reader reader = new MDLRXNV3000Reader(); - assertTrue(reader.accepts(ChemModel.class)); - assertTrue(reader.accepts(Reaction.class)); + Assert.assertTrue(reader.accepts(ChemModel.class)); + Assert.assertTrue(reader.accepts(Reaction.class)); } /** * @cdk.bug 1849925 */ - public void testReadReactions1() throws Exception { + @Test public void testReadReactions1() throws Exception { String filename1 = "data/mdl/reaction_v3.rxn"; logger.info("Testing: " + filename1); InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename1); @@ -80,17 +74,17 @@ reaction1 = (IReaction)reader1.read(reaction1); reader1.close(); - assertNotNull(reaction1); - assertEquals(1, reaction1.getReactantCount()); - assertEquals(1, reaction1.getProductCount()); + Assert.assertNotNull(reaction1); + Assert.assertEquals(1, reaction1.getReactantCount()); + Assert.assertEquals(1, reaction1.getProductCount()); IAtomContainer reactant = reaction1.getReactants().getAtomContainer(0); - assertNotNull(reactant); - assertEquals(32, reactant.getAtomCount()); - assertEquals(29, reactant.getBondCount()); + Assert.assertNotNull(reactant); + Assert.assertEquals(32, reactant.getAtomCount()); + Assert.assertEquals(29, reactant.getBondCount()); IAtomContainer product = reaction1.getProducts().getAtomContainer(0); - assertNotNull(product); - assertEquals(32, product.getAtomCount()); - assertEquals(29, product.getBondCount()); + Assert.assertNotNull(product); + Assert.assertEquals(32, product.getAtomCount()); + Assert.assertEquals(29, product.getBondCount()); } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNWriterTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNWriterTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLRXNWriterTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -30,21 +30,17 @@ import java.io.StringReader; import java.io.StringWriter; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.Reaction; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; -import org.openscience.cdk.io.MDLRXNReader; -import org.openscience.cdk.io.MDLRXNWriter; import org.openscience.cdk.nonotify.NNReactionSet; -import org.openscience.cdk.CDKTestCase; /** * TestCase for the writer MDL rxn files using one test file. @@ -53,28 +49,21 @@ * * @see org.openscience.cdk.io.MDLRXNWriter */ -public class MDLRXNWriterTest extends CDKTestCase { +public class MDLRXNWriterTest extends ChemObjectIOTest { - private IChemObjectBuilder builder; + private static IChemObjectBuilder builder; - public MDLRXNWriterTest(String name) { - super(name); + @BeforeClass public static void setup() { + builder = DefaultChemObjectBuilder.getInstance(); + setChemObjectIO(new MDLRXNWriter()); } - public void setUp() { - builder = DefaultChemObjectBuilder.getInstance(); - } - - public static Test suite() { - return new TestSuite(MDLRXNWriterTest.class); - } - - public void testAccepts() throws Exception { + @Test public void testAccepts() throws Exception { MDLRXNWriter reader = new MDLRXNWriter(); - assertTrue(reader.accepts(Reaction.class)); + Assert.assertTrue(reader.accepts(Reaction.class)); } - public void testRoundtrip() throws Exception { + @Test public void testRoundtrip() throws Exception { IReaction reaction = builder.newReaction(); IMolecule hydroxide = builder.newMolecule(); hydroxide.addAtom(builder.newAtom("O")); @@ -94,7 +83,7 @@ mdlWriter.close(); file = writer.toString(); - assertTrue(file.length() > 0); + Assert.assertTrue(file.length() > 0); // now deserialize the MDL RXN output IReaction reaction2 = builder.newReaction(); @@ -102,11 +91,11 @@ reaction2 = (IReaction)reader.read(reaction2); reader.close(); - assertEquals(2, reaction2.getReactantCount()); - assertEquals(1, reaction2.getProductCount()); + Assert.assertEquals(2, reaction2.getReactantCount()); + Assert.assertEquals(1, reaction2.getProductCount()); } - public void testReactionSet_1() throws Exception { + @Test public void testReactionSet_1() throws Exception { IReaction reaction11 = builder.newReaction(); IMolecule hydroxide = builder.newMolecule(); hydroxide.addAtom(builder.newAtom("O")); @@ -130,7 +119,7 @@ mdlWriter.close(); file = writer.toString(); - assertTrue(file.length() > 0); + Assert.assertTrue(file.length() > 0); // now deserialize the MDL RXN output IReaction reaction2 = builder.newReaction(); @@ -138,15 +127,15 @@ reaction2 = (IReaction)reader.read(reaction2); reader.close(); - assertEquals(2, reaction2.getReactantCount()); - assertEquals(1, reaction2.getReactants().getMolecule(0).getAtomCount()); - assertEquals(1, reaction2.getReactants().getMolecule(1).getAtomCount()); - assertEquals(1, reaction2.getProductCount()); - assertEquals(1, reaction2.getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, reaction2.getReactantCount()); + Assert.assertEquals(1, reaction2.getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, reaction2.getReactants().getMolecule(1).getAtomCount()); + Assert.assertEquals(1, reaction2.getProductCount()); + Assert.assertEquals(1, reaction2.getProducts().getMolecule(0).getAtomCount()); } - public void testReactionSet_2() throws Exception { + @Test public void testReactionSet_2() throws Exception { IReaction reaction11 = builder.newReaction(); IMolecule hydroxide = builder.newMolecule(); hydroxide.addAtom(builder.newAtom("O")); @@ -184,7 +173,7 @@ mdlWriter.close(); file = writer.toString(); - assertTrue(file.length() > 0); + Assert.assertTrue(file.length() > 0); // now deserialize the MDL RXN output IReactionSet reactionSetF = builder.newReactionSet(); @@ -192,11 +181,11 @@ reactionSetF = (IReactionSet)reader.read(reactionSetF); reader.close(); - assertEquals(2, reactionSetF.getReactionCount()); - assertEquals(1, reactionSetF.getReaction(0).getReactants().getMolecule(0).getAtomCount()); - assertEquals(1, reactionSetF.getReaction(0).getReactants().getMolecule(1).getAtomCount()); - assertEquals(1, reactionSetF.getReaction(0).getProductCount()); - assertEquals(1, reactionSetF.getReaction(0).getProducts().getMolecule(0).getAtomCount()); + Assert.assertEquals(2, reactionSetF.getReactionCount()); + Assert.assertEquals(1, reactionSetF.getReaction(0).getReactants().getMolecule(0).getAtomCount()); + Assert.assertEquals(1, reactionSetF.getReaction(0).getReactants().getMolecule(1).getAtomCount()); + Assert.assertEquals(1, reactionSetF.getReaction(0).getProductCount()); + Assert.assertEquals(1, reactionSetF.getReaction(0).getProducts().getMolecule(0).getAtomCount()); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -32,11 +32,10 @@ import java.util.Properties; import java.util.Set; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemModel; import org.openscience.cdk.ChemObject; @@ -55,6 +54,7 @@ import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.io.listener.PropertiesListener; import org.openscience.cdk.nonotify.NNMolecule; +import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -67,230 +67,226 @@ * @see org.openscience.cdk.io.MDLV2000Reader * @see org.openscience.cdk.io.SDFReaderTest */ -public class MDLV2000ReaderTest extends CDKTestCase { +public class MDLV2000ReaderTest extends ChemObjectIOTest { - private org.openscience.cdk.tools.LoggingTool logger; + private static LoggingTool logger; - public MDLV2000ReaderTest(String name) { - super(name); - logger = new org.openscience.cdk.tools.LoggingTool(this); + @BeforeClass public static void setup() { + logger = new LoggingTool(MDLV2000ReaderTest.class); + setChemObjectIO(new MDLV2000Reader()); } - public static Test suite() { - return new TestSuite(MDLV2000ReaderTest.class); - } - - public void testAccepts() { + @Test public void testAccepts() { MDLV2000Reader reader = new MDLV2000Reader(); - assertTrue(reader.accepts(ChemFile.class)); - assertTrue(reader.accepts(ChemModel.class)); - assertTrue(reader.accepts(Molecule.class)); + Assert.assertTrue(reader.accepts(ChemFile.class)); + Assert.assertTrue(reader.accepts(ChemModel.class)); + Assert.assertTrue(reader.accepts(Molecule.class)); } /** * @cdk.bug 682233 */ - public void testBug682233() throws Exception { + @Test public void testBug682233() throws Exception { String filename = "data/mdl/bug682233.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(4, m.getAtomCount()); - assertEquals(2, m.getBondCount()); + Assert.assertNotNull(m); + Assert.assertEquals(4, m.getAtomCount()); + Assert.assertEquals(2, m.getBondCount()); // test reading of formal charges org.openscience.cdk.interfaces.IAtom a = m.getAtom(0); - assertNotNull(a); - assertEquals("Na", a.getSymbol()); - assertEquals(1, a.getFormalCharge().intValue()); + Assert.assertNotNull(a); + Assert.assertEquals("Na", a.getSymbol()); + Assert.assertEquals(1, a.getFormalCharge().intValue()); a = m.getAtom(2); - assertNotNull(a); - assertEquals("O", a.getSymbol()); - assertEquals(-1, a.getFormalCharge().intValue()); + Assert.assertNotNull(a); + Assert.assertEquals("O", a.getSymbol()); + Assert.assertEquals(-1, a.getFormalCharge().intValue()); } - public void testAPinene() throws Exception { + @Test public void testAPinene() throws Exception { String filename = "data/mdl/a-pinene.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testAlkane() throws Exception { + @Test public void testAlkane() throws Exception { String filename = "data/mdl/shortest_path_test.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); + Assert.assertEquals(1, containersList.size()); IAtomContainer container = (IAtomContainer)containersList.get(0); - assertEquals(10, container.getAtomCount()); - assertEquals(9, container.getBondCount()); + Assert.assertEquals(10, container.getAtomCount()); + Assert.assertEquals(9, container.getBondCount()); Iterator<IAtom> atoms = container.atoms(); while (atoms.hasNext()) { - assertEquals("C", atoms.next().getSymbol()); + Assert.assertEquals("C", atoms.next().getSymbol()); } Iterator<IBond> bonds = container.bonds(); while (bonds.hasNext()) { - assertEquals(CDKConstants.BONDORDER_SINGLE, bonds.next().getOrder()); + Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bonds.next().getOrder()); } } - public void testReadTitle() throws Exception { + @Test public void testReadTitle() throws Exception { String filename = "data/mdl/a-pinene.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - assertEquals("a-pinen.mol", mol.getProperty(CDKConstants.TITLE)); + Assert.assertEquals("a-pinen.mol", mol.getProperty(CDKConstants.TITLE)); } - public void testFourRing() throws Exception { + @Test public void testFourRing() throws Exception { String filename = "data/mdl/four-ring-5x10.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testHydrozyamino() throws Exception { + @Test public void testHydrozyamino() throws Exception { String filename = "data/mdl/hydroxyamino.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testMethylBenzol() throws Exception { + @Test public void testMethylBenzol() throws Exception { String filename = "data/mdl/methylbenzol.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testPolycarpol() throws Exception { + @Test public void testPolycarpol() throws Exception { String filename = "data/mdl/polycarpol.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testReserpine() throws Exception { + @Test public void testReserpine() throws Exception { String filename = "data/mdl/reserpine.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testSixRing() throws Exception { + @Test public void testSixRing() throws Exception { String filename = "data/mdl/six-ring-4x4.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testSuperspiro() throws Exception { + @Test public void testSuperspiro() throws Exception { String filename = "data/mdl/superspiro.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testGhemicalOutput() throws Exception { + @Test public void testGhemicalOutput() throws Exception { String filename = "data/mdl/butanoic_acid.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); - assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0); } - public void testUsesGivenMolecule() throws Exception { + @Test public void testUsesGivenMolecule() throws Exception { String filename = "data/mdl/superspiro.mol"; // just a random file InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); Molecule superspiro = new Molecule(); superspiro.setID("superspiro"); Molecule result = (Molecule)reader.read(superspiro); - assertEquals(superspiro.getID(), result.getID()); + Assert.assertEquals(superspiro.getID(), result.getID()); } /** * @cdk.bug 835571 */ - public void testReadFromStringReader () throws Exception { + @Test public void testReadFromStringReader () throws Exception { String mdl = "cyclopropane.mol\n" + "\n" + @@ -317,60 +313,60 @@ "M END\n"; MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl)); ChemFile chemFile = (ChemFile) reader.read(new ChemFile()); - assertNotNull(chemFile); - assertEquals(1, chemFile.getChemSequenceCount()); + Assert.assertNotNull(chemFile); + Assert.assertEquals(1, chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); - assertNotNull(seq); - assertEquals(1, seq.getChemModelCount()); + Assert.assertNotNull(seq); + Assert.assertEquals(1, seq.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); - assertNotNull(model); + Assert.assertNotNull(model); org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet(); - assertNotNull(som); - assertEquals(1, som.getMoleculeCount()); + Assert.assertNotNull(som); + Assert.assertEquals(1, som.getMoleculeCount()); org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0); - assertNotNull(m); - assertEquals(9, m.getAtomCount()); - assertEquals(9, m.getBondCount()); + Assert.assertNotNull(m); + Assert.assertEquals(9, m.getAtomCount()); + Assert.assertEquals(9, m.getBondCount()); } - public void testRGroup() throws Exception { + @Test public void testRGroup() throws Exception { String filename = "data/mdl/SARGROUPTEST.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - assertEquals("R2",((PseudoAtom)mol.getAtom(19)).getLabel()); + Assert.assertEquals("R2",((PseudoAtom)mol.getAtom(19)).getLabel()); } - public void testAliasPropertyGroup() throws Exception { + @Test public void testAliasPropertyGroup() throws Exception { String filename = "data/mdl/AliasPropertyRGroup.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); IAtom atom = mol.getAtom(3); - assertTrue(atom instanceof PseudoAtom); - assertEquals("R1", ((PseudoAtom)atom).getLabel()); + Assert.assertTrue(atom instanceof PseudoAtom); + Assert.assertEquals("R1", ((PseudoAtom)atom).getLabel()); } /** * @cdk.bug 1587283 */ - public void testBug1587283() throws Exception { + @Test public void testBug1587283() throws Exception { String filename = "data/mdl/bug1587283.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertEquals(15, ((IAtomContainer)containersList.get(0)).getAtomCount()); - assertEquals(16, ((IAtomContainer)containersList.get(0)).getBondCount()); + Assert.assertEquals(1, containersList.size()); + Assert.assertEquals(15, ((IAtomContainer)containersList.get(0)).getAtomCount()); + Assert.assertEquals(16, ((IAtomContainer)containersList.get(0)).getBondCount()); } - public void testReadProton() throws Exception { + @Test public void testReadProton() throws Exception { String mdl = "proton.mol\n" + "\n" + @@ -381,60 +377,59 @@ "M END\n"; MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl)); Molecule mol = (Molecule)reader.read(new Molecule()); - assertNotNull(mol); - assertEquals(1, mol.getAtomCount()); - assertEquals(0, mol.getBondCount()); - assertEquals(1, AtomContainerManipulator.getTotalFormalCharge(mol)); + Assert.assertNotNull(mol); + Assert.assertEquals(1, mol.getAtomCount()); + Assert.assertEquals(0, mol.getBondCount()); + Assert.assertEquals(1, AtomContainerManipulator.getTotalFormalCharge(mol)); IAtom atom = mol.getAtom(0); - assertEquals(1, atom.getFormalCharge().intValue()); + Assert.assertEquals(1, atom.getFormalCharge().intValue()); } - public void testReadingCharges() throws CDKException { + @Test public void testReadingCharges() throws CDKException { String filename = "data/mdl/withcharges.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); IChemFile chemFile = (IChemFile) reader.read((IChemObject) new org.openscience.cdk.ChemFile()); - assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(6).getFormalCharge().intValue()); - assertEquals(-1, chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(8).getFormalCharge().intValue()); + Assert.assertEquals(1, chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(6).getFormalCharge().intValue()); + Assert.assertEquals(-1, chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(8).getFormalCharge().intValue()); } - public void testEmptyString() throws Exception { + @Test public void testEmptyString() throws Exception { String emptyString = ""; MDLV2000Reader reader = new MDLV2000Reader(new StringReader(emptyString)); IMolecule mol = (IMolecule) reader.read(new NNMolecule()); - assertNull(mol); + Assert.assertNull(mol); } - public void testNoAtomCase() throws CDKException { + @Test public void testNoAtomCase() throws CDKException { String filename = "data/mdl/emptyStructure.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); + Assert.assertEquals(1, containersList.size()); IAtomContainer container = (IAtomContainer) containersList.get(0); - assertNotNull(container); - assertEquals(0, container.getAtomCount()); - assertEquals(0, container.getBondCount()); + Assert.assertNotNull(container); + Assert.assertEquals(0, container.getAtomCount()); + Assert.assertEquals(0, container.getBondCount()); Map<Object,Object> props = container.getProperties(); Set<Object> keys = props.keySet(); - assertTrue(keys.contains("SubstanceType")); - assertTrue(keys.contains("TD50 Rat")); - assertTrue(keys.contains("ChemCount")); + Assert.assertTrue(keys.contains("SubstanceType")); + Assert.assertTrue(keys.contains("TD50 Rat")); + Assert.assertTrue(keys.contains("ChemCount")); } /** * @cdk.bug 1732307 - */ - public void testZeroZCoordinates() throws CDKException { + @Test public void testZeroZCoordinates() throws CDKException { String filename = "data/mdl/nozcoord.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); @@ -446,24 +441,24 @@ reader.customizeJob(); IMolecule mol = (IMolecule) reader.read(DefaultChemObjectBuilder.getInstance().newMolecule()); - assertNotNull(mol); - assertEquals(5, mol.getAtomCount()); + Assert.assertNotNull(mol); + Assert.assertEquals(5, mol.getAtomCount()); boolean has3d = GeometryTools.has3DCoordinates(mol); - assertTrue(has3d); + Assert.assertTrue(has3d); } /** * @cdk.bug 1826577 */ - public void testHisotopes_Strict() throws Exception { + @Test public void testHisotopes_Strict() throws Exception { String filename = "data/mdl/hisotopes.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); try { MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT); reader.read((ChemObject)new ChemFile()); - fail("Expected a CDKException"); + Assert.fail("Expected a CDKException"); } catch (Exception exception) { // OK, that's what's is supposed to happen } @@ -472,34 +467,34 @@ /** * @cdk.bug 1826577 */ - public void testHisotopes_Relaxed() throws Exception { + @Test public void testHisotopes_Relaxed() throws Exception { String filename = "data/mdl/hisotopes.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.RELAXED); IChemFile chemFile = (IChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertNotNull(containersList.get(0)); - assertFalse((containersList.get(0)).getAtom(1) instanceof IPseudoAtom); - assertFalse((containersList.get(0)).getAtom(2) instanceof IPseudoAtom); + Assert.assertNotNull(containersList.get(0)); + Assert.assertFalse((containersList.get(0)).getAtom(1) instanceof IPseudoAtom); + Assert.assertFalse((containersList.get(0)).getAtom(2) instanceof IPseudoAtom); } /** * * @throws Exception */ - public void testReadRadical() throws Exception { + @Test public void testReadRadical() throws Exception { String filename = "data/mdl/332727182.radical.mol"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); - assertNotNull(chemFile); + Assert.assertNotNull(chemFile); List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); - assertEquals(1, containersList.size()); - assertTrue((containersList.get(0)).getAtomCount() > 0); - assertTrue((containersList.get(0)).getBondCount() > 0); - assertTrue((containersList.get(0)).getSingleElectronCount() > 0); + Assert.assertEquals(1, containersList.size()); + Assert.assertTrue((containersList.get(0)).getAtomCount() > 0); + Assert.assertTrue((containersList.get(0)).getBondCount() > 0); + Assert.assertTrue((containersList.get(0)).getSingleElectronCount() > 0); } } Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498) +++ cdk/trunk/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java 2008-07-04 12:01:02 UTC (rev 11499) @@ -27,16 +27,14 @@ import java.io.InputStream; import java.io.StringReader; -import junit.framework.Test; -import junit.framework.TestSuite; - +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.io.MDLV3000Reader; import org.openscience.cdk.nonotify.NNMolecule; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.LoggingTool; /** @@ -4... [truncated message content] |
From: <eg...@us...> - 2008-07-15 17:14:56
|
Revision: 11595 http://cdk.svn.sourceforge.net/cdk/?rev=11595&view=rev Author: egonw Date: 2008-07-15 10:14:54 -0700 (Tue, 15 Jul 2008) Log Message: ----------- Added unit testing for the render module Added Paths: ----------- cdk/trunk/src/test/org/openscience/cdk/RenderCoverageTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MrenderTests.java cdk/trunk/src/test/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java cdk/trunk/src/test/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java Added: cdk/trunk/src/test/org/openscience/cdk/RenderCoverageTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/RenderCoverageTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/RenderCoverageTest.java 2008-07-15 17:14:54 UTC (rev 11595) @@ -0,0 +1,52 @@ +/* $Revision: 10775 $ $Author: egonw $ $Date: 2008-05-03 08:57:44 +0200 (Sat, 03 May 2008) $ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk; + +import junit.framework.Test; +import junit.framework.TestSuite; + +/** + * @cdk.module test-render + */ +public class RenderCoverageTest extends CoverageAnnotationTest { + + private final static String CLASS_LIST = "render.javafiles"; + + public RenderCoverageTest(String name) { + super(name); + } + + protected void setUp() throws Exception { + super.setUp(); + super.loadClassList(CLASS_LIST); + } + + public static Test suite() { + TestSuite suite = new TestSuite(); + suite.addTestSuite(RenderCoverageTest.class); + return suite; + } + + public void testCoverage() { + assertTrue(super.runCoverageTest()); + } + +} \ No newline at end of file Added: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MrenderTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MrenderTests.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MrenderTests.java 2008-07-15 17:14:54 UTC (rev 11595) @@ -0,0 +1,52 @@ +/* $Revision: 10837 $ $Author: miguelrojasch $ $Date: 2008-05-05 22:55:01 +0200 (Mon, 05 May 2008) $ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.modulesuites; + +import junit.framework.JUnit4TestAdapter; +import junit.framework.Test; +import junit.framework.TestSuite; + +import org.openscience.cdk.RenderCoverageTest; +import org.openscience.cdk.renderer.color.CDKAtomColorsTest; +import org.openscience.cdk.renderer.color.CPKAtomColorsTest; + +/** + * TestSuite that runs all the tests for the CDK <code>render</code> module. + * + * @cdk.module test-render + * @cdk.depends log4j.jar + * @cdk.depends junit.jar + */ +public class MrenderTests { + + public static Test suite() { + TestSuite suite= new TestSuite("CDK render Tests"); + + suite.addTest(new JUnit4TestAdapter(RenderCoverageTest.class)); + + // from cdk.render.color + suite.addTest(new JUnit4TestAdapter(CPKAtomColorsTest.class)); + suite.addTest(new JUnit4TestAdapter(CDKAtomColorsTest.class)); + + return suite; + } + +} Added: cdk/trunk/src/test/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java 2008-07-15 17:14:54 UTC (rev 11595) @@ -0,0 +1,50 @@ +/* $Revision: 10234 $ $Author: egonw $ $Date: 2008-02-25 14:11:58 +0100 (Mon, 25 Feb 2008) $ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.renderer.color; + +import java.awt.Color; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.Atom; +import org.openscience.cdk.NewCDKTestCase; +import org.openscience.cdk.interfaces.IAtom; + +/** + * @cdk.module test-render + */ +public class CDKAtomColorsTest extends NewCDKTestCase { + + @Test public void testGetAtomColor() { + CDKAtomColors colors = new CDKAtomColors(); + Assert.assertNotNull(colors); + IAtom hydrogen = new Atom("H"); hydrogen.setAtomicNumber(1); + Assert.assertEquals(Color.white, colors.getAtomColor(hydrogen)); + IAtom helium = new Atom("He"); helium.setAtomicNumber(2); + Assert.assertEquals(Color.darkGray, colors.getAtomColor(helium)); + } + +} + Added: cdk/trunk/src/test/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java (rev 0) +++ cdk/trunk/src/test/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java 2008-07-15 17:14:54 UTC (rev 11595) @@ -0,0 +1,47 @@ +/* $Revision: 10234 $ $Author: egonw $ $Date: 2008-02-25 14:11:58 +0100 (Mon, 25 Feb 2008) $ + * + * Copyright (C) 2008 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.renderer.color; + +import java.awt.Color; + +import org.junit.Assert; +import org.junit.Test; +import org.openscience.cdk.Atom; +import org.openscience.cdk.NewCDKTestCase; + +/** + * @cdk.module test-render + */ +public class CPKAtomColorsTest extends NewCDKTestCase { + + @Test public void testGetAtomColor() { + CPKAtomColors colors = new CPKAtomColors(); + Assert.assertNotNull(colors); + Assert.assertEquals(Color.WHITE, colors.getAtomColor(new Atom("H"))); + Assert.assertEquals(Color.PINK, colors.getAtomColor(new Atom("He"))); + } + +} + This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |