/**
* Test reading from a XML config file with content like:
*
* <pre>
* <atomType id="C">
* <!-- for example in CC-->
* <atom elementType="C" formalCharge="0">
* <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
* <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:valency">4</scalar>
* </atom>
* <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:DA">-</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:sphericalMatcher">[CSP]-[0-4][-]?+;[A-Za-z\+\-&&[^=%]]{0,6}[(].*+</scalar>
* </atomType>
* </pre>
*
* @throws Exception if the atom typ info cannot be loaded
*/
@Test
public void testGetAtomTypeFromMM2() throws Exception {
AtomTypeFactory factory;
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mm2_atomtypes.xml", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C", atomType.getAtomTypeName());
Assert.assertEquals(
"[CSP]-[0-4][-]?+;[A-Za-z\\+\\-&&[^=%]]{0,6}[(].*+",
atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP3, atomType.getHybridization());
atomType = factory.getAtomType("Sthi");
Assert.assertNotNull(atomType);
Assert.assertEquals("S", atomType.getSymbol());
Assert.assertEquals("Sthi", atomType.getAtomTypeName());
Assert.assertEquals(
"S-[2];[H]{0,3}+=C.*+", atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP2, atomType.getHybridization());
Assert.assertTrue(atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
Assert.assertEquals(5, atomType.getProperty(CDKConstants.PART_OF_RING_OF_SIZE));
}
@Test
public void testGetInstance_String_IChemObjectBuilder() throws Exception {
String configFile = "org/openscience/cdk/config/data/structgen_atomtypes.xml";
AtomTypeFactory atf = AtomTypeFactory.getInstance(configFile, new ChemObject().getBuilder());
Assert.assertNotNull(atf);
Assert.assertNotSame(0, atf.getSize());
}
@Test
public void testGetAllAtomTypes() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
IAtomType[] types = atf.getAllAtomTypes();
Assert.assertNotNull(types);
Assert.assertNotSame(0, types.length);
}
@Test
public void testGetInstance_InputStream_String_IChemObjectBuilder() throws Exception {
String configFile = "org/openscience/cdk/config/data/structgen_atomtypes.xml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(configFile);
AtomTypeFactory atf = AtomTypeFactory.getInstance(ins, "xml", new ChemObject().getBuilder());
Assert.assertNotNull(atf);
Assert.assertNotSame(0, atf.getSize());
}
@Test
public void testGetAtomTypeFromJmol() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("H");
Assert.assertNotNull(atomType);
Assert.assertEquals("H", atomType.getSymbol());
Assert.assertEquals("H", atomType.getAtomTypeName());
}
@Test
public void testConfigure_IAtom() throws Exception {
IAtomType atomType;
IAtom atom = new org.openscience.cdk.Atom("X");
atom.setAtomTypeName("C.ar");
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mol2_atomtypes.xml", new ChemObject().getBuilder());
atomType = factory.configure(atom);
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atom.getSymbol());
}
@Test
public void testGetAtomTypeFromOWL() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/cdk-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.sp3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.sp3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
0, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.sp2.radical");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.sp2.radical", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP2, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(1, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(1, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.planar3");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.planar3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.PLANAR3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(3, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
}
@Test
public void testGetInstance_IChemObjectBuilder() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
Assert.assertNotNull(atf);
}
/**
* Checks the functionality of the AtomTypeFactory.
*
* @cdk.module test-core
*/
public class AtomTypeFactoryTest extends CDKTestCase {
static final AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
private static final String JAXP_SCHEMA_LANGUAGE =
"http://java.sun.com/xml/jaxp/properties/schemaLanguage";
private static final String W3C_XML_SCHEMA = "http://www.w3.org/2001/XMLSchema";
static File tmpCMLSchema;
static {
try {
InputStream in =
AtomTypeFactoryTest.class
.getClassLoader()
.getResourceAsStream("org/openscience/cdk/io/cml/data/cml25b1.xsd");
tmpCMLSchema = copyFileToTmp("cml2.5.b1", ".xsd", in, null, null);
} catch (IOException e) {
e.printStackTrace();
}
}
@Test
public void testAtomTypeFactory() {
Assert.assertNotNull(atf);
Assert.assertNotSame(atf.getSize(), 0);
}
@Test
public void testGetInstance_InputStream_String_IChemObjectBuilder() throws Exception {
String configFile = "org/openscience/cdk/config/data/structgen_atomtypes.xml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(configFile);
AtomTypeFactory atf = AtomTypeFactory.getInstance(ins, "xml", new ChemObject().getBuilder());
Assert.assertNotNull(atf);
Assert.assertNotSame(0, atf.getSize());
}
@Test
public void testGetInstance_String_IChemObjectBuilder() throws Exception {
String configFile = "org/openscience/cdk/config/data/structgen_atomtypes.xml";
AtomTypeFactory atf = AtomTypeFactory.getInstance(configFile, new ChemObject().getBuilder());
Assert.assertNotNull(atf);
Assert.assertNotSame(0, atf.getSize());
}
@Test
public void testGetInstance_IChemObjectBuilder() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
Assert.assertNotNull(atf);
}
@Test
public void testGetSize() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
Assert.assertNotSame(0, atf.getSize());
}
@Test
public void testGetAllAtomTypes() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
IAtomType[] types = atf.getAllAtomTypes();
Assert.assertNotNull(types);
Assert.assertNotSame(0, types.length);
}
@Test
public void testGetAtomType_String() throws Exception {
IAtomType atomType = atf.getAtomType("C4");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C4", atomType.getAtomTypeName());
Assert.assertEquals(4.0, atomType.getBondOrderSum(), 0.001);
Assert.assertEquals(IBond.Order.TRIPLE, atomType.getMaxBondOrder());
}
@Test
public void testGetAtomTypes_String() throws Exception {
IAtomType[] atomTypes = atf.getAtomTypes("C");
Assert.assertNotNull(atomTypes);
Assert.assertTrue(0 < atomTypes.length);
Assert.assertEquals("C", atomTypes[0].getSymbol());
}
@Test
public void testGetAtomTypeFromPDB() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/pdb_atomtypes.xml", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("ALA.CA");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("ALA.CA", atomType.getAtomTypeName());
}
@Test
public void testGetAtomTypeFromOWL() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/cdk-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.sp3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.sp3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
0, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.sp2.radical");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.sp2.radical", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP2, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(1, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(1, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.planar3");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.planar3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.PLANAR3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(3, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
}
@Test
public void testGetAtomTypeFromOWL_Sybyl() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/sybyl-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.3", atomType.getAtomTypeName());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
0, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
}
@Test
public void testGetAtomTypeFromJmol() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("H");
Assert.assertNotNull(atomType);
Assert.assertEquals("H", atomType.getSymbol());
Assert.assertEquals("H", atomType.getAtomTypeName());
}
@Test
public void testConfigure_IAtom() throws Exception {
IAtomType atomType;
IAtom atom = new org.openscience.cdk.Atom("X");
atom.setAtomTypeName("C.ar");
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mol2_atomtypes.xml", new ChemObject().getBuilder());
atomType = factory.configure(atom);
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atom.getSymbol());
}
/**
* Test reading from a XML config file with content like:
*
* <pre>
* <atomType id="C">
* <!-- for example in CC-->
* <atom elementType="C" formalCharge="0">
* <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
* <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:valency">4</scalar>
* </atom>
* <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:DA">-</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:sphericalMatcher">[CSP]-[0-4][-]?+;[A-Za-z\+\-&&[^=%]]{0,6}[(].*+</scalar>
* </atomType>
* </pre>
*
* @throws Exception if the atom typ info cannot be loaded
*/
@Test
public void testGetAtomTypeFromMM2() throws Exception {
AtomTypeFactory factory;
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mm2_atomtypes.xml", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C", atomType.getAtomTypeName());
Assert.assertEquals(
"[CSP]-[0-4][-]?+;[A-Za-z\\+\\-&&[^=%]]{0,6}[(].*+",
atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP3, atomType.getHybridization());
atomType = factory.getAtomType("Sthi");
Assert.assertNotNull(atomType);
Assert.assertEquals("S", atomType.getSymbol());
Assert.assertEquals("Sthi", atomType.getAtomTypeName());
Assert.assertEquals(
"S-[2];[H]{0,3}+=C.*+", atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP2, atomType.getHybridization());
Assert.assertTrue(atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
Assert.assertEquals(5, atomType.getProperty(CDKConstants.PART_OF_RING_OF_SIZE));
}
@Test
public void testCanReadCMLSchema() throws Exception {
InputStream cmlSchema = new FileInputStream(tmpCMLSchema);
Assert.assertNotNull("Could not find the CML schema", cmlSchema);
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// make sure the schema is read
Document schemaDoc = parser.parse(cmlSchema);
Assert.assertNotNull(schemaDoc.getFirstChild());
Assert.assertEquals("xsd:schema", schemaDoc.getFirstChild().getNodeName());
}
@Test
public void testXMLValidityMM2() throws Exception {
assertValidCML("org/openscience/cdk/config/data/mm2_atomtypes.xml", "MM2");
}
@Test
public void testXMLValidityMMFF94() throws Exception {
assertValidCML("org/openscience/cdk/config/data/mmff94_atomtypes.xml", "MMFF94");
}
@Test
public void testXMLValidityMol2() throws Exception {
assertValidCML("org/openscience/cdk/config/data/mol2_atomtypes.xml", "Mol2");
}
@Test
public void testXMLValidityPDB() throws Exception {
assertValidCML("org/openscience/cdk/config/data/pdb_atomtypes.xml", "PDB");
}
@Test
public void testXMLValidityStructGen() throws Exception {
assertValidCML("org/openscience/cdk/config/data/structgen_atomtypes.xml", "StructGen");
}
private void assertValidCML(String atomTypeList, String shortcut) throws Exception {
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(atomTypeList);
File tmpInput =
copyFileToTmp(
shortcut,
".cmlinput",
ins,
"../../io/cml/data/cml25b1.xsd",
"file://" + tmpCMLSchema.getAbsolutePath());
Assert.assertNotNull("Could not find the atom type list CML source", ins);
if (System.getProperty("java.version").indexOf("1.6") != -1
|| System.getProperty("java.version").indexOf("1.7") != -1) {
InputStream cmlSchema = new FileInputStream(tmpCMLSchema);
Assert.assertNotNull("Could not find the CML schema", cmlSchema);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
factory.setValidating(true);
factory.setAttribute(JAXP_SCHEMA_LANGUAGE, W3C_XML_SCHEMA);
factory.setAttribute(JAXP_SCHEMA_LANGUAGE, cmlSchema);
factory.setFeature("http://apache.org/xml/features/validation/schema", true);
DocumentBuilder parser = factory.newDocumentBuilder();
parser.setErrorHandler(new SAXValidityErrorHandler(shortcut));
parser.parse(new FileInputStream(tmpInput));
} else if (System.getProperty("java.version").indexOf("1.5") != -1) {
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document document = parser.parse(tmpInput);
SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Source schemaFile = new StreamSource(tmpCMLSchema);
Schema schema = factory.newSchema(schemaFile);
Validator validator = schema.newValidator();
validator.validate(new DOMSource(document));
} else {
Assert.fail(
"Don't know how to validate with Java version: " + System.getProperty("java.version"));
}
}
/**
* Copies a file to TMP (whatever that is on your platform), and optionally replaces a String on
* the fly. The temporary file will be named prefix+suffix
*
* @param prefix Prefix of the temporary file name
* @param suffix Suffix of the temporary file name
* @param in InputStream to copy from
* @param toReplace String to replace. Null, if nothing needs to be replaced.
* @param replaceWith String that replaces the toReplace. Null, if nothing needs to be replaced.
* @return The temporary file/
* @throws IOException if the temp file cannot be created
*/
private static File copyFileToTmp(
String prefix, String suffix, InputStream in, String toReplace, String replaceWith)
throws IOException {
File tmpFile = File.createTempFile(prefix, suffix);
FileOutputStream out = new FileOutputStream(tmpFile);
byte[] buf = new byte[4096];
int i;
while ((i = in.read(buf)) != -1) {
if (toReplace != null
&& replaceWith != null
&& i >= toReplace.length()
&& new String(buf).contains(toReplace)) {
// a replacement has been defined
String newString = new String(buf).replaceAll(toReplace, replaceWith);
out.write(newString.getBytes());
} else {
// no replacement needs to be done
out.write(buf, 0, i);
}
}
in.close();
out.close();
tmpFile.deleteOnExit();
return tmpFile;
}
class SAXValidityErrorHandler implements ErrorHandler {
private String atomTypeList;
public SAXValidityErrorHandler(String atomTypeList) {
this.atomTypeList = atomTypeList;
}
public void error(SAXParseException arg0) throws SAXException {
Assert.fail(
atomTypeList
+ " is not valid on line "
+ arg0.getLineNumber()
+ ": "
+ arg0.getMessage());
}
public void fatalError(SAXParseException arg0) throws SAXException {
Assert.fail(
atomTypeList
+ " is not valid on line "
+ arg0.getLineNumber()
+ ": "
+ arg0.getMessage());
}
public void warning(SAXParseException arg0) throws SAXException {
// warnings are fine
}
}
}
@Test
public void testGetSize() throws Exception {
AtomTypeFactory atf = AtomTypeFactory.getInstance(new ChemObject().getBuilder());
Assert.assertNotSame(0, atf.getSize());
}