/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2003-2008 Egon Willighagen <egonw@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.validate;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
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.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IIsotope;
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.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Engine that performs the validation by traversing the IChemObject
* hierarchy. Basic use of the ValidatorEngine is:
* <pre>
* ValidatorEngine engine = new ValidatorEngine();
* engine.addValidator(new BasicValidator());
* ValidationReport report = engine.validateMolecule(new Molecule());
* </pre>
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.githash
* @cdk.created 2003-08-22
*/
public class ValidatorEngine implements IValidator {
private Map<String,IValidator> validators;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(ValidatorEngine.class);
public ValidatorEngine() {
validators = new Hashtable<String,IValidator>();
}
public void addValidator(IValidator validator) {
logger.info("Registering validator: " + validator.getClass().getName());
String validatorName = validator.getClass().getName();
if (validators.containsKey(validatorName)) {
logger.warn(" already registered.");
} else {
validators.put(validatorName, validator);
}
}
public void removeValidator(IValidator validator) {
logger.info("Removing validator: " + validator.getClass().getName());
String validatorName = validator.getClass().getName();
if (!validators.containsKey(validatorName)) {
logger.warn(" not in list.");
} else {
validators.remove(validatorName);
}
}
public ValidationReport validateAtom(IAtom subject) {
logger.info("Validating org.openscience.cdk.Atom");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateAtom(subject));
}
// traverse into super class
report.addReport(validateAtomType(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateAtomContainer(IAtomContainer subject) {
logger.info("Validating org.openscience.cdk.AtomContainer");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateAtomContainer(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
Iterator<IAtom> atoms = subject.atoms().iterator();
while (atoms.hasNext()) {
report.addReport(validateAtom((IAtom)atoms.next()));
}
Iterator<IBond> bonds = subject.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
report.addReport(validateBond(bond));
}
return report;
}
public ValidationReport validateAtomType(IAtomType subject) {
logger.info("Validating org.openscience.cdk.AtomType");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateAtomType(subject));
}
// traverse into super class
report.addReport(validateIsotope(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateBond(IBond subject) {
logger.info("Validating org.openscience.cdk.Bond");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateBond(subject));
}
// traverse into super class
report.addReport(validateElectronContainer(subject));
// traverse into hierarchy
Iterator<IAtom> atoms = subject.atoms().iterator();
while (atoms.hasNext()) {
report.addReport(validateAtom((IAtom)atoms.next()));
}
return report;
}
public ValidationReport validateChemFile(IChemFile subject) {
logger.info("Validating org.openscience.cdk.ChemFile");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateChemFile(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
for (int i=0; i< subject.getChemSequenceCount(); i++) {
report.addReport(validateChemSequence(subject.getChemSequence(i)));
}
return report;
}
public ValidationReport validateChemModel(IChemModel subject) {
logger.info("Validating org.openscience.cdk.ChemModel");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateChemModel(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
ICrystal crystal = subject.getCrystal();
if (crystal != null) {
report.addReport(validateCrystal(crystal));
}
IReactionSet reactionSet = subject.getReactionSet();
if (reactionSet != null) {
report.addReport(validateReactionSet(reactionSet));
}
IMoleculeSet moleculeSet = subject.getMoleculeSet();
if (moleculeSet != null) {
report.addReport(validateMoleculeSet(moleculeSet));
}
return report;
}
public ValidationReport validateChemObject(IChemObject subject) {
logger.info("Validating org.openscience.cdk.ChemObject");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateChemObject(subject));
}
// traverse into super class
// traverse into hierarchy
return report;
}
public ValidationReport validateChemSequence(IChemSequence subject) {
logger.info("Validating org.openscience.cdk.ChemSequence");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateChemSequence(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
Iterator<IChemModel> models = subject.chemModels().iterator();
while (models.hasNext()) {
report.addReport(validateChemModel(models.next()));
}
return report;
}
public ValidationReport validateCrystal(ICrystal subject) {
logger.info("Validating org.openscience.cdk.Crystal");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateCrystal(subject));
}
// traverse into super class
report.addReport(validateAtomContainer(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateElectronContainer(IElectronContainer subject) {
logger.info("Validating org.openscience.cdk.ElectronContainer");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateElectronContainer(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateElement(IElement subject) {
logger.info("Validating org.openscience.cdk.Element");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateElement(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateIsotope(IIsotope subject) {
logger.info("Validating org.openscience.cdk.Isotope");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateIsotope(subject));
}
// traverse into super class
report.addReport(validateElement(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateMolecule(IMolecule subject) {
logger.info("Validating org.openscience.cdk.Molecule");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateMolecule(subject));
}
// traverse into super class
report.addReport(validateAtomContainer(subject));
// traverse into hierarchy
return report;
}
public ValidationReport validateReaction(IReaction subject) {
logger.info("Validating org.openscience.cdk.Reaction");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateReaction(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
IMoleculeSet reactants = subject.getReactants();
for (int i=0; i<reactants.getAtomContainerCount(); i++) {
report.addReport(validateMolecule(reactants.getMolecule(i)));
}
IMoleculeSet products = subject.getProducts();
for (int i=0; i<products.getAtomContainerCount(); i++) {
report.addReport(validateMolecule(products.getMolecule(i)));
}
return report;
}
public ValidationReport validateMoleculeSet(IMoleculeSet subject) {
logger.info("Validating org.openscience.cdk.MoleculeSet");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateMoleculeSet(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
for (int i=0; i<subject.getAtomContainerCount(); i++) {
report.addReport(validateMolecule(subject.getMolecule(i)));
}
return report;
}
public ValidationReport validateReactionSet(IReactionSet subject) {
logger.info("Validating org.openscience.cdk.ReactionSet");
ValidationReport report = new ValidationReport();
// apply validators
for (IValidator test : validators.values()) {
report.addReport(test.validateReactionSet(subject));
}
// traverse into super class
report.addReport(validateChemObject(subject));
// traverse into hierarchy
for (Iterator<IReaction> iter = subject.reactions().iterator(); iter.hasNext();) {
report.addReport(validateReaction((IReaction)iter.next()));
}
return report;
}
}