org.openscience.cdk.debug.DebugChemObjectBuilder Maven / Gradle / Ivy
/* Copyright (C) 2010 Egon Willighagen
* 2012 John May
*
* Contact: [email protected]
*
* 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.openscience.cdk.DynamicFactory;
import org.openscience.cdk.interfaces.IAdductFormula;
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.IAtomType;
import org.openscience.cdk.interfaces.IBioPolymer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ICDKObject;
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.IDoubleBondStereochemistry;
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.IMapping;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecularFormulaSet;
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.ISubstance;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.stereo.DoubleBondStereochemistry;
import org.openscience.cdk.stereo.TetrahedralChirality;
/**
* A helper class to instantiate a {@link IChemObject} for the original CDK
* implementation. The factory create debug objects which will log their
* behaviour when used.
*
*
* {@code
* IChemObjectBuilder builder = DebugChemObjectBuilder.getInstance();
*
* IAtom a = builder.newInstance(IAtom.class);
* IAtom c12 = builder.newInstance(IAtom.class, "C");
* IAtom c13 = builder.newInstance(IAtom.class,
* builder.newInstance(IIsotope.class,
* "C", 13));
* }
*
*
* @author egonw
* @author john may
* @cdk.module datadebug
* @cdk.githash
*/
public class DebugChemObjectBuilder implements IChemObjectBuilder {
private static volatile IChemObjectBuilder instance = null;
private static final Object LOCK = new Object();
private final DynamicFactory factory = new DynamicFactory(200);
private DebugChemObjectBuilder() {
// self reference required for stereo-elements
final IChemObjectBuilder self = this;
// elements
factory.register(IAtom.class, DebugAtom.class);
factory.register(IPseudoAtom.class, DebugPseudoAtom.class);
factory.register(IElement.class, DebugElement.class);
factory.register(IAtomType.class, DebugAtomType.class);
factory.register(IFragmentAtom.class, DebugFragmentAtom.class);
factory.register(IPDBAtom.class, DebugPDBAtom.class);
factory.register(IIsotope.class, DebugIsotope.class);
// electron containers
factory.register(IBond.class, DebugBond.class);
factory.register(IElectronContainer.class, DebugElectronContainer.class);
factory.register(ISingleElectron.class, DebugSingleElectron.class);
factory.register(ILonePair.class, DebugLonePair.class);
// atom containers
factory.register(IAtomContainer.class, DebugAtomContainer.class);
factory.register(IRing.class, DebugRing.class);
factory.register(ICrystal.class, DebugCrystal.class);
factory.register(IPolymer.class, DebugPolymer.class);
factory.register(IPDBPolymer.class, DebugPDBPolymer.class);
factory.register(IMonomer.class, DebugMonomer.class);
factory.register(IPDBMonomer.class, DebugPDBMonomer.class);
factory.register(IBioPolymer.class, DebugBioPolymer.class);
factory.register(IPDBStructure.class, DebugPDBStructure.class);
factory.register(IAminoAcid.class, DebugAminoAcid.class);
factory.register(IStrand.class, DebugStrand.class);
// reactions
factory.register(IReaction.class, DebugReaction.class);
factory.register(IReactionScheme.class, DebugReactionScheme.class);
// formula
factory.register(IMolecularFormula.class, DebugMolecularFormula.class);
factory.register(IAdductFormula.class, DebugAdductFormula.class);
// chem object sets
factory.register(IAtomContainerSet.class, DebugAtomContainerSet.class);
factory.register(IMolecularFormulaSet.class, DebugMolecularFormulaSet.class);
factory.register(IReactionSet.class, DebugReactionSet.class);
factory.register(IRingSet.class, DebugRingSet.class);
factory.register(IChemModel.class, DebugChemModel.class);
factory.register(IChemFile.class, DebugChemFile.class);
factory.register(IChemSequence.class, DebugChemSequence.class);
factory.register(ISubstance.class, DebugSubstance.class);
// stereo components (requires some modification after instantiation)
factory.register(ITetrahedralChirality.class, TetrahedralChirality.class,
new DynamicFactory.CreationModifier() {
@Override
public void modify(TetrahedralChirality instance) {
instance.setBuilder(self);
}
});
factory.register(IDoubleBondStereochemistry.class, DoubleBondStereochemistry.class,
new DynamicFactory.CreationModifier() {
@Override
public void modify(DoubleBondStereochemistry instance) {
instance.setBuilder(self);
}
});
// miscellaneous
factory.register(IMapping.class, DebugMapping.class);
factory.register(IChemObject.class, DebugChemObject.class);
}
/**
* Access the singleton instance of this DebugChemObjectBuilder.
* {@code
*
* // get the builder instance
* IChemObjectBuilder builder = DebugChemObjectBuilder.getInstance();
*
* // using the builder...
* // create an IAtom using the default constructor
* IAtom atom = builder.newInstance(IAtom.class);
*
* // create a carbon atom
* IAtom c1 = builder.newInstance(IAtom.class, "C");
* }
*
* @return a DebugChemObjectBuilder instance
*/
public static IChemObjectBuilder getInstance() {
IChemObjectBuilder result = instance;
if (result == null) {
result = instance;
synchronized (LOCK) {
if (result == null) {
instance = result = new DebugChemObjectBuilder();
}
}
}
return result;
}
/**
* @inheritDoc
*/
@Override
public T newInstance(Class clazz, Object... params) {
return factory.ofClass(clazz, params);
}
}
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