/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2005-2007 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.debug;
import java.util.Map;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Debugging data class.
*
* @author egonw
* @cdk.module datadebug
* @cdk.githash
*/
public class DebugMoleculeSet extends MoleculeSet
implements IMoleculeSet {
private static final long serialVersionUID = -2925577323304207688L;
ILoggingTool logger =
LoggingToolFactory.createLoggingTool(DebugMoleculeSet.class);
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}
public int getListenerCount() {
logger.debug("Getting listener count: ", super.getListenerCount());
return super.getListenerCount();
}
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
public Object getProperty(Object description) {
logger.debug("Getting property: ", description + "=" + super.getProperty(description));
return super.getProperty(description);
}
public Map<Object,Object> getProperties() {
logger.debug("Getting properties");
return super.getProperties();
}
public String getID() {
logger.debug("Getting ID: ", super.getID());
return super.getID();
}
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}
public void setFlag(int flag_type, boolean flag_value) {
logger.debug("Setting flag: ", flag_type + "=" + flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
return super.getFlag(flag_type);
}
public void setProperties(Map<Object,Object> properties) {
logger.debug("Setting properties: ", properties);
super.setProperties(properties);
}
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
public boolean[] getFlags() {
logger.debug("Getting flags:", super.getFlags().length);
return super.getFlags();
}
public Object clone() throws CloneNotSupportedException {
Object clone = null;
try {
clone = super.clone();
} catch (Exception exception) {
logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
}
public IChemObjectBuilder getBuilder() {
return DebugChemObjectBuilder.getInstance();
}
public void addAtomContainer(IAtomContainer atomContainer) {
logger.debug("Adding atom container: ", atomContainer);
super.addAtomContainer(atomContainer);
}
public void removeAtomContainer(IAtomContainer atomContainer) {
logger.debug("Removing atom container: ", atomContainer);
super.removeAtomContainer(atomContainer);
}
public void removeAllAtomContainers() {
logger.debug("Removing all atom containers");
super.removeAllAtomContainers();
}
public void removeAtomContainer(int pos) {
logger.debug("Removing atom container at pos: ", pos);
super.removeAtomContainer(pos);
}
public void replaceAtomContainer(int position, IAtomContainer container) {
logger.debug("Replacing atom container at pos: ", position);
super.replaceAtomContainer(position, container);
}
public boolean setMultiplier(IAtomContainer container, Double multiplier) {
logger.debug("Setting multiplier for atomcontainer: ", container, ""+multiplier);
return super.setMultiplier(container, multiplier);
}
public void setMultiplier(int position, Double multiplier) {
logger.debug("Setting multiplier for atomcontainer at pos: ", ""+position, ""+multiplier);
super.setMultiplier(position, multiplier);
}
public Double[] getMultipliers() {
logger.debug("Getting multipliers array: ", super.getMultipliers().length);
return super.getMultipliers();
}
public boolean setMultipliers(Double[] newMultipliers) {
logger.debug("Setting mulipliers array: ", newMultipliers.length);
return super.setMultipliers(newMultipliers);
}
public void addAtomContainer(IAtomContainer atomContainer, double multiplier) {
logger.debug("Adding atom container with multiplier: ", ""+multiplier, atomContainer);
super.addAtomContainer(atomContainer, multiplier);
}
public void add(IAtomContainerSet atomContainerSet) {
logger.debug("Adding set of atom containers: ", atomContainerSet);
super.add(atomContainerSet);
}
public Iterable<IAtomContainer> atomContainers() {
logger.debug("Getting atom container iterator");
return super.atomContainers();
}
public IAtomContainer getAtomContainer(int number) {
logger.debug("Getting atom container at: ", number);
return super.getAtomContainer(number);
}
public Double getMultiplier(int number) {
logger.debug("Getting multiplier at: ", number);
return super.getMultiplier(number);
}
public Double getMultiplier(IAtomContainer container) {
logger.debug("Getting multiplier for atom container: ", container);
return super.getMultiplier(container);
}
public int getAtomContainerCount() {
logger.debug("Getting atom container count: ", super.getAtomContainerCount());
return super.getAtomContainerCount();
}
public void addMolecule(IMolecule molecule) {
logger.debug("Adding molecule: ", molecule);
super.addMolecule(molecule);
}
public void add(IMoleculeSet moleculeSet) {
logger.debug("Adding set of molecules: ", moleculeSet);
super.add(moleculeSet);
}
public void setMolecules(IMolecule[] molecules) {
logger.debug("Setting molecule array: ", molecules.length);
super.setMolecules(molecules);
}
public Iterable<IAtomContainer> molecules() {
logger.debug("Getting molecule iterator");
return super.molecules();
}
public IMolecule getMolecule(int number) {
logger.debug("Getting molecule at: ", number);
return super.getMolecule(number);
}
public int getMoleculeCount() {
logger.debug("Getting molecule count: ", super.getMoleculeCount());
return super.getMoleculeCount();
}
}