/* $Revision$ $Author$ $Date$
*
* 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.AtomType;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Debugging data class.
*
* @author egonw
* @cdk.module datadebug
* @cdk.githash
*/
public class DebugAtomType extends AtomType
implements IAtomType {
private static final long serialVersionUID = 1427549696666679540L;
ILoggingTool logger =
LoggingToolFactory.createLoggingTool(DebugAtomType.class);
public DebugAtomType(String elementSymbol) {
super(elementSymbol);
logger.debug("Instantiated a DebugAtomType: symbol= ", elementSymbol);
}
public DebugAtomType(String identifier, String elementSymbol) {
super(elementSymbol); // cannot use super(identifier, elementSymbol); that gives a NPE
logger.debug("Instantiated a DebugAtomType: identifier= " + identifier + " symbol= ", elementSymbol);
this.setSymbol(elementSymbol);
this.setAtomTypeName(identifier);
}
public DebugAtomType(IElement element) {
super(element);
logger.debug("Instantiated a DebugAtomType: element= ", element);
}
public Integer getAtomicNumber() {
logger.debug("Getting atomic number: ", super.getAtomicNumber());
return super.getAtomicNumber();
}
public void setAtomicNumber(Integer atomicNumber) {
logger.debug("Setting atomic number: ", atomicNumber);
super.setAtomicNumber(atomicNumber);
}
public String getSymbol() {
logger.debug("Getting symbol: ", super.getSymbol());
return super.getSymbol();
}
public void setSymbol(String symbol) {
logger.debug("Setting symbol: ", symbol);
super.setSymbol(symbol);
}
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 setNaturalAbundance(Double naturalAbundance) {
logger.debug("Setting natural abundance: ", naturalAbundance);
super.setNaturalAbundance(naturalAbundance);
}
public void setExactMass(Double exactMass) {
logger.debug("Setting exact mass: ", exactMass);
super.setExactMass(exactMass);
}
public Double getNaturalAbundance() {
logger.debug("Getting natural abundance: ", super.getNaturalAbundance());
return super.getNaturalAbundance();
}
public Double getExactMass() {
logger.debug("Getting exact mass: ", super.getExactMass());
return super.getExactMass();
}
public Integer getMassNumber() {
logger.debug("Getting mass number: ", super.getMassNumber());
return super.getMassNumber();
}
public void setMassNumber(Integer massNumber) {
logger.debug("Setting mass number: ", massNumber);
super.setMassNumber(massNumber);
}
public void setAtomTypeName(String identifier) {
logger.debug("Setting atom type name: ", identifier);
super.setAtomTypeName(identifier);
}
public void setMaxBondOrder(IBond.Order maxBondOrder) {
logger.debug("Setting max bond order: ", maxBondOrder);
super.setMaxBondOrder(maxBondOrder);
}
public void setBondOrderSum(Double bondOrderSum) {
logger.debug("Setting bond order sum: ", bondOrderSum);
super.setBondOrderSum(bondOrderSum);
}
public String getAtomTypeName() {
logger.debug("Getting atom type name: ", super.getAtomTypeName());
return super.getAtomTypeName();
}
public IBond.Order getMaxBondOrder() {
logger.debug("Getting max bond order: ", super.getMaxBondOrder());
return super.getMaxBondOrder();
}
public Double getBondOrderSum() {
logger.debug("Getting bond order sum: ", super.getBondOrderSum());
return super.getBondOrderSum();
}
public void setFormalCharge(Integer charge) {
logger.debug("Setting formal charge: ", charge);
super.setFormalCharge(charge);
}
public Integer getFormalCharge() {
logger.debug("Getting formal charge: ", super.getFormalCharge());
return super.getFormalCharge();
}
public void setFormalNeighbourCount(Integer count) {
logger.debug("Setting forml neighbour count: ", count);
super.setFormalNeighbourCount(count);
}
public Integer getFormalNeighbourCount() {
logger.debug("Getting formal neighbour count: ", super.getFormalNeighbourCount());
return super.getFormalNeighbourCount();
}
public void setHybridization(IAtomType.Hybridization hybridization) {
logger.debug("Setting hybridization: ", hybridization);
super.setHybridization(hybridization);
}
public IAtomType.Hybridization getHybridization() {
logger.debug("Getting hybridization: ", super.getHybridization());
return super.getHybridization();
}
public void setCovalentRadius(Double radius) {
logger.debug("Setting covalent radius: ", radius);
super.setCovalentRadius(radius);
}
public Double getCovalentRadius() {
logger.debug("Getting covalent radius: ", super.getCovalentRadius());
return super.getCovalentRadius();
}
public void setValency(Integer valency) {
logger.debug("Setting valency: ", valency);
super.setValency(valency);
}
public Integer getValency() {
logger.debug("Getting valency: ", super.getValency());
return super.getValency();
}
}