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DebugAtomType.java

/* $Revision: 7636 $ $Author: egonw $ $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 *
 * 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.Hashtable;

import org.openscience.cdk.interfaces.IAtomType;
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.LoggingTool;

/**
 * Debugging data class.
 * 
 * @author     egonw
 * @cdk.module datadebug
 */
00038 public class DebugAtomType extends org.openscience.cdk.AtomType
    implements IAtomType {

00041     private static final long serialVersionUID = 1427549696666679540L;
    
    LoggingTool logger = new LoggingTool(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);
      }

00062       public int getAtomicNumber() {
            logger.debug("Getting atomic number: ", super.getAtomicNumber());
            return super.getAtomicNumber();
      }

00067       public void setAtomicNumber(int atomicNumber) {
            logger.debug("Setting atomic number: ", atomicNumber);
            super.setAtomicNumber(atomicNumber);
      }

00072       public String getSymbol() {
            logger.debug("Getting symbol: ", super.getSymbol());
            return super.getSymbol();
      }

00077       public void setSymbol(String symbol) {
            logger.debug("Setting symbol: ", symbol);
            super.setSymbol(symbol);
      }

00082       public void addListener(IChemObjectListener col) {
            logger.debug("Adding listener: ", col);
            super.addListener(col);
      }

00087       public int getListenerCount() {
            logger.debug("Getting listener count: ", super.getListenerCount());
            return super.getListenerCount();
      }

00092       public void removeListener(IChemObjectListener col) {
            logger.debug("Removing listener: ", col);
            super.removeListener(col);
      }

00097       public void notifyChanged() {
            logger.debug("Notifying changed");
            super.notifyChanged();
      }

00102       public void notifyChanged(IChemObjectChangeEvent evt) {
            logger.debug("Notifying changed event: ", evt);
            super.notifyChanged(evt);
      }

00107       public void setProperty(Object description, Object property) {
            logger.debug("Setting property: ", description + "=" + property);
            super.setProperty(description, property);
      }

00112       public void removeProperty(Object description) {
            logger.debug("Removing property: ", description);
            super.removeProperty(description);
      }

00117       public Object getProperty(Object description) {
            logger.debug("Getting property: ", description + "=" + super.getProperty(description));
            return super.getProperty(description);
      }

00122       public Hashtable getProperties() {
            logger.debug("Getting properties");
            return super.getProperties();
      }

00127       public String getID() {
            logger.debug("Getting ID: ", super.getID());
            return super.getID();
      }

00132       public void setID(String identifier) {
            logger.debug("Setting ID: ", identifier);
            super.setID(identifier);
      }

00137       public void setFlag(int flag_type, boolean flag_value) {
            logger.debug("Setting flag: ", flag_type + "=" + flag_value);
            super.setFlag(flag_type, flag_value);
      }

00142       public boolean getFlag(int flag_type) {
            logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
            return super.getFlag(flag_type);
      }

00147       public void setProperties(Hashtable properties) {
            logger.debug("Setting properties: ", properties);
            super.setProperties(properties);
      }

00152       public void setFlags(boolean[] flagsNew) {
            logger.debug("Setting flags:", flagsNew.length);
            super.setFlags(flagsNew);
      }

00157       public boolean[] getFlags() {
            logger.debug("Getting flags:", super.getFlags().length);
            return super.getFlags();
      }

00162       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;
      }

00173       public IChemObjectBuilder getBuilder() {
            return DebugChemObjectBuilder.getInstance();
      }

00177       public void setNaturalAbundance(double naturalAbundance) {
            logger.debug("Setting natural abundance: ", naturalAbundance);
            super.setNaturalAbundance(naturalAbundance);
      }

00182       public void setExactMass(double exactMass) {
            logger.debug("Setting exact mass: ", exactMass);
            super.setExactMass(exactMass);
            
      }

00188       public double getNaturalAbundance() {
            logger.debug("Getting natural abundance: ", super.getNaturalAbundance());
            return super.getNaturalAbundance();
      }

00193       public double getExactMass() {
            logger.debug("Getting exact mass: ", super.getExactMass());
            return super.getExactMass();
      }

00198       public int getMassNumber() {
            logger.debug("Getting mass number: ", super.getMassNumber());
            return super.getMassNumber();
      }

00203       public void setMassNumber(int massNumber) {
            logger.debug("Setting mass number: ", massNumber);
            super.setMassNumber(massNumber);
      }

00208       public void setAtomTypeName(String identifier) {
            logger.debug("Setting atom type name: ", identifier);
            super.setAtomTypeName(identifier);
      }

00213       public void setMaxBondOrder(double maxBondOrder) {
            logger.debug("Setting max bond order: ", maxBondOrder);
            super.setMaxBondOrder(maxBondOrder);
      }

00218       public void setBondOrderSum(double bondOrderSum) {
            logger.debug("Setting bond order sum: ", bondOrderSum);
            super.setBondOrderSum(bondOrderSum);
      }

00223       public String getAtomTypeName() {
            logger.debug("Getting atom type name: ", super.getAtomTypeName());
            return super.getAtomTypeName();
      }

00228       public double getMaxBondOrder() {
            logger.debug("Getting max bond order: ", super.getMaxBondOrder());
            return super.getMaxBondOrder();
      }

00233       public double getBondOrderSum() {
            logger.debug("Getting bond order sum: ", super.getBondOrderSum());
            return super.getBondOrderSum();
      }

00238       public void setFormalCharge(int charge) {
            logger.debug("Setting formal charge: ", charge);
            super.setFormalCharge(charge);
      }

00243       public int getFormalCharge() {
            logger.debug("Getting formal charge: ", super.getFormalCharge());
            return super.getFormalCharge();
      }

00248       public void setFormalNeighbourCount(int count) {
            logger.debug("Setting forml neighbour count: ", count);
            super.setFormalNeighbourCount(count);
      }

00253       public int getFormalNeighbourCount() {
            logger.debug("Getting formal neighbour count: ", super.getFormalNeighbourCount());
            return super.getFormalNeighbourCount();
      }

00258       public void setHybridization(int hybridization) {
            logger.debug("Setting hybridization: ", hybridization);
            super.setHybridization(hybridization);
      }

00263       public int getHybridization() {
            logger.debug("Getting hybridization: ", super.getHybridization());
            return super.getHybridization();
      }

00268       public void setVanderwaalsRadius(double radius) {
            logger.debug("Setting vanderwaals radius: ", radius);
            super.setVanderwaalsRadius(radius);
      }

00273       public double getVanderwaalsRadius() {
            logger.debug("Getting vanderwaals radius: ", super.getVanderwaalsRadius());
            return super.getVanderwaalsRadius();
      }

00278       public void setCovalentRadius(double radius) {
            logger.debug("Setting covalent radius: ", radius);
            super.setCovalentRadius(radius);
      }

00283       public double getCovalentRadius() {
            logger.debug("Getting covalent radius: ", super.getCovalentRadius());
            return super.getCovalentRadius();
      }

00288       public void setValency(int valency) {
            logger.debug("Setting valency: ", valency);
            super.setValency(valency);
      }

00293       public int getValency() {
            logger.debug("Getting valency: ", super.getValency());
            return super.getValency();
      }


}

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