DebugPseudoAtom.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 javax.vecmath.Point2d;
import javax.vecmath.Point3d;

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.interfaces.IPseudoAtom;
import org.openscience.cdk.tools.LoggingTool;

/**
 * Debugging data class.
 * 
 * @author     egonw
 * @cdk.module datadebug
 */
00041 public class DebugPseudoAtom extends org.openscience.cdk.PseudoAtom 
    implements IPseudoAtom {

00044     private static final long serialVersionUID = -5935090219383862070L;
    
    LoggingTool logger = new LoggingTool(DebugPseudoAtom.class);
      
      public DebugPseudoAtom() {
            super();
            logger.debug("Instantiated a DebugAtom");
      }
      
      public DebugPseudoAtom(IElement element) {
            super(element);
            logger.debug("Instantiated a DebugAtom: element= ", element);
      }

      public DebugPseudoAtom(String symbol) {
            super(symbol);
            logger.debug("Instantiated a DebugAtom: symbol= ", symbol);
      }
      
      public DebugPseudoAtom(String symbol, Point2d point2d) {
            super(symbol, point2d);
            logger.debug("Instantiated a DebugAtom: symbol= ", symbol + " point2d=" + point2d);
      }
      
      public DebugPseudoAtom(String symbol, Point3d point3d) {
            super(symbol, point3d);
            logger.debug("Instantiated a DebugAtom: symbol= ", symbol + " point3d=" + point3d);
      }
      
00073       public void setCharge(double charge) {
            logger.debug("Setting charge: ", charge);
            super.setCharge(charge);
      }

00078       public double getCharge() {
            logger.debug("Setting charge: ", super.getCharge());
            return super.getCharge();
      }

00083       public void setHydrogenCount(int hydrogenCount) {
            logger.debug("Setting hydrogen count: ", hydrogenCount);
            super.setHydrogenCount(hydrogenCount);
      }

00088       public int getHydrogenCount() {
            logger.debug("Getting hydrogen count: ", super.getHydrogenCount());
            return super.getHydrogenCount();
      }

00093       public void setPoint2d(Point2d point2d) {
            logger.debug("Setting point2d: x=" + point2d.x + 
                             ", y=" + point2d.y);
            super.setPoint2d(point2d);
      }

00099       public void setPoint3d(Point3d point3d) {
            logger.debug("Setting point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            super.setPoint3d(point3d);
      }

00105       public void setFractionalPoint3d(Point3d point3d) {
            logger.debug("Setting fractional point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            super.setFractionalPoint3d(point3d);
      }

00111       public void setStereoParity(int stereoParity) {
            logger.debug("Setting stereoParity: ", stereoParity);
            super.setStereoParity(stereoParity);
      }

00116       public Point2d getPoint2d() {
            Point2d point2d = super.getPoint2d();
            if (point2d == null) {
                  logger.debug("Getting point2d: null");
            } else {
                  logger.debug("Getting point2d: x=" + point2d.x + 
                       ", y=" + point2d.y);
            }
            return point2d;
      }

00127       public Point3d getPoint3d() {
            Point3d point3d = super.getPoint3d();
            if (point3d == null) {
                  logger.debug("Getting point3d: null");
            } else {
                  logger.debug("Getting point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            }
            return point3d;
      }

00138       public Point3d getFractionalPoint3d() {
            Point3d point3d = super.getFractionalPoint3d();
            if (point3d == null) {
                  logger.debug("Getting fractional point3d: null");
            } else {
                  logger.debug("Getting fractional point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            }
            return point3d;
      }

00149       public int getStereoParity() {
            logger.debug("Getting stereo parity: ", super.getStereoParity());
            return super.getStereoParity();
      }

00154       public void setAtomTypeName(String identifier) {
            logger.debug("Setting atom type name: ", identifier);
            super.setAtomTypeName(identifier);
      }

00159       public void setMaxBondOrder(double maxBondOrder) {
            logger.debug("Setting max bond order: ", maxBondOrder);
            super.setMaxBondOrder(maxBondOrder);
      }

00164       public void setBondOrderSum(double bondOrderSum) {
            logger.debug("Setting bond order sum: ", bondOrderSum);
            super.setBondOrderSum(bondOrderSum);
      }

00169       public String getAtomTypeName() {
            logger.debug("Getting atom type name: ", super.getAtomTypeName());
            return super.getAtomTypeName();
      }

00174       public double getMaxBondOrder() {
            logger.debug("Getting max bond order: ", super.getMaxBondOrder());
            return super.getMaxBondOrder();
      }

00179       public double getBondOrderSum() {
            logger.debug("Getting bond order sum: ", super.getBondOrderSum());
            return super.getBondOrderSum();
      }

00184       public void setFormalCharge(int charge) {
            logger.debug("Setting formal charge: ", charge);
            super.setFormalCharge(charge);
      }

00189       public int getFormalCharge() {
            logger.debug("Getting formal charge: ", super.getFormalCharge());
            return super.getFormalCharge();
      }

00194       public void setFormalNeighbourCount(int count) {
            logger.debug("Setting forml neighbour count: ", count);
            super.setFormalNeighbourCount(count);
      }

00199       public int getFormalNeighbourCount() {
            logger.debug("Getting formal neighbour count: ", super.getFormalNeighbourCount());
            return super.getFormalNeighbourCount();
      }

00204       public void setHybridization(int hybridization) {
            logger.debug("Setting hybridization: ", hybridization);
            super.setHybridization(hybridization);
      }

00209       public int getHybridization() {
            logger.debug("Getting hybridization: ", super.getHybridization());
            return super.getHybridization();
      }

00214       public void setVanderwaalsRadius(double radius) {
            logger.debug("Setting vanderwaals radius: ", radius);
            super.setVanderwaalsRadius(radius);
      }

00219       public double getVanderwaalsRadius() {
            logger.debug("Getting vanderwaals radius: ", super.getVanderwaalsRadius());
            return super.getVanderwaalsRadius();
      }

00224       public void setCovalentRadius(double radius) {
            logger.debug("Setting covalent radius: ", radius);
            super.setCovalentRadius(radius);
      }

00229       public double getCovalentRadius() {
            logger.debug("Getting covalent radius: ", super.getCovalentRadius());
            return super.getCovalentRadius();
      }

00234       public void setValency(int valency) {
            logger.debug("Setting valency: ", valency);
            super.setValency(valency);
      }

00239       public int getValency() {
            logger.debug("Getting valency: ", super.getValency());
            return super.getValency();
      }

00244       public void setNaturalAbundance(double naturalAbundance) {
            logger.debug("Setting natural abundance: ", naturalAbundance);
            super.setNaturalAbundance(naturalAbundance);
      }

00249       public void setExactMass(double exactMass) {
            logger.debug("Setting exact mass: ", exactMass);
            super.setExactMass(exactMass);
            
      }

00255       public double getNaturalAbundance() {
            logger.debug("Getting natural abundance: ", super.getNaturalAbundance());
            return super.getNaturalAbundance();
      }

00260       public double getExactMass() {
            logger.debug("Getting exact mass: ", super.getExactMass());
            return super.getExactMass();
      }

00265       public int getMassNumber() {
            logger.debug("Getting mass number: ", super.getMassNumber());
            return super.getMassNumber();
      }

00270       public void setMassNumber(int massNumber) {
            logger.debug("Setting mass number: ", massNumber);
            super.setMassNumber(massNumber);
      }

00275       public int getAtomicNumber() {
            logger.debug("Getting atomic number: ", super.getAtomicNumber());
            return super.getAtomicNumber();
      }

00280       public void setAtomicNumber(int atomicNumber) {
            logger.debug("Setting atomic number: ", atomicNumber);
            super.setAtomicNumber(atomicNumber);
      }

00285       public String getSymbol() {
            logger.debug("Getting symbol: ", super.getSymbol());
            return super.getSymbol();
      }

00290       public void setSymbol(String symbol) {
            logger.debug("Setting symbol: ", symbol);
            super.setSymbol(symbol);
      }

00295       public void addListener(IChemObjectListener col) {
            logger.debug("Adding listener: ", col);
            super.addListener(col);
      }

00300       public int getListenerCount() {
            logger.debug("Getting listener count: ", super.getListenerCount());
            return super.getListenerCount();
      }

00305       public void removeListener(IChemObjectListener col) {
            logger.debug("Removing listener: ", col);
            super.removeListener(col);
      }

00310       public void notifyChanged() {
            logger.debug("Notifying changed");
            super.notifyChanged();
      }

00315       public void notifyChanged(IChemObjectChangeEvent evt) {
            logger.debug("Notifying changed event: ", evt);
            super.notifyChanged(evt);
      }

00320       public void setProperty(Object description, Object property) {
            logger.debug("Setting property: ", description + "=" + property);
            super.setProperty(description, property);
      }

00325       public void removeProperty(Object description) {
            logger.debug("Removing property: ", description);
            super.removeProperty(description);
      }

00330       public Object getProperty(Object description) {
            logger.debug("Getting property: ", description + "=" + super.getProperty(description));
            return super.getProperty(description);
      }

00335       public Hashtable getProperties() {
            logger.debug("Getting properties");
            return super.getProperties();
      }

00340       public String getID() {
            logger.debug("Getting ID: ", super.getID());
            return super.getID();
      }

00345       public void setID(String identifier) {
            logger.debug("Setting ID: ", identifier);
            super.setID(identifier);
      }

00350       public void setFlag(int flag_type, boolean flag_value) {
            logger.debug("Setting flag: ", flag_type + "=" + flag_value);
            super.setFlag(flag_type, flag_value);
      }

00355       public boolean getFlag(int flag_type) {
            logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
            return super.getFlag(flag_type);
      }

00360       public void setProperties(Hashtable properties) {
            logger.debug("Setting properties: ", properties);
            super.setProperties(properties);
      }

00365       public void setFlags(boolean[] flagsNew) {
            logger.debug("Setting flags:", flagsNew.length);
            super.setFlags(flagsNew);
      }

00370       public boolean[] getFlags() {
            logger.debug("Getting flags:", super.getFlags().length);
            return super.getFlags();
      }

00375       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;
      }

00386       public IChemObjectBuilder getBuilder() {
            return DebugChemObjectBuilder.getInstance();
      }

00390       public String getLabel() {
            logger.debug("Getting label: ", super.getLabel());
            return super.getLabel();
      }

00395       public void setLabel(String label) {
            logger.debug("Setting label: ", label);
            super.setLabel(label);
      }

}