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DebugFragmentAtom.java

/* $Revision$ $Author$$Date$
 *
 * Copyright (C) 2006-2008  Egon Willighagen <ewilligh@uni-koeln.de>
 * 
 * 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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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 javax.vecmath.Point2d;
import javax.vecmath.Point3d;

import org.openscience.cdk.FragmentAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
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.tools.LoggingTool;

/**
 * Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
 * like the MDL molfile <code>Group</code> concept.
 * 
 * @cdk.module datadebug
 * @cdk.githash
 * 
 * @author egonw
 */
00050 public class DebugFragmentAtom extends FragmentAtom {

00052       private static final long serialVersionUID = 0L;

      LoggingTool logger = new LoggingTool(DebugFragmentAtom.class);

      public DebugFragmentAtom() {
            super();
            logger.debug("Instantiated a DebugFragmentAtom");
      }
      
00061       public boolean isExpanded() {
            logger.debug("Getting isExpanded state...");
            return super.isExpanded();
      }
      
      public void setExpanded(boolean bool) {
            logger.debug("Setting the isExpanded state: " + bool);
            super.setExpanded(bool);
      }

00071       public IAtomContainer getFragment() {
            logger.debug("Getting the fragment...");
            return super.getFragment();
      }

00076       public void setFragment(IAtomContainer fragment) {
            logger.debug("Setting the fragment: ", fragment);
            super.setFragment(fragment);
      }
      
00081       public void setCharge(Double charge) {
            logger.debug("Setting charge: ", charge);
            super.setCharge(charge);
      }

00086       public Double getCharge() {
            logger.debug("Setting charge: ", super.getCharge());
            return super.getCharge();
      }

00091       public void setHydrogenCount(Integer hydrogenCount) {
            logger.debug("Setting hydrogen count: ", hydrogenCount);
            super.setHydrogenCount(hydrogenCount);
      }

00096       public Integer getHydrogenCount() {
            logger.debug("Getting hydrogen count: ", super.getHydrogenCount());
            return super.getHydrogenCount();
      }

00101       public void setPoint2d(Point2d point2d) {
            logger.debug("Setting point2d: x=" + point2d.x + 
                             ", y=" + point2d.y);
            super.setPoint2d(point2d);
      }

00107       public void setPoint3d(Point3d point3d) {
            logger.debug("Setting point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            super.setPoint3d(point3d);
      }

00113       public void setFractionalPoint3d(Point3d point3d) {
            logger.debug("Setting fractional point3d: x=" + point3d.x + 
                       ", y=" + point3d.y, ", z=" + point3d.z);
            super.setFractionalPoint3d(point3d);
      }

00119       public void setStereoParity(Integer stereoParity) {
            logger.debug("Setting stereoParity: ", stereoParity);
            super.setStereoParity(stereoParity);
      }

00124       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;
      }

00135       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;
      }

00146       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;
      }

00157       public Integer getStereoParity() {
            logger.debug("Getting stereo parity: ", super.getStereoParity());
            return super.getStereoParity();
      }

00162       public void setAtomTypeName(String identifier) {
            logger.debug("Setting atom type name: ", identifier);
            super.setAtomTypeName(identifier);
      }

00167       public void setMaxBondOrder(IBond.Order maxBondOrder) {
            logger.debug("Setting max bond order: ", maxBondOrder);
            super.setMaxBondOrder(maxBondOrder);
      }

00172       public void setBondOrderSum(Double bondOrderSum) {
            logger.debug("Setting bond order sum: ", bondOrderSum);
            super.setBondOrderSum(bondOrderSum);
      }

00177       public String getAtomTypeName() {
            logger.debug("Getting atom type name: ", super.getAtomTypeName());
            return super.getAtomTypeName();
      }

00182       public IBond.Order getMaxBondOrder() {
            logger.debug("Getting max bond order: ", super.getMaxBondOrder());
            return super.getMaxBondOrder();
      }

00187       public Double getBondOrderSum() {
            logger.debug("Getting bond order sum: ", super.getBondOrderSum());
            return super.getBondOrderSum();
      }

00192       public void setFormalCharge(Integer charge) {
            logger.debug("Setting formal charge: ", charge);
            super.setFormalCharge(charge);
      }

00197       public Integer getFormalCharge() {
            logger.debug("Getting formal charge: ", super.getFormalCharge());
            return super.getFormalCharge();
      }

00202       public void setFormalNeighbourCount(Integer count) {
            logger.debug("Setting forml neighbour count: ", count);
            super.setFormalNeighbourCount(count);
      }

00207       public Integer getFormalNeighbourCount() {
            logger.debug("Getting formal neighbour count: ", super.getFormalNeighbourCount());
            return super.getFormalNeighbourCount();
      }

00212       public void setHybridization(IAtomType.Hybridization hybridization) {
            logger.debug("Setting hybridization: ", hybridization);
            super.setHybridization(hybridization);
      }

00217       public IAtomType.Hybridization getHybridization() {
            logger.debug("Getting hybridization: ", super.getHybridization());
            return super.getHybridization();
      }

00222       public void setCovalentRadius(Double radius) {
            logger.debug("Setting covalent radius: ", radius);
            super.setCovalentRadius(radius);
      }

00227       public Double getCovalentRadius() {
            logger.debug("Getting covalent radius: ", super.getCovalentRadius());
            return super.getCovalentRadius();
      }

00232       public void setValency(Integer valency) {
            logger.debug("Setting valency: ", valency);
            super.setValency(valency);
      }

00237       public Integer getValency() {
            logger.debug("Getting valency: ", super.getValency());
            return super.getValency();
      }

00242       public void setNaturalAbundance(Double naturalAbundance) {
            logger.debug("Setting natural abundance: ", naturalAbundance);
            super.setNaturalAbundance(naturalAbundance);
      }

00247       public void setExactMass(Double exactMass) {
            logger.debug("Setting exact mass: ", exactMass);
            super.setExactMass(exactMass);
            
      }

00253       public Double getNaturalAbundance() {
            logger.debug("Getting natural abundance: ", super.getNaturalAbundance());
            return super.getNaturalAbundance();
      }

00258       public Double getExactMass() {
            logger.debug("Getting exact mass: ", super.getExactMass());
            return super.getExactMass();
      }

00263       public Integer getMassNumber() {
            logger.debug("Getting mass number: ", super.getMassNumber());
            return super.getMassNumber();
      }

00268       public void setMassNumber(Integer massNumber) {
            logger.debug("Setting mass number: ", massNumber);
            super.setMassNumber(massNumber);
      }

00273       public Integer getAtomicNumber() {
            logger.debug("Getting atomic number: ", super.getAtomicNumber());
            return super.getAtomicNumber();
      }

00278       public void setAtomicNumber(Integer atomicNumber) {
            logger.debug("Setting atomic number: ", atomicNumber);
            super.setAtomicNumber(atomicNumber);
      }

00283       public String getSymbol() {
            logger.debug("Getting symbol: ", super.getSymbol());
            return super.getSymbol();
      }

00288       public void setSymbol(String symbol) {
            logger.debug("Setting symbol: ", symbol);
            super.setSymbol(symbol);
      }

00293       public void addListener(IChemObjectListener col) {
            logger.debug("Adding listener: ", col);
            super.addListener(col);
      }

00298       public int getListenerCount() {
            logger.debug("Getting listener count: ", super.getListenerCount());
            return super.getListenerCount();
      }

00303       public void removeListener(IChemObjectListener col) {
            logger.debug("Removing listener: ", col);
            super.removeListener(col);
      }

00308       public void notifyChanged() {
            logger.debug("Notifying changed");
            super.notifyChanged();
      }

00313       public void notifyChanged(IChemObjectChangeEvent evt) {
            logger.debug("Notifying changed event: ", evt);
            super.notifyChanged(evt);
      }

00318       public void setProperty(Object description, Object property) {
            logger.debug("Setting property: ", description + "=" + property);
            super.setProperty(description, property);
      }

00323       public void removeProperty(Object description) {
            logger.debug("Removing property: ", description);
            super.removeProperty(description);
      }

00328       public Object getProperty(Object description) {
            logger.debug("Getting property: ", description + "=" + super.getProperty(description));
            return super.getProperty(description);
      }

00333       public Map<Object,Object> getProperties() {
            logger.debug("Getting properties");
            return super.getProperties();
      }

00338       public String getID() {
            logger.debug("Getting ID: ", super.getID());
            return super.getID();
      }

00343       public void setID(String identifier) {
            logger.debug("Setting ID: ", identifier);
            super.setID(identifier);
      }

00348       public void setFlag(int flag_type, boolean flag_value) {
            logger.debug("Setting flag: ", flag_type + "=" + flag_value);
            super.setFlag(flag_type, flag_value);
      }

00353       public boolean getFlag(int flag_type) {
            logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
            return super.getFlag(flag_type);
      }

00358       public void setProperties(Map<Object,Object> properties) {
            logger.debug("Setting properties: ", properties);
            super.setProperties(properties);
      }

00363       public void setFlags(boolean[] flagsNew) {
            logger.debug("Setting flags:", flagsNew.length);
            super.setFlags(flagsNew);
      }

00368       public boolean[] getFlags() {
            logger.debug("Getting flags:", super.getFlags().length);
            return super.getFlags();
      }

00373       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;
      }

00384       public IChemObjectBuilder getBuilder() {
            return DebugChemObjectBuilder.getInstance();
      }

00388       public String getLabel() {
            logger.debug("Getting label: ", super.getLabel());
            return super.getLabel();
      }

00393       public void setLabel(String label) {
            logger.debug("Setting label: ", label);
            super.setLabel(label);
      }
}

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