org.openscience.cdk.debug.DebugFragmentAtom Maven / Gradle / Ivy
/* Copyright (C) 2006-2008 Egon Willighagen
*
* Contact: [email protected]
*
* 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.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IFragmentAtom;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
* like the MDL molfile Group concept.
*
* @cdk.module datadebug
* @cdk.githash
*
* @author egonw
*/
public class DebugFragmentAtom extends FragmentAtom {
private static final long serialVersionUID = 0L;
ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugFragmentAtom.class);
public DebugFragmentAtom() {
super();
logger.debug("Instantiated a DebugFragmentAtom");
}
/** {@inheritDoc} */
@Override
public boolean isExpanded() {
logger.debug("Getting isExpanded state...");
return super.isExpanded();
}
/** {@inheritDoc} */
@Override
public void setExpanded(boolean bool) {
logger.debug("Setting the isExpanded state: " + bool);
super.setExpanded(bool);
}
/** {@inheritDoc} */
@Override
public IAtomContainer getFragment() {
logger.debug("Getting the fragment...");
return super.getFragment();
}
/** {@inheritDoc} */
@Override
public void setFragment(IAtomContainer fragment) {
logger.debug("Setting the fragment: ", fragment);
super.setFragment(fragment);
}
/** {@inheritDoc} */
@Override
public void setCharge(Double charge) {
logger.debug("Setting charge: ", charge);
super.setCharge(charge);
}
/** {@inheritDoc} */
@Override
public Double getCharge() {
logger.debug("Setting charge: ", super.getCharge());
return super.getCharge();
}
/** {@inheritDoc} */
@Override
public void setImplicitHydrogenCount(Integer hydrogenCount) {
logger.debug("Setting hydrogen count: ", hydrogenCount);
super.setImplicitHydrogenCount(hydrogenCount);
}
/** {@inheritDoc} */
@Override
public Integer getImplicitHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getImplicitHydrogenCount());
return super.getImplicitHydrogenCount();
}
/** {@inheritDoc} */
@Override
public void setPoint2d(Point2d point2d) {
logger.debug("Setting point2d: x=" + point2d.x + ", y=" + point2d.y);
super.setPoint2d(point2d);
}
/** {@inheritDoc} */
@Override
public void setPoint3d(Point3d point3d) {
logger.debug("Setting point3d: x=" + point3d.x + ", y=" + point3d.y, ", z=" + point3d.z);
super.setPoint3d(point3d);
}
/** {@inheritDoc} */
@Override
public void setFractionalPoint3d(Point3d point3d) {
logger.debug("Setting fractional point3d: x=" + point3d.x + ", y=" + point3d.y, ", z=" + point3d.z);
super.setFractionalPoint3d(point3d);
}
/** {@inheritDoc} */
@Override
public void setStereoParity(Integer stereoParity) {
logger.debug("Setting stereoParity: ", stereoParity);
super.setStereoParity(stereoParity);
}
/** {@inheritDoc} */
@Override
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;
}
/** {@inheritDoc} */
@Override
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;
}
/** {@inheritDoc} */
@Override
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;
}
/** {@inheritDoc} */
@Override
public Integer getStereoParity() {
logger.debug("Getting stereo parity: ", super.getStereoParity());
return super.getStereoParity();
}
/** {@inheritDoc} */
@Override
public void setAtomTypeName(String identifier) {
logger.debug("Setting atom type name: ", identifier);
super.setAtomTypeName(identifier);
}
/** {@inheritDoc} */
@Override
public void setMaxBondOrder(IBond.Order maxBondOrder) {
logger.debug("Setting max bond order: ", maxBondOrder);
super.setMaxBondOrder(maxBondOrder);
}
/** {@inheritDoc} */
@Override
public void setBondOrderSum(Double bondOrderSum) {
logger.debug("Setting bond order sum: ", bondOrderSum);
super.setBondOrderSum(bondOrderSum);
}
/** {@inheritDoc} */
@Override
public String getAtomTypeName() {
logger.debug("Getting atom type name: ", super.getAtomTypeName());
return super.getAtomTypeName();
}
/** {@inheritDoc} */
@Override
public IBond.Order getMaxBondOrder() {
logger.debug("Getting max bond order: ", super.getMaxBondOrder());
return super.getMaxBondOrder();
}
/** {@inheritDoc} */
@Override
public Double getBondOrderSum() {
logger.debug("Getting bond order sum: ", super.getBondOrderSum());
return super.getBondOrderSum();
}
/** {@inheritDoc} */
@Override
public void setFormalCharge(Integer charge) {
logger.debug("Setting formal charge: ", charge);
super.setFormalCharge(charge);
}
/** {@inheritDoc} */
@Override
public Integer getFormalCharge() {
logger.debug("Getting formal charge: ", super.getFormalCharge());
return super.getFormalCharge();
}
/** {@inheritDoc} */
@Override
public void setFormalNeighbourCount(Integer count) {
logger.debug("Setting forml neighbour count: ", count);
super.setFormalNeighbourCount(count);
}
/** {@inheritDoc} */
@Override
public Integer getFormalNeighbourCount() {
logger.debug("Getting formal neighbour count: ", super.getFormalNeighbourCount());
return super.getFormalNeighbourCount();
}
/** {@inheritDoc} */
@Override
public void setHybridization(IAtomType.Hybridization hybridization) {
logger.debug("Setting hybridization: ", hybridization);
super.setHybridization(hybridization);
}
/** {@inheritDoc} */
@Override
public IAtomType.Hybridization getHybridization() {
logger.debug("Getting hybridization: ", super.getHybridization());
return super.getHybridization();
}
/** {@inheritDoc} */
@Override
public void setCovalentRadius(Double radius) {
logger.debug("Setting covalent radius: ", radius);
super.setCovalentRadius(radius);
}
/** {@inheritDoc} */
@Override
public Double getCovalentRadius() {
logger.debug("Getting covalent radius: ", super.getCovalentRadius());
return super.getCovalentRadius();
}
/** {@inheritDoc} */
@Override
public void setValency(Integer valency) {
logger.debug("Setting valency: ", valency);
super.setValency(valency);
}
/** {@inheritDoc} */
@Override
public Integer getValency() {
logger.debug("Getting valency: ", super.getValency());
return super.getValency();
}
/** {@inheritDoc} */
@Override
public void setNaturalAbundance(Double naturalAbundance) {
logger.debug("Setting natural abundance: ", naturalAbundance);
super.setNaturalAbundance(naturalAbundance);
}
/** {@inheritDoc} */
@Override
public void setExactMass(Double exactMass) {
logger.debug("Setting exact mass: ", exactMass);
super.setExactMass(exactMass);
}
/** {@inheritDoc} */
@Override
public Double getNaturalAbundance() {
logger.debug("Getting natural abundance: ", super.getNaturalAbundance());
return super.getNaturalAbundance();
}
/** {@inheritDoc} */
@Override
public Double getExactMass() {
logger.debug("Getting exact mass: ", super.getExactMass());
return super.getExactMass();
}
/** {@inheritDoc} */
@Override
public Integer getMassNumber() {
logger.debug("Getting mass number: ", super.getMassNumber());
return super.getMassNumber();
}
/** {@inheritDoc} */
@Override
public void setMassNumber(Integer massNumber) {
logger.debug("Setting mass number: ", massNumber);
super.setMassNumber(massNumber);
}
/** {@inheritDoc} */
@Override
public Integer getAtomicNumber() {
logger.debug("Getting atomic number: ", super.getAtomicNumber());
return super.getAtomicNumber();
}
/** {@inheritDoc} */
@Override
public void setAtomicNumber(Integer atomicNumber) {
logger.debug("Setting atomic number: ", atomicNumber);
super.setAtomicNumber(atomicNumber);
}
/** {@inheritDoc} */
@Override
public String getSymbol() {
logger.debug("Getting symbol: ", super.getSymbol());
return super.getSymbol();
}
/** {@inheritDoc} */
@Override
public void setSymbol(String symbol) {
logger.debug("Setting symbol: ", symbol);
super.setSymbol(symbol);
}
/** {@inheritDoc} */
@Override
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}
/** {@inheritDoc} */
@Override
public int getListenerCount() {
logger.debug("Getting listener count: ", super.getListenerCount());
return super.getListenerCount();
}
/** {@inheritDoc} */
@Override
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
/** {@inheritDoc} */
@Override
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
/** {@inheritDoc} */
@Override
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
/** {@inheritDoc} */
@Override
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
/** {@inheritDoc} */
@Override
public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
/** {@inheritDoc} */
@Override
public T getProperty(Object description) {
logger.debug("Getting property: ", description + "=" + super.getProperty(description));
return super.getProperty(description);
}
/** {@inheritDoc} */
@Override
public Map getProperties() {
logger.debug("Getting properties");
return super.getProperties();
}
/** {@inheritDoc} */
@Override
public String getID() {
logger.debug("Getting ID: ", super.getID());
return super.getID();
}
/** {@inheritDoc} */
@Override
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}
/** {@inheritDoc} */
@Override
public void setFlag(int flagType, boolean flagValue) {
logger.debug("Setting flag: ", flagType + "=" + flagValue);
super.setFlag(flagType, flagValue);
}
/** {@inheritDoc} */
@Override
public boolean getFlag(int flagType) {
logger.debug("Setting flag: ", flagType + "=" + super.getFlag(flagType));
return super.getFlag(flagType);
}
/** {@inheritDoc} */
@Override
public void addProperties(Map properties) {
logger.debug("Setting properties: ", properties);
super.addProperties(properties);
}
/** {@inheritDoc} */
@Override
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
/** {@inheritDoc} */
@Override
public boolean[] getFlags() {
logger.debug("Getting flags:", super.getFlags().length);
return super.getFlags();
}
/** {@inheritDoc} */
@Override
public IFragmentAtom 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 (IFragmentAtom) clone;
}
/** {@inheritDoc} */
@Override
public IChemObjectBuilder getBuilder() {
return DebugChemObjectBuilder.getInstance();
}
/** {@inheritDoc} */
@Override
public String getLabel() {
logger.debug("Getting label: ", super.getLabel());
return super.getLabel();
}
/** {@inheritDoc} */
@Override
public void setLabel(String label) {
logger.debug("Setting label: ", label);
super.setLabel(label);
}
}
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