/* $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); } }