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/* $Revision: 7636 $ $Author: egonw $ $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
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* Copyright (C) 2005-2007 Egon Willighagen <egonw@users.sf.net>
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.debug;
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import java.util.Collection;
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import java.util.Hashtable;
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import java.util.List;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IAtomParity;
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import org.openscience.cdk.interfaces.IBond;
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import org.openscience.cdk.interfaces.IChemObjectBuilder;
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import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
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import org.openscience.cdk.interfaces.IChemObjectListener;
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import org.openscience.cdk.interfaces.IElectronContainer;
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import org.openscience.cdk.interfaces.ILonePair;
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import org.openscience.cdk.interfaces.IMonomer;
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import org.openscience.cdk.interfaces.ISingleElectron;
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import org.openscience.cdk.interfaces.IStrand;
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import org.openscience.cdk.tools.LoggingTool;
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* Debugging data class.
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* @cdk.module datadebug
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public class DebugStrand extends org.openscience.cdk.Strand
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private static final long serialVersionUID = 1794588804926192427L;
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LoggingTool logger = new LoggingTool(DebugAtomContainer.class);
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public void addAtomParity(IAtomParity parity) {
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logger.debug("Adding atom parity: ", parity);
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super.addAtomParity(parity);
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public IAtomParity getAtomParity(IAtom atom) {
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logger.debug("Getting atom parity: ", atom);
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return super.getAtomParity(atom);
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public void setAtoms(IAtom[] atoms) {
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logger.debug("Setting atoms: ", atoms.length);
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super.setAtoms(atoms);
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// public void setElectronContainers(IElectronContainer[] electronContainers) {
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// logger.debug("Setting electron containers: ", electronContainers.length);
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// super.setElectronContainers(electronContainers);
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public void setAtom(int number, IAtom atom) {
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logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
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super.setAtom(number, atom);
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public IAtom getAtom(int number) {
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logger.debug("Getting atom at: ", number);
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return super.getAtom(number);
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public IBond getBond(int number) {
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logger.debug("Getting bond at: ", number);
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return super.getBond(number);
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public ILonePair getLonePair(int number) {
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logger.debug("Getting lone pair at: ", number);
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return super.getLonePair(number);
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public ISingleElectron getSingleElectron(int number) {
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logger.debug("Getting single electron at: ", number);
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return super.getSingleElectron(number);
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// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
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// super.setElectronContainer(number, electronContainer);
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// public void setElectronContainerCount(int electronContainerCount) {
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// logger.debug("Setting electron container count: ", electronContainerCount);
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// super.setElectronContainerCount(electronContainerCount);
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// public void setAtomCount(int atomCount) {
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// logger.debug("Settting atom count: ", atomCount);
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// super.setAtomCount(atomCount);
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public java.util.Iterator atoms() {
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logger.debug("Getting atoms iterator");
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return super.atoms();
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public java.util.Iterator bonds() {
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logger.debug("Getting bonds iterator");
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return super.bonds();
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public java.util.Iterator lonePairs() {
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logger.debug("Getting lone pairs iterator");
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return super.lonePairs();
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public java.util.Iterator singleElectrons() {
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logger.debug("Getting single electrons iterator");
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return super.singleElectrons();
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public java.util.Iterator electronContainers() {
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logger.debug("Getting electron containers iterator");
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return super.electronContainers();
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public IAtom getFirstAtom() {
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logger.debug("Getting first atom: ", super.getFirstAtom());
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return super.getFirstAtom();
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public IAtom getLastAtom() {
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logger.debug("Getting last atom: ", super.getLastAtom());
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return super.getLastAtom();
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public int getAtomNumber(IAtom atom) {
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logger.debug("Getting atom number: ", atom);
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return super.getAtomNumber(atom);
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public int getBondNumber(IAtom atom1, IAtom atom2) {
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logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
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return super.getBondNumber(atom1, atom2);
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public int getBondNumber(IBond bond) {
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logger.debug("Getting bond number: ", bond);
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return super.getBondNumber(bond);
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public int getLonePairNumber(ILonePair bond) {
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logger.debug("Getting lone pair number: ", bond);
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return super.getLonePairNumber(bond);
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public int getSingleElectronNumber(ISingleElectron bond) {
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logger.debug("Getting single electron number: ", bond);
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return super.getSingleElectronNumber(bond);
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public IElectronContainer getElectronContainer(int number) {
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logger.debug("Getting electron container at: ", number);
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return super.getElectronContainer(number);
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public IBond getBond(IAtom atom1, IAtom atom2) {
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logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
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return super.getBond(atom1, atom2);
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public int getAtomCount() {
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logger.debug("Getting atom count");
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return super.getAtomCount();
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public int getBondCount() {
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logger.debug("Getting bond count");
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return super.getBondCount();
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public int getLonePairCount() {
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logger.debug("Getting lone pair count");
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return super.getLonePairCount();
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public int getSingleElectronCount() {
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logger.debug("Getting single electron count");
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return super.getSingleElectronCount();
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public int getElectronContainerCount() {
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logger.debug("Getting electron container count");
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return super.getElectronContainerCount();
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// public IAtom[] getConnectedAtoms(IAtom atom) {
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// logger.debug("Getting connected atoms for atom: ", atom);
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// return super.getConnectedAtoms(atom);
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public List getConnectedAtomsList(IAtom atom) {
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logger.debug("Getting connecting atoms vector for atom: ", atom);
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return super.getConnectedAtomsList(atom);
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// public IBond[] getConnectedBonds(IAtom atom) {
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// logger.debug("Getting connected bonds for atom: ", atom);
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// return super.getConnectedBonds(atom);
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public List getConnectedBondsList(IAtom atom) {
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logger.debug("Getting connected bonds vector for atom: ", atom);
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return super.getConnectedBondsList(atom);
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public List getConnectedLonePairsList(IAtom atom) {
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logger.debug("Getting lone pairs at atom: atom=" + atom, " lone pairs=" + super.getConnectedLonePairsCount(atom));
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return super.getConnectedLonePairsList(atom);
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public List getConnectedSingleElectronsList(IAtom atom) {
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logger.debug("Getting single electrons at atom: atom=" + atom, " single electrons=" + super.getConnectedSingleElectronsCount(atom));
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return super.getConnectedSingleElectronsList(atom);
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public java.util.List getConnectedElectronContainersList(IAtom atom) {
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logger.debug("Getting connected electron containers for atom: ", atom);
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return super.getConnectedElectronContainersList(atom);
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public int getConnectedAtomsCount(IAtom atom) {
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logger.debug("Getting connected atoms count for atom: ", atom);
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return super.getConnectedAtomsCount(atom);
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public int getConnectedBondsCount(IAtom atom) {
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logger.debug("Getting connected bonds count for atom: ", atom);
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return super.getConnectedBondsCount(atom);
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public int getConnectedLonePairsCount(IAtom atom) {
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logger.debug("Getting connected lone pairs count for atom: ", atom);
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return super.getConnectedLonePairsCount(atom);
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public int getConnectedSingleElectronsCount(IAtom atom) {
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logger.debug("Getting connected single electrons count for atom: ", atom);
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return super.getConnectedSingleElectronsCount(atom);
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public double getBondOrderSum(IAtom atom) {
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logger.debug("Getting bond order sum for atom: ", atom);
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return super.getBondOrderSum(atom);
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public double getMaximumBondOrder(IAtom atom) {
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logger.debug("Getting maximum bond order for atom: ", atom);
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return super.getMaximumBondOrder(atom);
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public double getMinimumBondOrder(IAtom atom) {
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logger.debug("Getting minimum bond order for atom: ", atom);
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return super.getMinimumBondOrder(atom);
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// public void addElectronContainers(IAtomContainer atomContainer) {
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// logger.debug("Adding electron containers from atom container: ", atomContainer);
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// super.addElectronContainers(atomContainer);
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public void add(IAtomContainer atomContainer) {
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logger.debug("Adding atom container: ", atomContainer);
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super.add(atomContainer);
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public void addAtom(IAtom atom) {
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logger.debug("Adding atom: ", atom);
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public void addBond(IBond bond) {
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logger.debug("Adding bond: ", bond);
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public void addLonePair(ILonePair ec) {
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logger.debug("Adding lone pair: ", ec);
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super.addLonePair(ec);
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public void addSingleElectron(ISingleElectron ec) {
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logger.debug("Adding single electron: ", ec);
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super.addSingleElectron(ec);
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public void addElectronContainer(IElectronContainer electronContainer) {
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logger.debug("Adding electron container: ", electronContainer);
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super.addElectronContainer(electronContainer);
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public void remove(IAtomContainer atomContainer) {
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logger.debug("Removing atom container: ", atomContainer);
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super.remove(atomContainer);
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public IElectronContainer removeElectronContainer(int position) {
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logger.debug("Removing electronContainer: ", position);
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return super.removeElectronContainer(position);
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public void removeElectronContainer(IElectronContainer electronContainer) {
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logger.debug("Removing electron container: ", electronContainer);
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super.removeElectronContainer(electronContainer);
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public void removeAtom(int position) {
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logger.debug("Removing atom: ", position);
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super.removeAtom(position);
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public void removeAtom(IAtom atom) {
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logger.debug("Removing atom: ", atom);
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super.removeAtom(atom);
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public IBond removeBond(int pos) {
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logger.debug("Removing bond at " + pos);
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return super.removeBond(pos);
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public IBond removeBond(IAtom atom1, IAtom atom2) {
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logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
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return super.removeBond(atom1, atom2);
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public void removeBond(IBond bond) {
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logger.debug("Removing bond=" + bond);
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super.removeBond(bond);
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public ILonePair removeLonePair(int pos) {
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logger.debug("Removing bond at " + pos);
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return super.removeLonePair(pos);
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public void removeLonePair(ILonePair ec) {
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logger.debug("Removing bond=" + ec);
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super.removeLonePair(ec);
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public ISingleElectron removeSingleElectron(int pos) {
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logger.debug("Removing bond at " + pos);
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return super.removeSingleElectron(pos);
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public void removeSingleElectron(ISingleElectron ec) {
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logger.debug("Removing bond=" + ec);
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super.removeSingleElectron(ec);
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public void removeAtomAndConnectedElectronContainers(IAtom atom) {
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logger.debug("Removing atom and connected electron containers: ", atom);
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super.removeAtomAndConnectedElectronContainers(atom);
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public void removeAllElements() {
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logger.debug("Removing all elements");
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super.removeAllElements();
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public void removeAllElectronContainers() {
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logger.debug("Removing all electron containers");
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super.removeAllElectronContainers();
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public void removeAllBonds() {
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logger.debug("Removing all bonds");
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super.removeAllBonds();
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public void addBond(int atom1, int atom2, double order, int stereo) {
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logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
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super.addBond(atom1, atom2, order, stereo);
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public void addBond(int atom1, int atom2, double order) {
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logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
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super.addBond(atom1, atom2, order);
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public void addLonePair(int atomID) {
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logger.debug("Adding lone pair: ", atomID);
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super.addLonePair(atomID);
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public void addSingleElectron(int atomID) {
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logger.debug("Adding single electron: ", atomID);
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super.addSingleElectron(atomID);
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public boolean contains(IAtom atom) {
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logger.debug("Contains atom: ", atom);
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return super.contains(atom);
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public boolean contains(IBond bond) {
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logger.debug("Contains bond: ", bond);
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return super.contains(bond);
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public boolean contains(ILonePair ec) {
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logger.debug("Contains lone pair: ", ec);
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return super.contains(ec);
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public boolean contains(ISingleElectron ec) {
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logger.debug("Contains single electron: ", ec);
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return super.contains(ec);
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public boolean contains(IElectronContainer electronContainer) {
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logger.debug("Contains electron container: ", electronContainer);
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return super.contains(electronContainer);
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public void addListener(IChemObjectListener col) {
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logger.debug("Adding listener: ", col);
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super.addListener(col);
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public int getListenerCount() {
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logger.debug("Getting listener count: ", super.getListenerCount());
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return super.getListenerCount();
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public void removeListener(IChemObjectListener col) {
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logger.debug("Removing listener: ", col);
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super.removeListener(col);
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public void notifyChanged() {
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logger.debug("Notifying changed");
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super.notifyChanged();
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public void notifyChanged(IChemObjectChangeEvent evt) {
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logger.debug("Notifying changed event: ", evt);
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super.notifyChanged(evt);
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public void setProperty(Object description, Object property) {
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logger.debug("Setting property: ", description + "=" + property);
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super.setProperty(description, property);
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public void removeProperty(Object description) {
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logger.debug("Removing property: ", description);
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super.removeProperty(description);
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public Object getProperty(Object description) {
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logger.debug("Getting property: ", description + "=" + super.getProperty(description));
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return super.getProperty(description);
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public Hashtable getProperties() {
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logger.debug("Getting properties");
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return super.getProperties();
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public String getID() {
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logger.debug("Getting ID: ", super.getID());
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return super.getID();
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public void setID(String identifier) {
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logger.debug("Setting ID: ", identifier);
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super.setID(identifier);
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public void setFlag(int flag_type, boolean flag_value) {
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logger.debug("Setting flag: ", flag_type + "=" + flag_value);
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super.setFlag(flag_type, flag_value);
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public boolean getFlag(int flag_type) {
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logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
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return super.getFlag(flag_type);
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public void setProperties(Hashtable properties) {
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logger.debug("Setting properties: ", properties);
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super.setProperties(properties);
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public void setFlags(boolean[] flagsNew) {
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logger.debug("Setting flags:", flagsNew.length);
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super.setFlags(flagsNew);
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public boolean[] getFlags() {
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logger.debug("Getting flags:", super.getFlags().length);
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return super.getFlags();
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public Object clone() throws CloneNotSupportedException {
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clone = super.clone();
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} catch (Exception exception) {
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logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
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logger.debug(exception);
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public IChemObjectBuilder getBuilder() {
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return DebugChemObjectBuilder.getInstance();
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public String getStrandName() {
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logger.debug("Getting strand name: ", super.getStrandName());
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return super.getStrandName();
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public String getStrandType() {
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logger.debug("Getting strand type: ", super.getStrandType());
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return super.getStrandType();
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public void setStrandName(String cStrandName) {
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logger.debug("Setting strand name to: ", cStrandName);
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super.setStrandName(cStrandName);
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public void setStrandType(String cStrandType) {
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logger.debug("Setting strand type to: ", cStrandType);
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super.setStrandType(cStrandType);
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public void addAtom(IAtom oAtom, IMonomer oMonomer) {
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logger.debug("Adding atom to monomer: ", oAtom, oMonomer);
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super.addAtom(oAtom, oMonomer);
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public int getMonomerCount() {
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logger.debug("Getting monomer count: ", super.getMonomerCount());
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return super.getMonomerCount();
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public IMonomer getMonomer(String cName) {
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logger.debug("Getting monomer for String: ", cName);
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return super.getMonomer(cName);
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public Collection getMonomerNames() {
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logger.debug("Getting monomer names");
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return super.getMonomerNames();
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public void removeMonomer(String name) {
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logger.debug("Removing monomer by string: ", name);
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super.removeMonomer(name);
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public Hashtable getMonomers() {
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logger.debug("Getting monomers as hashtable");
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return super.getMonomers();
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public void stateChanged(IChemObjectChangeEvent event) {
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logger.debug("Receiving state changed event: ", event);
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super.stateChanged(event);
added
removed
src/org/openscience/cdk/debug/DebugStrand.java
