org.openscience.cdk.debug.DebugBioPolymer Maven / Gradle / Ivy
/* Copyright (C) 2005-2007 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.
*
* 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.Collection;
import java.util.List;
import java.util.Map;
import org.openscience.cdk.BioPolymer;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
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.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMonomer;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.IStrand;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Debugging data class.
*
* @author egonw
* @cdk.module datadebug
* @cdk.githash
*/
public class DebugBioPolymer extends BioPolymer implements IBioPolymer {
private static final long serialVersionUID = 5349870327516864575L;
ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugAtomContainer.class);
/** {@inheritDoc} */
@Override
public void addStereoElement(IStereoElement parity) {
logger.debug("Adding stereo element: ", parity);
super.addStereoElement(parity);
}
/** {@inheritDoc} */
@Override
public Iterable stereoElements() {
logger.debug("Getting stereo elements.");
return super.stereoElements();
}
/** {@inheritDoc} */
@Override
public void setAtoms(IAtom[] atoms) {
logger.debug("Setting atoms: ", atoms.length);
super.setAtoms(atoms);
}
// public void setElectronContainers(IElectronContainer[] electronContainers) {
// logger.debug("Setting electron containers: ", electronContainers.length);
// super.setElectronContainers(electronContainers);
// }
/** {@inheritDoc} */
@Override
public void setAtom(int number, IAtom atom) {
logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
super.setAtom(number, atom);
}
/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
}
/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
}
/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
}
/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
}
// public void setElectronContainer(int number, IElectronContainer electronContainer) {
// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
// super.setElectronContainer(number, electronContainer);
// }
// public void setElectronContainerCount(int electronContainerCount) {
// logger.debug("Setting electron container count: ", electronContainerCount);
// super.setElectronContainerCount(electronContainerCount);
// }
// public void setAtomCount(int atomCount) {
// logger.debug("Settting atom count: ", atomCount);
// super.setAtomCount(atomCount);
// }
/** {@inheritDoc} */
@Override
public Iterable atoms() {
logger.debug("Getting atoms iterator");
return super.atoms();
}
/** {@inheritDoc} */
@Override
public Iterable bonds() {
logger.debug("Getting bonds iterator");
return super.bonds();
}
/** {@inheritDoc} */
@Override
public Iterable lonePairs() {
logger.debug("Getting lone pairs iterator");
return super.lonePairs();
}
/** {@inheritDoc} */
@Override
public Iterable singleElectrons() {
logger.debug("Getting single electrons iterator");
return super.singleElectrons();
}
/** {@inheritDoc} */
@Override
public Iterable electronContainers() {
logger.debug("Getting electron containers iterator");
return super.electronContainers();
}
/** {@inheritDoc} */
@Override
public IAtom getFirstAtom() {
logger.debug("Getting first atom: ", super.getFirstAtom());
return super.getFirstAtom();
}
/** {@inheritDoc} */
@Override
public IAtom getLastAtom() {
logger.debug("Getting last atom: ", super.getLastAtom());
return super.getLastAtom();
}
/** {@inheritDoc} */
@Override
public int getAtomNumber(IAtom atom) {
logger.debug("Getting atom number: ", atom);
return super.getAtomNumber(atom);
}
/** {@inheritDoc} */
@Override
public int getBondNumber(IAtom atom1, IAtom atom2) {
logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
return super.getBondNumber(atom1, atom2);
}
/** {@inheritDoc} */
@Override
public int getBondNumber(IBond bond) {
logger.debug("Getting bond number: ", bond);
return super.getBondNumber(bond);
}
/** {@inheritDoc} */
@Override
public int getLonePairNumber(ILonePair bond) {
logger.debug("Getting lone pair number: ", bond);
return super.getLonePairNumber(bond);
}
/** {@inheritDoc} */
@Override
public int getSingleElectronNumber(ISingleElectron bond) {
logger.debug("Getting single electron number: ", bond);
return super.getSingleElectronNumber(bond);
}
/** {@inheritDoc} */
@Override
public IElectronContainer getElectronContainer(int number) {
logger.debug("Getting electron container at: ", number);
return super.getElectronContainer(number);
}
/** {@inheritDoc} */
@Override
public IBond getBond(IAtom atom1, IAtom atom2) {
logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
return super.getBond(atom1, atom2);
}
/** {@inheritDoc} */
@Override
public int getAtomCount() {
logger.debug("Getting atom count");
return super.getAtomCount();
}
/** {@inheritDoc} */
@Override
public int getBondCount() {
logger.debug("Getting bond count");
return super.getBondCount();
}
/** {@inheritDoc} */
@Override
public int getLonePairCount() {
logger.debug("Getting lone pair count");
return super.getLonePairCount();
}
/** {@inheritDoc} */
@Override
public int getSingleElectronCount() {
logger.debug("Getting single electron count");
return super.getSingleElectronCount();
}
/** {@inheritDoc} */
@Override
public int getElectronContainerCount() {
logger.debug("Getting electron container count");
return super.getElectronContainerCount();
}
// public IAtom[] getConnectedAtoms(IAtom atom) {
// logger.debug("Getting connected atoms for atom: ", atom);
// return super.getConnectedAtoms(atom);
// }
/** {@inheritDoc} */
@Override
public List getConnectedAtomsList(IAtom atom) {
logger.debug("Getting connecting atoms vector for atom: ", atom);
return super.getConnectedAtomsList(atom);
}
// public IBond[] getConnectedBonds(IAtom atom) {
// logger.debug("Getting connected bonds for atom: ", atom);
// return super.getConnectedBonds(atom);
// }
/** {@inheritDoc} */
@Override
public List getConnectedBondsList(IAtom atom) {
logger.debug("Getting connected bonds vector for atom: ", atom);
return super.getConnectedBondsList(atom);
}
/** {@inheritDoc} */
@Override
public List getConnectedLonePairsList(IAtom atom) {
logger.debug("Getting lone pairs at atom: atom=" + atom,
" lone pairs=" + super.getConnectedLonePairsCount(atom));
return super.getConnectedLonePairsList(atom);
}
/** {@inheritDoc} */
@Override
public List getConnectedSingleElectronsList(IAtom atom) {
logger.debug("Getting single electrons at atom: atom=" + atom,
" single electrons=" + super.getConnectedSingleElectronsCount(atom));
return super.getConnectedSingleElectronsList(atom);
}
/** {@inheritDoc} */
@Override
public List getConnectedElectronContainersList(IAtom atom) {
logger.debug("Getting connected electron containers for atom: ", atom);
return super.getConnectedElectronContainersList(atom);
}
/** {@inheritDoc} */
@Override
public int getConnectedAtomsCount(IAtom atom) {
logger.debug("Getting connected atoms count for atom: ", atom);
return super.getConnectedAtomsCount(atom);
}
/** {@inheritDoc} */
@Override
public int getConnectedBondsCount(IAtom atom) {
logger.debug("Getting connected bonds count for atom: ", atom);
return super.getConnectedBondsCount(atom);
}
/** {@inheritDoc} */
@Override
public int getConnectedLonePairsCount(IAtom atom) {
logger.debug("Getting connected lone pairs count for atom: ", atom);
return super.getConnectedLonePairsCount(atom);
}
/** {@inheritDoc} */
@Override
public int getConnectedSingleElectronsCount(IAtom atom) {
logger.debug("Getting connected single electrons count for atom: ", atom);
return super.getConnectedSingleElectronsCount(atom);
}
/** {@inheritDoc} */
@Override
public double getBondOrderSum(IAtom atom) {
logger.debug("Getting bond order sum for atom: ", atom);
return super.getBondOrderSum(atom);
}
/** {@inheritDoc} */
@Override
public Order getMaximumBondOrder(IAtom atom) {
logger.debug("Getting maximum bond order for atom: ", atom);
return super.getMaximumBondOrder(atom);
}
/** {@inheritDoc} */
@Override
public Order getMinimumBondOrder(IAtom atom) {
logger.debug("Getting minimum bond order for atom: ", atom);
return super.getMinimumBondOrder(atom);
}
// public void addElectronContainers(IAtomContainer atomContainer) {
// logger.debug("Adding electron containers from atom container: ", atomContainer);
// super.addElectronContainers(atomContainer);
// }
/** {@inheritDoc} */
@Override
public void add(IAtomContainer atomContainer) {
logger.debug("Adding atom container: ", atomContainer);
super.add(atomContainer);
}
/** {@inheritDoc} */
@Override
public void addAtom(IAtom atom) {
logger.debug("Adding atom: ", atom);
super.addAtom(atom);
}
/** {@inheritDoc} */
@Override
public void addBond(IBond bond) {
logger.debug("Adding bond: ", bond);
super.addBond(bond);
}
/** {@inheritDoc} */
@Override
public void addLonePair(ILonePair ec) {
logger.debug("Adding lone pair: ", ec);
super.addLonePair(ec);
}
/** {@inheritDoc} */
@Override
public void addSingleElectron(ISingleElectron ec) {
logger.debug("Adding single electron: ", ec);
super.addSingleElectron(ec);
}
/** {@inheritDoc} */
@Override
public void addElectronContainer(IElectronContainer electronContainer) {
logger.debug("Adding electron container: ", electronContainer);
super.addElectronContainer(electronContainer);
}
/** {@inheritDoc} */
@Override
public void remove(IAtomContainer atomContainer) {
logger.debug("Removing atom container: ", atomContainer);
super.remove(atomContainer);
}
/** {@inheritDoc} */
@Override
public IElectronContainer removeElectronContainer(int position) {
logger.debug("Removing electronContainer: ", position);
return super.removeElectronContainer(position);
}
/** {@inheritDoc} */
@Override
public void removeElectronContainer(IElectronContainer electronContainer) {
logger.debug("Removing electron container: ", electronContainer);
super.removeElectronContainer(electronContainer);
}
/** {@inheritDoc} */
@Override
public void removeAtom(int position) {
logger.debug("Removing atom: ", position);
super.removeAtom(position);
}
/** {@inheritDoc} */
@Override
public void removeAtom(IAtom atom) {
logger.debug("Removing atom: ", atom);
super.removeAtom(atom);
}
/** {@inheritDoc} */
@Override
public IBond removeBond(int pos) {
logger.debug("Removing bond at " + pos);
return super.removeBond(pos);
}
/** {@inheritDoc} */
@Override
public IBond removeBond(IAtom atom1, IAtom atom2) {
logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
return super.removeBond(atom1, atom2);
}
/** {@inheritDoc} */
@Override
public void removeBond(IBond bond) {
logger.debug("Removing bond=" + bond);
super.removeBond(bond);
}
/** {@inheritDoc} */
@Override
public ILonePair removeLonePair(int pos) {
logger.debug("Removing bond at " + pos);
return super.removeLonePair(pos);
}
/** {@inheritDoc} */
@Override
public void removeLonePair(ILonePair ec) {
logger.debug("Removing bond=" + ec);
super.removeLonePair(ec);
}
/** {@inheritDoc} */
@Override
public ISingleElectron removeSingleElectron(int pos) {
logger.debug("Removing bond at " + pos);
return super.removeSingleElectron(pos);
}
/** {@inheritDoc} */
@Override
public void removeSingleElectron(ISingleElectron ec) {
logger.debug("Removing bond=" + ec);
super.removeSingleElectron(ec);
}
/** {@inheritDoc} */
@Override
public void removeAtomAndConnectedElectronContainers(IAtom atom) {
logger.debug("Removing atom and connected electron containers: ", atom);
super.removeAtomAndConnectedElectronContainers(atom);
}
/** {@inheritDoc} */
@Override
public void removeAllElements() {
logger.debug("Removing all elements");
super.removeAllElements();
}
/** {@inheritDoc} */
@Override
public void removeAllElectronContainers() {
logger.debug("Removing all electron containers");
super.removeAllElectronContainers();
}
/** {@inheritDoc} */
@Override
public void removeAllBonds() {
logger.debug("Removing all bonds");
super.removeAllBonds();
}
/** {@inheritDoc} */
@Override
public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) {
logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
super.addBond(atom1, atom2, order, stereo);
}
/** {@inheritDoc} */
@Override
public void addBond(int atom1, int atom2, IBond.Order order) {
logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
super.addBond(atom1, atom2, order);
}
/** {@inheritDoc} */
@Override
public void addLonePair(int atomID) {
logger.debug("Adding lone pair: ", atomID);
super.addLonePair(atomID);
}
/** {@inheritDoc} */
@Override
public void addSingleElectron(int atomID) {
logger.debug("Adding single electron: ", atomID);
super.addSingleElectron(atomID);
}
/** {@inheritDoc} */
@Override
public boolean contains(IAtom atom) {
logger.debug("Contains atom: ", atom);
return super.contains(atom);
}
/** {@inheritDoc} */
@Override
public boolean contains(IBond bond) {
logger.debug("Contains bond: ", bond);
return super.contains(bond);
}
/** {@inheritDoc} */
@Override
public boolean contains(ILonePair ec) {
logger.debug("Contains lone pair: ", ec);
return super.contains(ec);
}
/** {@inheritDoc} */
@Override
public boolean contains(ISingleElectron ec) {
logger.debug("Contains single electron: ", ec);
return super.contains(ec);
}
/** {@inheritDoc} */
@Override
public boolean contains(IElectronContainer electronContainer) {
logger.debug("Contains electron container: ", electronContainer);
return super.contains(electronContainer);
}
/** {@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 IBioPolymer clone() throws CloneNotSupportedException {
IBioPolymer clone = null;
try {
clone = super.clone();
} catch (Exception exception) {
logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
}
/** {@inheritDoc} */
@Override
public IChemObjectBuilder getBuilder() {
return DebugChemObjectBuilder.getInstance();
}
/** {@inheritDoc} */
@Override
public void stateChanged(IChemObjectChangeEvent event) {
logger.debug("Receiving state changed event: ", event);
super.stateChanged(event);
}
/** {@inheritDoc} */
@Override
public void addAtom(IAtom oAtom, IMonomer oMonomer) {
logger.debug("Adding atom to monomer: ", oAtom, oMonomer);
super.addAtom(oAtom, oMonomer);
}
/** {@inheritDoc} */
@Override
public int getMonomerCount() {
logger.debug("Getting monomer count: ", super.getMonomerCount());
return super.getMonomerCount();
}
/** {@inheritDoc} */
@Override
public IMonomer getMonomer(String cName) {
logger.debug("Getting monomer for String: ", cName);
return super.getMonomer(cName);
}
/** {@inheritDoc} */
@Override
public Collection getMonomerNames() {
logger.debug("Getting monomer names");
return super.getMonomerNames();
}
/** {@inheritDoc} */
@Override
public void removeMonomer(String name) {
logger.debug("Removing monomer by string: ", name);
super.removeMonomer(name);
}
/** {@inheritDoc} */
@Override
public void addAtom(IAtom oAtom, IStrand oStrand) {
logger.debug("Adding stoms to strand: ", oAtom, oStrand);
super.addAtom(oAtom, oStrand);
}
/** {@inheritDoc} */
@Override
public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) {
logger.debug("Adding stoms to strand/monomer: ", oAtom, oMonomer, oStrand);
super.addAtom(oAtom, oMonomer, oStrand);
}
/** {@inheritDoc} */
@Override
public IMonomer getMonomer(String monName, String strandName) {
logger.debug("Getting monomer from strand: ", monName, strandName);
return super.getMonomer(monName, strandName);
}
/** {@inheritDoc} */
@Override
public int getStrandCount() {
logger.debug("Getting strand count: ", super.getStrandCount());
return super.getStrandCount();
}
/** {@inheritDoc} */
@Override
public IStrand getStrand(String cName) {
logger.debug("Getting strand by name: ", cName);
return super.getStrand(cName);
}
/** {@inheritDoc} */
@Override
public Collection getStrandNames() {
logger.debug("Getting strand names: ", super.getStrandNames());
return super.getStrandNames();
}
/** {@inheritDoc} */
@Override
public void removeStrand(String name) {
logger.debug("Removing strand by name: ", name);
super.removeStrand(name);
}
/** {@inheritDoc} */
@Override
public Map getStrands() {
logger.debug("Getting strands: ", super.getStrands());
return super.getStrands();
}
}
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