/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2003-2007 Egon Willighagen <egonw@users.sf.net>
* 2008 Aleksey Tarkhov <bayern7105@yahoo.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.tools;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.tools.manipulator.*;
import java.util.Iterator;
import java.util.List;
/**
* Class that provides methods to give unique IDs to ChemObjects.
* Methods are implemented for Atom, Bond, AtomContainer, AtomContainerSet
* and Reaction. It will only create missing IDs. If you want to create new
* IDs for all ChemObjects, you need to delete them first.
*
* @cdk.module standard
* @cdk.githash
*
* @author Egon Willighagen
* @cdk.created 2003-04-01
*
* @cdk.keyword id, creation
*/
@TestClass("org.openscience.cdk.tools.IDCreatorTest")
public abstract class IDCreator {
// counters for generated in current session IDs
private static int REACTION_COUNT = 0;
private static int ATOM_COUNT = 0;
private static int BOND_COUNT = 0;
private static int ATOMCONTAINER_COUNT = 0;
private static int ATOMCONTAINERSET_COUNT = 0;
private static int REACTIONSET_COUNT = 0;
private static int CHEMMODEL_COUNT = 0;
private static int CHEMSEQUENCE_COUNT = 0;
private static int CHEMFILE_COUNT = 0;
// prefix to prepend every individual IDs
private final static String REACTION_PREFIX = "r";
private final static String ATOM_PREFIX = "a";
private final static String BOND_PREFIX = "b";
private final static String ATOMCONTAINER_PREFIX = "m";
private final static String ATOMCONTAINERSET_PREFIX = "molSet";
private final static String REACTIONSET_PREFIX = "rset";
private final static String CHEMMODEL_PREFIX = "model";
private final static String CHEMSEQUENCE_PREFIX = "seq";
private final static String CHEMFILE_PREFIX = "file";
/**
* Old ID generation policy - to generate IDs unique over the entire set
*/
public static final int SET_UNIQUE_POLICY = 0;
/**
* New ID generation policy - to generate IDs unique only in a molecule
*/
public static final int OBJECT_UNIQUE_POLICY = 1;
/**
* Internal flag identifying the IDs generation policy. The old policy
* is to generate IDs so that in a sequence of several molecules all the
* atoms and bonds will receive the unique IDs even across molecules, i.e.
* in a set of 2 molecules the first atom of the first molecule will be "a1"
* while the first atom of the second molecule will be "aX" where X equals
* to the number of atoms in the first molecule plus 1.
* <br/>
* The new policy is to keep the singularity of IDs only within a single
* molecule, i.e. in a set of two molecules first atoms of each will be "a1".
*/
private static int policy = SET_UNIQUE_POLICY;
/**
* Alters the policy of ID generation. The IDCreator should in any case
* preserve the already existing IDs therefore if one of objects already
* has an ID set, this ID will be skipped in all the cases when attempting to
* generate a new ID value
* @param policy new policy to be used
* @see #OBJECT_UNIQUE_POLICY
* @see #SET_UNIQUE_POLICY
*/
public static void setIDPolicy(int policy) {
IDCreator.policy = policy;
}
/**
* Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
* scheme often used in CML. Supports IAtomContainer, IAtomContainerSet,
* IChemFile, IChemModel, IChemSequence, IReaction, IReactionSet,
* and derived interfaces.
*
* @param chemObject IChemObject to create IDs for.
*/
@TestMethod("testCreateIDs_IChemObject,testKeepingIDs,testNoDuplicateCreation,testCallingTwice")
public static void createIDs(IChemObject chemObject) {
if (chemObject == null) return;
resetCounters();
if (chemObject instanceof IAtomContainer) {
createIDsForAtomContainer((IAtomContainer)chemObject, null);
} else if (chemObject instanceof IAtomContainerSet) {
createIDsForAtomContainerSet((IAtomContainerSet)chemObject, null);
} else if (chemObject instanceof IReaction) {
createIDsForReaction((IReaction)chemObject, null);
} else if (chemObject instanceof IReactionSet) {
createIDsForReactionSet((IReactionSet)chemObject, null);
} else if (chemObject instanceof IChemFile) {
createIDsForChemFile((IChemFile)chemObject, null);
} else if (chemObject instanceof IChemSequence) {
createIDsForChemSequence((IChemSequence)chemObject, null);
} else if (chemObject instanceof IChemModel) {
createIDsForChemModel((IChemModel)chemObject, null);
}
}
/**
* Reset the counters so that we keep generating simple IDs within
* single chem object or a set of them
*/
private static void resetCounters() {
ATOM_COUNT = 0;
BOND_COUNT = 0;
ATOMCONTAINER_COUNT = 0;
ATOMCONTAINERSET_COUNT = 0;
REACTION_COUNT = 0;
REACTIONSET_COUNT = 0;
CHEMMODEL_COUNT = 0;
CHEMSEQUENCE_COUNT = 0;
CHEMFILE_COUNT = 0;
}
/**
* Sets the ID on the object and adds it to the tabu list.
*
* @param object IChemObject to set the ID for
* @param tabuList Tabu list to add the ID to
*/
private static int setID(String prefix, int identifier, IChemObject object, List<String> tabuList) {
identifier += 1;
while (tabuList.contains(prefix + identifier)) {
identifier += 1;
}
object.setID(prefix + identifier);
tabuList.add(prefix + identifier);
return identifier;
}
/**
* Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
* scheme often used in CML.
*
* @see #createIDs(org.openscience.cdk.interfaces.IChemObject)
*/
private static void createIDsForAtomContainer(IAtomContainer container, List<String> tabuList) {
if (tabuList == null) tabuList = AtomContainerManipulator.getAllIDs(container);
if (null == container.getID()) {
// generate new ID and remember it
ATOMCONTAINER_COUNT = setID(ATOMCONTAINER_PREFIX, ATOMCONTAINER_COUNT, container, tabuList);
}
// the tabu list for the container should force singularity
// within a container only!
List internalTabuList = AtomContainerManipulator.getAllIDs(container);
if (policy == OBJECT_UNIQUE_POLICY) {
// start atom and bond indices within a container set always from 1
ATOM_COUNT = 0;
BOND_COUNT = 0;
} else {
internalTabuList = tabuList;
}
Iterator atoms = container.atoms().iterator();
while(atoms.hasNext()) {
IAtom atom = (IAtom)atoms.next();
if (null == atom.getID()) {
ATOM_COUNT = setID(ATOM_PREFIX, ATOM_COUNT, atom, internalTabuList);
}
}
Iterator bonds = container.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
if (null == bond.getID()) {
BOND_COUNT = setID(BOND_PREFIX, BOND_COUNT, bond, internalTabuList);
}
}
}
/**
* Labels the Atom's and Bond's in each AtomContainer using the a1, a2, b1, b2
* scheme often used in CML. It will also set id's for all AtomContainers, naming
* them m1, m2, etc.
* It will not the AtomContainerSet itself.
*/
private static void createIDsForAtomContainerSet(IAtomContainerSet containerSet, List<String> tabuList) {
if (tabuList == null) tabuList = AtomContainerSetManipulator.getAllIDs(containerSet);
if (null == containerSet.getID()) {
ATOMCONTAINERSET_COUNT = setID(ATOMCONTAINERSET_PREFIX, ATOMCONTAINERSET_COUNT, containerSet, tabuList);
}
if (policy == OBJECT_UNIQUE_POLICY) {
// start atom and bond indices within a container set always from 1
ATOM_COUNT = 0;
BOND_COUNT = 0;
}
Iterator<IAtomContainer> acs = containerSet.atomContainers().iterator();
while (acs.hasNext()) {
createIDsForAtomContainer((IAtomContainer)acs.next(), tabuList);
}
}
/**
* Labels the reactants and products in the Reaction m1, m2, etc, and the atoms
* accordingly, when no ID is given.
*/
private static void createIDsForReaction(IReaction reaction, List<String> tabuList) {
if (tabuList == null) tabuList = ReactionManipulator.getAllIDs(reaction);
if (null == reaction.getID()) {
// generate new ID
REACTION_COUNT = setID(REACTION_PREFIX, REACTION_COUNT, reaction, tabuList);
}
if (policy == OBJECT_UNIQUE_POLICY) {
// start atom and bond indices within a reaction set always from 1
ATOM_COUNT = 0;
BOND_COUNT = 0;
}
for (IAtomContainer reactant : reaction.getReactants().atomContainers()) {
createIDsForAtomContainer(reactant, tabuList);
}
for (IAtomContainer product : reaction.getReactants().atomContainers()) {
createIDsForAtomContainer(product, tabuList);
}
Iterator<IAtomContainer> agents = reaction.getAgents().atomContainers().iterator();
while (agents.hasNext()) {
createIDsForAtomContainer((IAtomContainer)agents.next(), tabuList);
}
}
private static void createIDsForReactionSet(IReactionSet reactionSet, List<String> tabuList) {
if (tabuList == null) tabuList = ReactionSetManipulator.getAllIDs(reactionSet);
if (null == reactionSet.getID()) {
// generate new ID for the set
REACTIONSET_COUNT = setID(REACTIONSET_PREFIX, REACTIONSET_COUNT, reactionSet, tabuList);
}
for (Iterator reaction = reactionSet.reactions().iterator(); reaction.hasNext();) {
createIDsForReaction((IReaction)reaction.next(), tabuList);
}
}
private static void createIDsForChemFile(IChemFile file, List<String> tabuList) {
if (tabuList == null) tabuList = ChemFileManipulator.getAllIDs(file);
if (null == file.getID()) {
CHEMFILE_COUNT = setID(CHEMFILE_PREFIX, CHEMFILE_COUNT, file, tabuList);
}
if (policy == OBJECT_UNIQUE_POLICY) {
// start indices within a chem file always from 1
CHEMSEQUENCE_COUNT = 0;
}
for (IChemSequence chemSequence : file.chemSequences()) {
createIDsForChemSequence(chemSequence, tabuList);
}
}
private static void createIDsForChemSequence(IChemSequence sequence, List<String> tabuList) {
if (tabuList == null) tabuList = ChemSequenceManipulator.getAllIDs(sequence);
if (null == sequence.getID()) {
CHEMSEQUENCE_COUNT = setID(CHEMSEQUENCE_PREFIX, CHEMSEQUENCE_COUNT, sequence, tabuList);
}
if (policy == OBJECT_UNIQUE_POLICY) {
// start indices within a chem file always from 1
CHEMSEQUENCE_COUNT = 0;
}
for (IChemModel chemModel : sequence.chemModels()) {
createIDsForChemModel(chemModel, tabuList);
}
}
private static void createIDsForChemModel(IChemModel model, List<String> tabuList) {
if (tabuList == null) tabuList = ChemModelManipulator.getAllIDs(model);
if (null == model.getID()) {
CHEMMODEL_COUNT = setID(CHEMMODEL_PREFIX, CHEMMODEL_COUNT, model, tabuList);
}
ICrystal crystal = model.getCrystal();
if (crystal != null) {
if (policy == OBJECT_UNIQUE_POLICY) {
ATOM_COUNT = 0;
BOND_COUNT = 0;
}
createIDsForAtomContainer(crystal, tabuList);
}
IMoleculeSet moleculeSet = model.getMoleculeSet();
if (moleculeSet != null) {
if (policy == OBJECT_UNIQUE_POLICY) {
ATOMCONTAINERSET_COUNT = 0;
ATOMCONTAINER_COUNT = 0;
}
createIDsForAtomContainerSet(moleculeSet, tabuList);
}
IReactionSet reactionSet = model.getReactionSet();
if (reactionSet != null) {
if (policy == OBJECT_UNIQUE_POLICY) {
REACTIONSET_COUNT = 0;
REACTION_COUNT = 0;
}
createIDsForReactionSet(reactionSet, tabuList);
}
}
}