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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools IDCreator.java,1.11,1.12
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From: Egon W. <eg...@us...> - 2004-02-25 15:15:09
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5460/src/org/openscience/cdk/tools Modified Files: IDCreator.java Log Message: IDCreator now creates missing IDs only. API highly changed: check JavaDoc Index: IDCreator.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/IDCreator.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- IDCreator.java 12 Feb 2004 10:20:46 -0000 1.11 +++ IDCreator.java 25 Feb 2004 15:00:06 -0000 1.12 @@ -28,6 +28,8 @@ */ package org.openscience.cdk.tools; +import java.util.Vector; + import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; @@ -38,7 +40,8 @@ /** * Class that provides methods to give unique IDs to ChemObjects. * Methods are implemented for Atom, Bond, AtomContainer, SetOfAtomContainers - * and Reaction. + * 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 * @@ -50,36 +53,62 @@ public class IDCreator { /** - * Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 - * scheme often used in CML. It will not set an id for the AtomContainer. - * - * @see #createAtomContainerAndAtomAndBondIDs(SetOfAtomContainers) + * A list of taken IDs. + */ + private Vector tabuList; + + /** + * Keep track of numbers. */ - public static void createAtomAndBondIDs(AtomContainer container) { - IDCreator.createAtomAndBondIDs(container, 0, 0); + int atomCount; + int bondCount; + int moleculeCount; + int reactionCount; + + public IDCreator() { + reset(); } - + + public void reset() { + tabuList = null; + atomCount = 0; + bondCount = 0; + moleculeCount = 0; + reactionCount = 0; + } + /** * Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 - * scheme often used in CML. It will not set an id for the AtomContainer. - * - * <p>An offset can be used to start numbering at, for example, a3 instead - * of a1 using an offset = 2. - * - * @param atomOffset Lowest ID number to be used for the Atoms - * @param bondOffset Lowest ID number to be used for the Bonds + * scheme often used in CML. * * @see #createAtomContainerAndAtomAndBondIDs(SetOfAtomContainers) */ - public static void createAtomAndBondIDs(AtomContainer container, - int atomOffset, int bondOffset) { + public void createIDs(AtomContainer container) { + if (tabuList == null) tabuList = AtomContainerManipulator.getAllIDs(container); + + if (container.getID() == null) { + moleculeCount++; + while (tabuList.contains("m" + moleculeCount)) moleculeCount++; + container.setID("m" + moleculeCount); + } + Atom[] atoms = container.getAtoms(); for (int i=0; i<atoms.length; i++) { - atoms[i].setID("a" + (i+1+atomOffset)); + Atom atom = atoms[i]; + if (atom.getID() == null) { + atomCount++; + while (tabuList.contains("a" + atomCount)) atomCount++; + atoms[i].setID("a" + atomCount); + } } Bond[] bonds = container.getBonds(); for (int i=0; i<bonds.length; i++) { - bonds[i].setID("b" + (i+1+bondOffset)); + Bond bond = bonds[i]; + if (bond.getID() == null) { + bondCount++; + while (tabuList.contains("b" + bondCount)) bondCount++; + atoms[i].setID("b" + bondCount); + } } } @@ -89,76 +118,49 @@ * them m1, m2, etc. * It will not the SetOfAtomContainers itself. */ - public static void createAtomContainerAndAtomAndBondIDs(SetOfAtomContainers containerSet) { - IDCreator.createAtomContainerAndAtomAndBondIDs(containerSet, 0, 0, 0); - } + public void createIDs(SetOfAtomContainers containerSet) { + if (containerSet.getID() == null) { + moleculeCount++; + while (tabuList.contains("molSet" + moleculeCount)) moleculeCount++; + containerSet.setID("molSet" + moleculeCount); + } - /** - * 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 SetOfAtomContainers itself. - * - * @param containerOffset Lowest ID number to be used for the AtomContainers - * @param atomOffset Lowest ID number to be used for the Atoms - * @param bondOffset Lowest ID number to be used for the Bonds - */ - public static void createAtomContainerAndAtomAndBondIDs(SetOfAtomContainers containerSet, - int containerOffset, int atomOffset, int bondOffset) { AtomContainer[] containers = containerSet.getAtomContainers(); - int atomCount = atomOffset; - int bondCount = bondOffset; for (int i=0; i<containers.length; i++) { AtomContainer container = containers[i]; - container.setID("m" + (i+1+containerOffset)); - IDCreator.createAtomAndBondIDs(container, atomCount, bondCount); - atomCount += container.getAtomCount(); - bondCount += container.getBondCount(); + if (container.getID() == null) { + createIDs(container); + } } } /** * Labels the reactants and products in the Reaction m1, m2, etc, and the atoms - * accordingly. It does not apply mapping such that mapped atoms have the same ID. + * accordingly, when no ID is given. */ - public static void createIDs(Reaction reaction) { - IDCreator.createIDs(reaction, 0, 0, 0); - } - public static void createIDs(Reaction reaction, - int containerOffset, int atomOffset, int bondOffset) { + public void createIDs(Reaction reaction) { + if (tabuList == null) tabuList = ReactionManipulator.getAllIDs(reaction); + + if (reaction.getID() == null) { + reactionCount++; + while (tabuList.contains("r" + reactionCount)) reactionCount++; + reaction.setID("r" + reactionCount); + } + AtomContainer[] reactants = reaction.getReactants().getAtomContainers(); - int atomCount = atomOffset; - int bondCount = bondOffset; for (int i=0; i<reactants.length; i++) { - AtomContainer container = reactants[i]; - container.setID("m" + (i+1+containerOffset)); - IDCreator.createAtomAndBondIDs(container, atomCount, bondCount); - atomCount += container.getAtomCount(); - bondCount += container.getBondCount(); + createIDs(reactants[i]); } AtomContainer[] products = reaction.getProducts().getAtomContainers(); for (int i=0; i<products.length; i++) { - AtomContainer container = products[i]; - container.setID("m" + (i+1+containerOffset)); - IDCreator.createAtomAndBondIDs(container, atomCount, bondCount); - atomCount += container.getAtomCount(); - bondCount += container.getBondCount(); + createIDs(products[i]); } } - public static void createIDs(SetOfReactions reactionSet) { + public void createIDs(SetOfReactions reactionSet) { Reaction[] reactions = reactionSet.getReactions(); - int containerCount = 0; - int atomCount = 0; - int bondCount = 0; for (int i=0; i<reactions.length; i++) { - Reaction reaction = reactions[i]; - reaction.setID("r" + (i+1)); - IDCreator.createIDs(reaction, containerCount, atomCount, bondCount); - containerCount += ReactionManipulator.getAllAtomContainers(reaction).length; - AtomContainer container = ReactionManipulator.getAllInOneContainer(reaction); - atomCount += container.getAtomCount(); - bondCount += container.getBondCount(); + createIDs(reactions[i]); } } |