InvPair.java

/*  $RCSfile$
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 *
 *  Copyright (C) 2002-2007  The Chemistry Development Kit (CDK) Project
 *
 *  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
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package org.openscience.cdk.smiles;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.math.Primes;

/**
 * This is used to hold the invariance numbers for the canonical labeling of
 * {@link IAtomContainer}s.
 *
 * @cdk.module standard
 * @cdk.githash
 */
@TestClass("org.openscience.cdk.smiles.InvPairTest")
public class InvPair implements java.io.Serializable{

    private static final long serialVersionUID = -1397634098919863122L;

  /** The description used to set the invariance numbers in the atom's property*/
  public final static String INVARIANCE_PAIR = "InvariancePair";
  public final static String CANONICAL_LABEL = "CanonicalLable";

  private long last = 0;

  private long curr = 0;

  private IAtom atom;

  private int prime;

  public InvPair() {
  }

  public InvPair(long c, IAtom a){
    curr = c;
    atom = a;
    a.setProperty(INVARIANCE_PAIR, this);
  }

    @TestMethod("testGetLast")
    public long getLast() {
        return last;
    }

    /**
     * Set the value of the seed.
     * <p/>
     * Note that use of this method implies that a new prime number is desired.
     * If so, make sure to call {@link #setPrime()} to ensure that a new prime
     * number is obtained using the new seed.
     * <p/>
     * Todo make the following robust!
     *
     * @see #getCurr()
     * @see #setPrime()
     */
    @TestMethod("testSetCurr_long")
    public void setCurr(long newCurr) {
        curr = newCurr;
    }

    /**
     * Get the current seed.
     *
     * @return The seed
     * @see #setCurr(long)
     * @see #setPrime()
     * @see #getPrime()
     */
    @TestMethod("testGetCurr")
    public long getCurr() {
        return curr;
    }

    /**
     * Check whether this instance equals another instance.
     *
     * @param e An instance of InvPair
     * @return true if they are equal, false otherwise
     */
    @TestMethod("testEquals_Object")
    public boolean equals(Object e) {
        if (e instanceof InvPair) {
            InvPair o = (InvPair) e;
//      logger.debug("Last " + last + "o.last " + o.getLast() + " curr " + curr + " o.curr " + o.getCurr() + " equals " +(last == o.getLast() && curr == o.getCurr()));
            return (last == o.getLast() && curr == o.getCurr());
        } else {
            return false;
        }
    }

    @TestMethod("testSetLast_long")
    public void setLast(long newLast) {
        last = newLast;
    }

    @TestMethod("testSetAtom_IAtom")
    public void setAtom(IAtom newAtom) {
        atom = newAtom;
    }

    @TestMethod("testGetAtom")
    public IAtom getAtom() {
        return atom;
    }

    @TestMethod("testCommit")
    public void commit() {
        atom.setProperty(CANONICAL_LABEL, Long.valueOf(curr));
    }

    /**
     * String representation.
     *
     * @return The string representation of the class.
     */
    @TestMethod("testToString")
    public String toString() {
        StringBuffer buff = new StringBuffer();
        buff.append(curr);
        buff.append("\t");
        return buff.toString();
    }

    /**
     * Get the current prime number.
     *
     * @return The current prime number
     * @see #setPrime()
     */
    @TestMethod("testGetPrime")
    public int getPrime() {
        return prime;
    }

    /**
     * Sets the prime number based on the current seed.
     * <p/>
     * Note that if you change the seed via {@link #setCurr(long)}, you should make
     * sure to call this method so that a new prime number is available via
     * {@link #getPrime()}
     *
     * @see #setCurr(long)
     * @see #getPrime()
     */
    @TestMethod("testSetPrime")
    public void setPrime() {
        prime = Primes.getPrimeAt((int) curr - 1);
    }
}