/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2002-2007 Christoph Steinbeck <steinbeck@users.sf.net>
*
* 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.fingerprint;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Tool with helper methods for IFingerprint.
*
* @author steinbeck
* @cdk.created 2002-02-24
* @cdk.keyword fingerprint
* @cdk.module standard
* @cdk.githash
*/
@TestClass("org.openscience.cdk.fingerprint.FingerprinterToolTest")
public class FingerprinterTool {
private final static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(FingerprinterTool.class);
/**
* Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1. If
* so, the molecular structure from which bs2 was generated is a possible
* substructure of bs1. <p>
*
* Example: <pre>
* Molecule mol = MoleculeFactory.makeIndole();
* BitSet bs = Fingerprinter.getFingerprint(mol);
* Molecule frag1 = MoleculeFactory.makePyrrole();
* BitSet bs1 = Fingerprinter.getFingerprint(frag1);
* if (Fingerprinter.isSubset(bs, bs1)) {
* System.out.println("Pyrrole is subset of Indole.");
* }
* </pre>
*
*@param bs1 The reference BitSet
*@param bs2 The BitSet which is compared with bs1
*@return True, if bs2 is a subset of bs1
*@cdk.keyword substructure search
*/
@TestMethod("testIsSubset_BitSet_BitSet")
public static boolean isSubset(BitSet bs1, BitSet bs2)
{
BitSet clone = (BitSet) bs1.clone();
clone.and(bs2);
if (clone.equals(bs2))
{
return true;
}
return false;
}
/**
* This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger
*
* @param bs1 First bitset
* @param bs2 Second bitset
* @return An arrayList of Integers
*/
@TestMethod("testListDifferences_BitSet_BitSet")
public static List<Integer> listDifferences(BitSet bs1, BitSet bs2)
{
List<Integer> l=new ArrayList<Integer>();
logger.debug("Listing bit positions set in bs2 but not in bs1");
for (int f = 0; f < bs2.size(); f++) {
if (bs2.get(f) && !bs1.get(f)) {
l.add(f);
logger.debug("Bit " + f + " not set in bs1");
}
}
return l;
}
}