org.xmlcml.cml.tools.MorganAtomMatcher Maven / Gradle / Ivy

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/**
 *    Copyright 2011 Peter Murray-Rust et. al.
 *
 *    Licensed under the Apache License, Version 2.0 (the "License");
 *    you may not use this file except in compliance with the License.
 *    You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0
 *
 *    Unless required by applicable law or agreed to in writing, software
 *    distributed under the License is distributed on an "AS IS" BASIS,
 *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *    See the License for the specific language governing permissions and
 *    limitations under the License.
 */

package org.xmlcml.cml.tools;

import java.util.List;

import org.xmlcml.cml.base.CMLConstants;
import org.xmlcml.cml.element.CMLAtom;
import org.xmlcml.cml.element.CMLAtomSet;
import org.xmlcml.cml.element.CMLLink;
import org.xmlcml.cml.element.CMLMap;

public class MorganAtomMatcher extends AtomMatcher {

	public MorganAtomMatcher() {
		super();
	}
	
	public CMLMap match(CMLAtomSet atomSet0, CMLAtomSet atomSet1, String title) {
		CMLLink cmlLink;
		CMLMap cmlMap = makeMap();
		Morgan morgan0 = new Morgan(atomSet0);
		List morganList0 = morgan0.getMorganList();
		List atomSetList0 = morgan0.getAtomSetList();
		Morgan morgan1 = new Morgan(atomSet1);
		List morganList1 = morgan1.getMorganList();
		List atomSetList1 = morgan1.getAtomSetList();
		if (morganList0.size() != morganList1.size()) {
			;// may be different as atomSets may have different
			// equivalences
		} else {
			for (int i = 0; i < morganList0.size(); i++) {
				if (morganList0.get(i).intValue() != morganList1.get(i)
						.intValue()) {
					throw new RuntimeException(
							"morgan numbers do not match; (Matching non-identical atomSets?)"
									+ " Failed.... " + i);
				}
				CMLAtomSet atomSetx0 = atomSetList0.get(i);
				CMLAtomSet atomSetx1 = atomSetList1.get(i);
				List atoms0 = atomSetx0.getAtoms();
				List atoms1 = atomSetx1.getAtoms();
				// atom sets are same size so we have an equivalence
				if (atomSetx0.size() == atomSetx1.size()) {
					cmlLink = new CMLLink();
					cmlLink.setTitle(title + CMLConstants.S_SPACE + atomSetx0.size());
					// if single atom we have exact match so add as link
					// if annotation is required add it outside
					if (atomSetx0.size() == 1) {
						cmlLink.setFrom(atoms0.get(0).getId());
						cmlLink.setTo(atoms1.get(0).getId());
					} else {
						String[] atomSet0S = atomSetx0.getXMLContent();
						String[] atomSet1S = atomSetx1.getXMLContent();
						cmlLink.setFromSet(atomSet0S);
						cmlLink.setToSet(atomSet1S);
					}
					cmlMap.addUniqueLink(cmlLink, CMLMap.Direction.EITHER);
				} else {
					throw new RuntimeException(
							"atom sets wrong size in Morga");
					// mismatched atom sets - match fails
				}
			}
		}
		return cmlMap;
	}

	
}