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The protein structure modules of BioJava.
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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.quaternary;

import java.util.Collections;
import java.util.List;


/** A class to resolve the operators for transformations
 *
 * @author Peter Rose
 *
 */
public class OperatorResolver {

	/**
	 * Unary operator expressions are parsed stored unary operations.
	 * For example the operator expression "(1,2,3,4)" is stored as a list 1,2,3,4
	 */
	private List unaryOperators = Collections.emptyList();
	/**
	 * Binary Operator expressions are parsed and stored as ordered pairs of
	 * binary operators. For example the operator expression "(1-60)(61-88)"
	 * is saved as a list of pairs {1,61}, {1,62}, .., {1,88}, ... {60,88}.
	 */
	private List> binaryOperators = Collections.emptyList();


	/**
	 * Parses the operator expression and save the operators as a list
	 * of unary or binary operators (i.e. matrix multiplication, see below).
	 * Operation expressions are given in a compact notation and specify
	 * matrices from the operations list.
	 * An operation expression can be a comma-separated list 1, 5, 9,
	 * a dash-delimited range 1-60 or a matrix multiplication involving two
	 * or more lists or ranges. For instance, (X0)(1-20) specifies the
	 * portion of the X174 procapsid crystal asymmetric unit belonging to
	 * the first independent virus particle and corresponds
	 * to the 20 transformations [X0][1], [X0][2], ... , [X0][20].
	 * See C. Lawson, Acta Cryst., D64, 874-882, 2008.
	 *
	 * @param operatorExpression the operator expression to be parsed
	 */
	public  void parseOperatorExpressionString(String operatorExpression) throws IllegalArgumentException {
		String expression = operatorExpression.trim();

		// remove single quotes, i.e. '(1-49)' in 1CGM
		expression = expression.replaceAll("'", "");

		if (BioAssemblyTools.isUnaryExpression(expression)) {
			unaryOperators = BioAssemblyTools.parseUnaryOperatorExpression(expression);
		} else {
			binaryOperators = BioAssemblyTools.parseBinaryOperatorExpression(expression);
		}

		//System.out.println("OperatorResolver: unary: " + unaryOperators + " | binary: " + binaryOperators);
	}





	public void setUnaryOperators(List unaryOperators) {
		this.unaryOperators = unaryOperators;
	}





	public void setBinaryOperators(List> binaryOperators) {
		this.binaryOperators = binaryOperators;
	}

	/**
	 * Returns a list of operators for this assembly. The operators
	 * refer to the transformations that should be applied to
	 * the asym ids to generate this macromolecular assembly.
	 * @return the unary operators for this assembly
	 */
	public List getUnaryOperators() {
		return unaryOperators;
	}

	/**
	 * Returns a list of operators for this assembly. The operators
	 * refer to the transformations that should be applied to
	 * the asym ids to generate this macromolecular assembly.
	 * Each ordered pair refers to the multiplication
	 * of the two transformation matrices in the
	 * pdbx_structure_oper_list category.
	 * @return the binary operators for this assembly
	 */
	public List> getBinaryOperators() {
		return binaryOperators;
	}


}