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Module to parse HELM Notation in the format 1 and 2.
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/**
 * *****************************************************************************
 * Copyright C 2015, The Pistoia Alliance
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 *****************************************************************************
 */
package org.helm.notation2.parser.notation;

import java.io.IOException;
import java.util.regex.Pattern;

import org.helm.notation2.parser.exceptionparser.NotationException;
import org.helm.notation2.parser.notation.polymer.BlobEntity;
import org.helm.notation2.parser.notation.polymer.ChemEntity;
import org.helm.notation2.parser.notation.polymer.GroupEntity;
import org.helm.notation2.parser.notation.polymer.HELMEntity;
import org.helm.notation2.parser.notation.polymer.MonomerNotation;
import org.helm.notation2.parser.notation.polymer.MonomerNotationGroupElement;
import org.helm.notation2.parser.notation.polymer.MonomerNotationGroupMixture;
import org.helm.notation2.parser.notation.polymer.MonomerNotationGroupOr;
import org.helm.notation2.parser.notation.polymer.MonomerNotationList;
import org.helm.notation2.parser.notation.polymer.MonomerNotationUnit;
import org.helm.notation2.parser.notation.polymer.MonomerNotationUnitRNA;
import org.helm.notation2.parser.notation.polymer.PeptideEntity;
import org.helm.notation2.parser.notation.polymer.RNAEntity;
import org.jdom2.JDOMException;

/**
 * Class containing validation methods
 *
 * @author hecht
 */
public final class ValidationMethod {

	/**
	 * Default constructor.
	 */
	private ValidationMethod() {

	}

	/**
	 * method to decide which of the MonomerNotation classes should be
	 * initialized
	 *
	 * @param str notation
	 * @param type polymer type
	 * @return MonomerNotation if monomer is not valid
	 * @throws NotationException if notation is not valid
	 */
	public static MonomerNotation decideWhichMonomerNotation(String str, String type)
			throws NotationException {
		MonomerNotation mon;
		/* group ? */
		if (str.startsWith("(") && str.endsWith(")")) {
			String str2 = str.substring(1, str.length() - 1);

			Pattern patternAND = Pattern.compile("\\+");
			Pattern patternOR = Pattern.compile(",");
			/* Mixture of elements */
			if (patternAND.matcher(str).find()) {
				mon = new MonomerNotationGroupMixture(str2, type);
			} /* or - groups */ else if (patternOR.matcher(str).find()) {
				mon = new MonomerNotationGroupOr(str2, type);
			} else {
				if (str.contains(".")) {
					mon = new MonomerNotationList(str2, type);
				} else {
					/* monomer unit is just in brackets */
					if (type == "RNA") {
						mon = new MonomerNotationUnitRNA(str2, type);
					} else {
						if (str2.length() > 1) {
							if (!(str2.startsWith("[") && str2.endsWith("]"))) {
								throw new NotationException("Monomers have to be in brackets: " + str);
							}
						}
						mon = new MonomerNotationUnit(str2, type);
					}
				}

			}
		} else {
			if (type == "RNA") {
				// if (str.startsWith("[") && str.endsWith("]")) {
				// mon = new MonomerNotationUnitRNA(str, type);
				// }
				mon = new MonomerNotationUnitRNA(str, type);
			} else if (type != "BLOB") {
				if (str.length() > 1) {
					if (!(str.startsWith("[") && str.endsWith("]"))) {
						throw new NotationException("Monomers have to be in brackets: " + str);
					}
				}
				mon = new MonomerNotationUnit(str, type);
			}
			else{
				mon = new MonomerNotationUnit(str, type);
			}

		}
		return mon;
	}

	/**
	 * method to decide which of the two Constructors of
	 * MonomerNotationGroupElement should be called
	 *
	 * @param str
	 *            Monomer
	 * @param type
	 *            polymer type of monomer          
	 * @param one
	 *            count of Monomer
	 * @param two
	 *            count of Monomer
	 * @param interval
	 *            Has the monomer instead of one count an interval
	 * @param isDefault
	 *            Is the count of the monomer default = 1
	 * @return MonomerNotationGroupElement
	 * @throws NotationException if notation is not valid
	 */
	public static MonomerNotationGroupElement decideWhichMonomerNotationInGroup(String str, String type, double one,
			double two, boolean interval, boolean isDefault) throws NotationException{
		MonomerNotation element;

		element = decideWhichMonomerNotation(str, type);

		if (interval) {
			return new MonomerNotationGroupElement(element, one, two);
		} else {
			return new MonomerNotationGroupElement(element, one, isDefault);
		}
	}

	/**
	 * method to decide which of the Entities classes should be initialized
	 *
	 * @param str
	 *            polymer ID
	 * @return Entity
	 * @throws NotationException if the HELMEntity is not known, ID is not in the right format
	 */
	public static HELMEntity decideWhichEntity(String str) throws NotationException {

		HELMEntity item;

		if (str.toUpperCase().matches("PEPTIDE[1-9][0-9]*")) {
			item = new PeptideEntity(str.toUpperCase());
		} else if (str.toUpperCase().matches("RNA[1-9][0-9]*")) {
			item = new RNAEntity(str.toUpperCase());
		} else if (str.toUpperCase().matches("BLOB[1-9][0-9]*")) {
			item = new BlobEntity(str.toUpperCase());
		} else if (str.toUpperCase().matches("CHEM[1-9][0-9]*")) {
			item = new ChemEntity(str.toUpperCase());
		} else if (str.toUpperCase().matches("G[1-9][0-9]*")) {
			item = new GroupEntity(str.toUpperCase());
		} else {
			throw new NotationException("ID is wrong: " + str);
		}

		return item;

	}

}