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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.polymer;

import java.io.IOException;
import java.util.List;

import org.helm.notation2.parser.exceptionparser.HELM1ConverterException;
import org.helm.notation2.parser.exceptionparser.NotationException;
import org.helm.notation2.parser.exceptionparser.SimplePolymerSectionException;
import org.jdom2.JDOMException;

import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonTypeInfo;

/**
 * PolymerElements
 *
 * @author hecht
 */
@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "classType")
public abstract class PolymerElements {

	@JsonIgnore
	public List listMonomerNotations = null;

	protected HELMEntity entity;

	public PolymerElements() {

	}

	public PolymerElements(HELMEntity entity) {
		this.entity = entity;
	}

	public void setListOfElements(List monomers) {
		this.listMonomerNotations = monomers;
	}

	/**
	 * method to get a list of all elements
	 *
	 * @return List{@link MonomerNotation} list of all monomer notations
	 */
	public abstract List getListOfElements();

	public HELMEntity getEntity() {
		return this.entity;
	}

	/**
	 * method to add a monomer to the polymer
	 *
	 * @param str
	 *            Monomer
	 * @throws SimplePolymerSectionException Simple Polymer Section is not valid
	 * @throws NotationException if HELM notation is not valid
	 */
	public abstract void addMonomerNotation(String str)
			throws SimplePolymerSectionException, NotationException;

	/**
	 * method to get the current monomer
	 *
	 * @return current Monomer
	 */
	@JsonIgnore
	public abstract MonomerNotation getCurrentMonomerNotation();

	/**
	 * method to change the current Monomer
	 *
	 * @param not
	 *            MonomerNotation
	 */
	public abstract void changeMonomerNotation(MonomerNotation not);

	/**
	 * method to generate a valid HELM2 of this object
	 *
	 * @return valid HELM2
	 */
	public String toHELM2() {
		StringBuilder notation = new StringBuilder();
		for (int i = 0; i < listMonomerNotations.size(); i++) {
			notation.append(listMonomerNotations.get(i).toHELM2() + ".");

		}

		notation.setLength(notation.length() - 1);
		return notation.toString();
	}

	/**
	 * @return PolymerElments in HELM format
	 * @throws HELM1ConverterException if one single object can not be downgraded to HELM1-Format
	 * 
	 */
	public String toHELM() throws HELM1ConverterException {
		StringBuilder notation = new StringBuilder();
		for (int i = 0; i < listMonomerNotations.size(); i++) {
			notation.append(listMonomerNotations.get(i).toHELM() + ".");

		}

		notation.setLength(notation.length() - 1);
		return notation.toString();
	}

}