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Module to parse HELM Notation in the format 1 and 2.
/**
* *****************************************************************************
* 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.text.DecimalFormat;
import org.helm.notation2.parser.exceptionparser.NotationException;
import org.jdom2.JDOMException;
/**
* MonomerNotationGroupOr class to represent an or group
*
* @author hecht
*/
public class MonomerNotationGroupOr extends MonomerNotationGroup {
/**
* Constructs with the given String an Or group
*
* @param str details about the group
* @param type type of the current polymer
* @throws NotationException if notation is not valid
*/
public MonomerNotationGroupOr(String str, String type) throws NotationException {
super(str, type);
/* Or elements are separated by , */
String[] parts = str.split(",");
boolean interval = false;
for (int i = 0; i < parts.length; ++i) {
/* Ratio can be defined -> default is 1 */
String[] item = parts[i].split(":");
double probability = 1;
double probability2 = 1;
boolean isDefault = true;
interval = false;
if (item.length > 1) {
/* an interval can be there or not */
if (item[1].split("-").length > 1) {
interval = true;
probability = Float.parseFloat(item[1].split("-")[0]);
probability2 = Float.parseFloat(item[1].split("-")[1]);
isDefault = false;
} else {
if ((Math.abs(Float.parseFloat(item[1]) - 1.0) > 0.00000001)) {
probability = Float.parseFloat(item[1]);
isDefault = false;
}
/* unknown ratio */
if (item[1].contains("?")) {
probability = -1;
isDefault = false;
}
}
}
/* Add element to the list */
addElement(item[0], type, probability, probability2, interval, isDefault);
}
}
/**
* {@inheritDoc}
*/
@Override
public String toHELM2() {
StringBuilder notation = new StringBuilder();
DecimalFormat d = new DecimalFormat("#.##");
notation.append("(");
for (int i = 0; i < elements.size(); i++) {
String text = elements.get(i).getMonomerNotation().getUnit();
if (!(elements.get(i).isDefaultValue())) {
String value = d.format(elements.get(i).getValue().get(0)).replace(',', '.');
if (elements.get(i).isInterval()) {
value += "-" + d.format(elements.get(i).getValue().get(1)).replace(',', '.');
}
if (value.equals("-1")) {
value = "?";
}
text += ":" + value;
}
notation.append(text + ",");
}
notation.setLength(notation.length() - 1);
notation.append(")");
if (!(isDefault)) {
notation.append("'" + count + "'");
}
if (isAnnotationHere) {
notation.append("\"" + annotation + "\"");
}
return notation.toString();
}
}