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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;
/**
* ConverterHELM1ToHELM2
*
* @author hecht
*/
public class ConverterHELM1ToHELM2 {
/**
* Constructor to convert HELM1 into HELM2
*/
public ConverterHELM1ToHELM2() {
}
/**
* method to convert the given string into the HELM2 format
*
* @param str HELM1 Notation
* @return HELM2 Notation
*/
public String doConvert(String str) {
//check for just missing V2.0
ParserHELM2 parser = new ParserHELM2();
try{
parser.parse(str + "V2.0");
return str + "V2.0";
}
catch(Exception e){
/* Use String Builder */
/* simple add character -> split works then */
String helm1 = str + "f";
StringBuilder helm2 = new StringBuilder();
String[] sections = helm1.split("}\\$");
/* Section 1 is accepted in full, no changes necessary, Section 1 has to be there */
helm2.append(sections[0] + "}$");
StringBuilder sb = new StringBuilder();
for (int i = 1; i < sections.length; i++) {
sb.append(sections[i] + "}$");
}
helm1 = "$" + sb.toString();
sections = helm1.split("\\$");
/*
* Section 2 connection section; section 3 is added to the second section,
* Section 2 is not necessary, is this section really there
*/
if (sections.length >= 2) {
if (!(sections[1].isEmpty())) {
helm2.append(sections[1]);
}
}
/* Add hydrogen bonds to the connection section */
if (sections.length >= 3) {
if (!(sections[2].isEmpty())) {
if (!(sections[1].isEmpty())) {
helm2.append("|" + sections[2]);
} else {
helm2.append(sections[2]);
}
}
/*Group section*/
helm2.append("$");
helm2.append("$");
/*Add annotation to the annotation section*/
if (sections.length >= 4) {
if (!(sections[3].isEmpty())) {
helm2.append(sections[3]);
}
}
}
/* Add version number to indicate HELM2 notation */
helm2.append("$V2.0");
return helm2.toString();
}
}
}