com.actelion.research.chem.io.pdb.parser.HetSynonymParser Maven / Gradle / Ivy

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package com.actelion.research.chem.io.pdb.parser;

import java.text.ParseException;
import java.util.HashMap;
import java.util.List;

/**
 * HetSynonymParser
 * Copyright: Idorsia Pharmaceuticals Ltd., Inc. All Rights Reserved
 * This software is the proprietary information of Idorsia Pharmaceuticals, Ltd.
 * Use is subject to license terms.
 * Created by korffmo1 on 11.04.18.
 */
public class HetSynonymParser {

    private int indexLine;

    private HashMap hmId_Synonyms;

    void parse(List liRaw, int indexLine) throws ParseException {

        hmId_Synonyms = new HashMap<>();

        String tag = PDBFileParser.TAG_HETSYN;

        String l0 = liRaw.get(indexLine);
        if(!l0.startsWith(tag)) {
            throw new RuntimeException("Error in parsing " + tag);
        }

        StringBuilder sb = new StringBuilder();

        int start = indexLine;

        String nameId = l0.substring(11, 14);

        for (int i = start; i < liRaw.size(); i++) {

            String l = liRaw.get(i);

            if(!l.startsWith(tag)) {
                break;
            }

            String nameIdLine = l.substring(11, 14);

            if(!nameId.equals(nameIdLine)) {

                String name = sb.toString();

                hmId_Synonyms.put(nameId, name);

                nameId = nameIdLine;

                sb = new StringBuilder();
            }

            if(sb.length()>0){
                sb.append(" ");
            }

            String nameLine = l.substring(15).trim();
            sb.append(nameLine);

            indexLine++;
        }

        if(sb.length()>0){
            String name = sb.toString();

            hmId_Synonyms.put(nameId, name);
        }

        this.indexLine = indexLine;
    }

    public int getIndexLine() {
        return indexLine;
    }

    public HashMap getHMId_Synonyms() {
        return hmId_Synonyms;
    }
}