package jsci.biology;

import java.lang.Double;
import java.io.IOException;
import java.util.Collections;
import java.util.Map;
import java.util.HashMap;
import javax.xml.parsers.*;

import jsci.chemistry.Molecule;

import org.w3c.dom.*;
import org.xml.sax.SAXException;

/**
 * This class provides access to amino acids.
 * @version 1.0
 * @author Silvere Martin-Michiellot
 * @author Mark Hale
 */
public final class AminoAcids {
        private static final Map table = new HashMap();
        private static Map symbols;

        private AminoAcids() {}
        /**
        * Returns the name for a symbol.
        */
        public static String getName(String symbol) {
                if(symbols == null)
                        symbols = loadIndex();
                return (String)symbols.get(symbol);
        }
    /**
     * Returns an amino acid.
     */
    public static AminoAcid getAminoAcid(String name) {
        name=name.toLowerCase();
        AminoAcid aminoacid = (AminoAcid) table.get(name);
        if(aminoacid==null) {
            aminoacid=loadAminoAcid("aminoacids/"+name.replace(' ', '-')+".xml");
                if(aminoacid != null)
            table.put(name,aminoacid);
        }
        return aminoacid;
    }
        /**
        * Loads the XML index.
        */
        private static Map loadIndex() {
                DocumentBuilderFactory docFactory=DocumentBuilderFactory.newInstance();
                try {
                        DocumentBuilder docBuilder=docFactory.newDocumentBuilder();
                        Document doc=docBuilder.parse(AminoAcids.class.getResource("aminoacids/index.xml").toString());
                        Node root=doc.getDocumentElement();
                        NodeList nl=root.getChildNodes();
                        Map index = new HashMap();
                        for(int i=0; i