JSci.biology.AminoAcids Maven / Gradle / Ivy
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JSci is a set of open source Java packages. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software.
It offers: abstract math interfaces, linear algebra (support for various matrix and vector types), statistics (including probability distributions), wavelets, newtonian mechanics, chart/graph components (AWT and Swing), MathML DOM implementation, ...
Note: some packages, like javax.comm, for the astro and instruments package aren't listed as dependencies (not available).
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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 org.w3c.dom.*;
import org.xml.sax.SAXException;
import JSci.chemistry.Molecule;
/**
* 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