KEGGのPathway MapのXMLをparseして，矢印の関係を書き出すJavaプログラム

KEGGのPathwayのデータ（ftp.genome.ad.jp/pub/kegg/xml/map 下の*.xmlとか，ftp.genome.ad.jp/pub/kegg/xml/organisms/*/*.xml とか）をparseして，KEGG上の図で矢印で現れている部分を表示するプログラム．

java KEGGRelation map05214.xml

とか動かすと

ko:K05087 -> ko:K00922 (activation)
ko:K05087 -> ko:K02649 (activation)
ko:K04361 -> ko:K05859 (activation,phosphorylation)
ko:K04363 -> ko:K05859 (activation,phosphorylation)

というふうに，結果が返ってくる．
細かいエラーハンドルは，なし．もちろん，DTDも無視．KGML 0.6.1以外では動くかどうか，わかりませんです，はい．
Bio** 使えって話もありますが，マニュアル見るより書いたほうが早かったので，書きました．
あと, 遺伝子（プロテイン）A,Bがcomplexで，遺伝子Cに向かって矢印が在る場合，A->C, B->Cの両方が出てきます．

import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.xml.sax.SAXException;


public class KEGGRelation {
	private String filename = "";
	private HashMap<Integer, Element> idToElement;

	public KEGGRelation(String string) {
		filename = string;
	}

	public static void main(String[] args) {
		KEGGRelation kegg = new KEGGRelation(args[0]);
		try {
			kegg.parse();
		} catch (Exception e) {
			e.printStackTrace();
			System.err.println("XML parse error");
		}
		
	}

	private void parse() throws ParserConfigurationException, SAXException, IOException {
		DocumentBuilderFactory dbfactory = DocumentBuilderFactory.newInstance();
		DocumentBuilder builder = dbfactory.newDocumentBuilder();
		Document doc = builder.parse(new File(filename));
		Element root = doc.getDocumentElement();
		// parse <entry ...></entry> elements
		parseEntry(root.getElementsByTagName("entry"));
		// parse and print <relation></relation> elements
		showRelations(root.getElementsByTagName("relation"));
	}

	private void parseEntry(NodeList entries) {
		idToElement = new HashMap<Integer, Element>(); 
		int length = entries.getLength();
		for(int i = 0; i < length; i++ ) {
			Element e = (Element)entries.item(i);
			idToElement.put(Integer.parseInt(e.getAttribute("id")), e);
		}
	}

	private void showRelations(NodeList relations) {
		int length = relations.getLength();
		for(int i = 0; i < length; i++ ) {
			Element e = (Element)relations.item(i);
			Element e1 = idToElement.get(
						Integer.parseInt(e.getAttribute("entry1")));
			Element e2 = idToElement.get(
						Integer.parseInt(e.getAttribute("entry2")));
			showSubRelations(e1, e2, e.getElementsByTagName("subtype"));
		}
	}

	private void showSubRelations(Element e1, Element e2,  NodeList subtypes) {
		NodeList componentsForE1 = e1.getElementsByTagName("component"); 
		NodeList componentsForE2 = e2.getElementsByTagName("component");
		if(componentsForE1.getLength() != 0 ) {
			// when e1 contains complex
			ArrayList<Integer> ids = extractComponentIds(componentsForE1);
			for(int i: ids) {
				  Element subE1 = idToElement.get(i);
				  showSubRelations(subE1, e2, subtypes);
			}
		} else if ( componentsForE2.getLength() != 0) {
			// when e2 contains complex
			ArrayList<Integer> ids = extractComponentIds(componentsForE2);
			for(int i: ids) {
				Element subE2 = idToElement.get(i);
				showSubRelations(e1, subE2, subtypes);
			}
		} else {
			// no sub component
			String[] e1names = e1.getAttribute("name").split(" ");
			String[] e2names = e2.getAttribute("name").split(" ");
			// subtype name
			String subtypeName = "";
			for(int i = 0; i < subtypes.getLength(); i++ ) 
				subtypeName += "," + ((Element)subtypes.item(i)).getAttribute("name");
			for(String e1name: e1names) 
				for(String e2name: e2names ) {
					System.out.println(e1name + " -> " + e2name + " (" + subtypeName.substring(1) + ")" );
				}
		}
	}

	private ArrayList<Integer> extractComponentIds(NodeList components) {
		ArrayList<Integer> ids = new ArrayList<Integer>();
		int length = components.getLength();
		for(int i = 0; i < length; i++ ) {
			Element e = (Element)components.item(i);
			ids.add(Integer.parseInt(e.getAttribute("id")));
		}
		return ids;
	}

}