org.biojava.nbio.protmod.io.ComponentXMLConverter Maven / Gradle / Ivy

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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.protmod.io;

import org.biojava.nbio.protmod.Component;
import org.biojava.nbio.core.util.PrettyXMLWriter;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.HashSet;
import java.util.Set;


public class ComponentXMLConverter {
	public static String toXML(Component component) throws IOException{
		StringWriter out = new StringWriter();

		PrettyXMLWriter xml = new PrettyXMLWriter(new PrintWriter(out));
		toXML(component, xml);

		return out.toString();
	}

	public static void toXML(Component component, PrettyXMLWriter xml) throws IOException{
		xml.openTag("component");

		xml.attribute("nTerminal" , component.isNTerminal()+"");
		xml.attribute("cTerminal", component.isCTerminal()+"");
		for (String pdbccId : component.getPdbccIds()){
			xml.openTag("pdbccID");
			xml.attribute("id", pdbccId);
			xml.closeTag("pdbccID");
		}

		xml.closeTag("component");
	}

	public static Component fromXML(String xml){
		return null;
	}

	public static Component fromXML(Node componentN) {

		String name = componentN.getNodeName();
		if ( ! name.equals("component"))
			throw new RuntimeException("did not get component element, but " + name);

		//String type = getAttribute(componentN, "type");
		String nTerminalS = getAttribute(componentN, "nTerminal");
		String cTerminalS = getAttribute(componentN, "cTerminal");

		boolean isNTerminal = Boolean.parseBoolean(nTerminalS);
		boolean isCTerminal = Boolean.parseBoolean(cTerminalS);

		SetpdbccIds = new HashSet();

		NodeList valList = componentN.getChildNodes();
		int numChildren  = valList.getLength();


		for ( int e =0; e< numChildren ; e++){
			Node  pdbccN = valList.item(e);

			if(!pdbccN.hasAttributes()) continue;


			if ( pdbccN.getNodeName().equals("pdbccID")) {
				String id = getAttribute(pdbccN, "id");
				pdbccIds.add(id);
			}

		}

		Component c = Component.of(pdbccIds, isNTerminal, isCTerminal);
		return c;

	}

	private static String getAttribute(Node node, String attr){
		if( ! node.hasAttributes())
			return null;

		NamedNodeMap atts = node.getAttributes();

		if ( atts == null)
			return null;

		Node att = atts.getNamedItem(attr);
		if ( att == null)
			return null;

		String value = att.getTextContent();

		return value;

	}
}