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The protein structure modules of BioJava.

There is a newer version: 7.2.2

/*
 *                    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.structure.align.xml;

import java.io.IOException;
import java.util.List;

import javax.vecmath.Matrix4d;

import org.biojava.nbio.core.util.PrettyXMLWriter;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.align.multiple.Block;
import org.biojava.nbio.structure.align.multiple.BlockSet;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
import org.biojava.nbio.structure.align.multiple.ScoresCache;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;

/**
 * Helper methods to convert all the hierarchy levels of a MultipleAlignment
 * into an XML format.
 * 
 * To convert a MultipleAlignment to an XML String use the
 * {@link MultipleAlignmentWriter#toXML(MultipleAlignmentEnsemble)} method.
 *
 * @author Aleix Lafita
 * @since 4.1.1
 *
 */
public class MultipleAlignmentXMLConverter {

	public synchronized static void printXMLensemble(PrettyXMLWriter xml,
			MultipleAlignmentEnsemble ensemble)	throws IOException {

		xml.openTag("MultipleAlignmentEnsemble");

		printXMLheader(xml,ensemble);

		for (MultipleAlignment msa:ensemble.getMultipleAlignments()){
			printXMLalignment(xml,msa);
		}
		printXMLscoresCache(xml,ensemble);

		xml.closeTag("MultipleAlignmentEnsemble");
	}

	public synchronized static void printXMLalignment(PrettyXMLWriter xml,
			MultipleAlignment msa) throws IOException {

		xml.openTag("MultipleAlignment");

		for(BlockSet bs:msa.getBlockSets()) {
			printXMLblockSet(xml, bs);
		}
		printXMLscoresCache(xml,msa);

		xml.closeTag("MultipleAlignment");
	}

	public synchronized static void printXMLblockSet(PrettyXMLWriter xml,
			BlockSet bs) throws IOException {

		xml.openTag("BlockSet");

		for(Block b:bs.getBlocks()) {
			printXMLblock(xml, b);
		}

		if (bs.getTransformations() != null){
			for(Matrix4d t:bs.getTransformations()){
				printXMLmatrix4d(xml, t);
			}
		}
		printXMLscoresCache(xml,bs);

		xml.closeTag("BlockSet");
	}

	public synchronized static void printXMLblock(PrettyXMLWriter xml,
			Block b) throws IOException {

		xml.openTag("Block");
		List> alignment = b.getAlignRes();

		for (int pos=0;pos