// TestCreateGCP_LocusCollection.java
//
// Created: January 2006
//
// This file is a component of the BioMoby project.
// Copyright Martin Senger (martin.senger@gmail.com).
//

package org.jmoby.tutorial.client;

import org.biomoby.shared.parser.MobyCollection;
import org.biomoby.shared.parser.MobySimple;
import org.biomoby.shared.datatypes.GCP_Locus;

import org.jdom.Document;
import org.jdom.output.XMLOutputter;
import org.jdom.output.Format;

/**
 * A example how to create a BioMoby input data using Moses
 * pre-generated data types. <p>
 *
 * @author <A HREF="mailto:martin.senger@gmail.com">Martin Senger</A>
 * @version $Id: TestCreateGCP_LocusCollection.java.txt,v 1.1 2007/05/21 00:56:15 senger Exp $
 */
public class TestCreateGCP_LocusCollection {

    public static void main (String [] args) {
	try {

	    // create a collection
	    MobyCollection collection = new MobyCollection();
	    collection.setName ("loci");

	    // and fill it with simple elements
	    String[] idsOfElements = new String[] { "a", "b" };
	    for (int i = 0; i < idsOfElements.length; i++) {
		GCP_Locus locus = new GCP_Locus();
		locus.setId (idsOfElements[i]);
		locus.setNamespace ("Tropgene_Banana");

		// here you can add some GCP_Alleles and/or
		// GCP_LinkageGroup to the just created locus by
		// calling methods locus.set_allele(...) and
		// locus.set_linkage_group(...)

		MobySimple simple = new MobySimple();
		simple.setData (locus);

		collection.addData (simple);
	    }

	    // and print it as a text...
	    System.out.println (collection);

	    // and print it as an XML
	    Document doc = new Document (collection.toXML());
	    XMLOutputter xo = new XMLOutputter();
	    xo.setFormat (Format.getPrettyFormat());
	    System.out.println (xo.outputString (doc));

	} catch (Exception e) {
	    System.err.println ("===ERROR===");
	    e.printStackTrace();
	    System.err.println ("===========");
	}
    }
}