/*
 *                  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/
 * 
 * Created on Mar 15, 2006
 *
 */
package org.biojava.dasobert.das2.io;

import java.util.ArrayList;
import java.util.List;

import org.biojava.dasobert.das2.Das2Capability;
import org.biojava.dasobert.das2.Das2CapabilityImpl;
import org.biojava.dasobert.das2.Das2Source;
import org.biojava.dasobert.das2.Das2SourceImpl;
import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
import org.biojava.dasobert.dasregistry.DasSource;
import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;

/** a parser for the DAS2 sources response
 * 
 * @author Andreas Prlic
 * @since 6:53:45 PM
 * @version %I% %G%
 */
public class DAS2SourceHandler extends DefaultHandler{

    List sources;
    Das2Source currentSource;
    List coordinates;
    List capabilities;
    List labels;

    public static final String LABELPROPERTY = "label";

    public DAS2SourceHandler() {
        super();
        
        sources       = new ArrayList();
        currentSource = new Das2SourceImpl();
        coordinates   = new ArrayList();
        capabilities  = new ArrayList();
	labels        = new ArrayList();
    }
    
    private void startSource (String uri, String name, String qName, Attributes atts){
        
        String id = atts.getValue("uri");
        String title = atts.getValue("title");
        String doc_ref = atts.getValue("doc_href");
        String description = atts.getValue("description");

           
        currentSource.setId(id);
        currentSource.setNickname(title);
        currentSource.setHelperurl(doc_ref);
        currentSource.setDescription(description);
        
    }
    
    private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
        // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6" 
        // source="Protein Sequence" authority="UniProt" test_range="P06213" />
        DasCoordinateSystem dcs = new DasCoordinateSystem();
        String id = atts.getValue("uri");
        dcs.setUniqueId(id);
        
        String source = atts.getValue("source");
        dcs.setCategory(source);
        
        String authority = atts.getValue("authority");
        dcs.setName(authority);
        
        String test_range = atts.getValue("test_range");
        dcs.setTestCode(test_range);
        
        try {
            String taxidstr = atts.getValue("taxid");
            int taxid = Integer.parseInt(taxidstr);
            dcs.setNCBITaxId(taxid);
        } catch (Exception e){}
        
        String version = atts.getValue("version");
        if ( version != null)
            dcs.setVersion(version);
        
        return dcs;
    }
    
    public void startElement (String uri, String name, String qName, Attributes atts){
        //System.out.println("new element "+qName);
        
        if (qName.equals("SOURCE")) {
            //System.out.println("new Source " + atts.getValue(uri));
            currentSource = new Das2SourceImpl();
            coordinates = new ArrayList();
            capabilities = new ArrayList();
            
            startSource(uri,name, qName, atts);
            
        } else if ( qName.equals("MAINTAINER")){
            String email = atts.getValue("email");
            currentSource.setAdminemail(email);
        } else if ( qName.equals("COORDINATES")){
            DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
            coordinates.add(dcs);
            
        } else if ( qName.equals("CAPABILITY")){
            Das2Capability cap = getCapability(uri,name,qName,atts);
            capabilities.add(cap);
        } else if (qName.equals("PROPERTY")) {
	    addProperty(uri,name,qName,atts);
	}                
    }
    
    private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
        // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
        Das2Capability cap = new Das2CapabilityImpl();
        
        String type = atts.getValue("type");
        cap.setCapability(type);
        String query_uri = atts.getValue("query_uri");
        cap.setQueryUri(query_uri);
        return cap;
        
    }
    
    private void addProperty(String uri, String name, String qName, Attributes atts){
	String pname = atts.getValue("name");
	String label = atts.getValue("value");
	if ( pname.equals(LABELPROPERTY) )
	    labels.add(label);
    }
    
    public void startDocument(){
        sources = new ArrayList();
        coordinates = new ArrayList();
        capabilities = new ArrayList();
    }
    
    public void endElement(String uri, String name, String qName) {
        if ( qName.equals("SOURCE")) {
            currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
            //System.out.println("got coordinates " + coordinates.size());
            currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));

	    currentSource.setLabels((String[])labels.toArray(new String[labels.size()]));
	    labels.clear();

            //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
            //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());    
            sources.add(currentSource);   
            currentSource = new Das2SourceImpl();
        } 		
    }
    
    public DasSource[] getSources(){    
        //System.out.println("Das2SourceHandler: source size: " + sources.size());
        return (DasSource[])sources.toArray(new DasSource[sources.size()]);
    }
    
    

}