/*
 *                    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.domain;

import org.biojava.nbio.structure.align.util.URLConnectionTools;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;

import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import java.io.*;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.SortedSet;
import java.util.TreeSet;


/**
 * Class to fetch domains through the RCSB's REST API.
 *
 * @author Spencer Bliven
 *
 */
public class PDBDomainProvider implements DomainProvider{
        public static final String DEFAULT_PDB_HOST = "http://www.rcsb.org";
        public static final String DEFAULT_PDB_API_URL = DEFAULT_PDB_HOST + "/pdb/rest/";

        private String base;
        private int cutoff;

        /**
         */
        public PDBDomainProvider() {
                this(DEFAULT_PDB_API_URL,40);
        }
        /**
         * @param base
         * @param cutoff
         */
        public PDBDomainProvider(String base, int cutoff) {
                this.base = base;
                this.cutoff = cutoff;
        }


        /**
         * Gets a list of domain representatives for a given PDB ID.
         */
        @Override
        public SortedSet<String> getDomainNames(String name) {
                if ( name.length() < 4)
                        throw new IllegalArgumentException("Can't interpret IDs that are shorter than 4 residues!");

                String url = String.format("%srepresentativeDomains?cluster=%s&structureId=%s",
                                base, cutoff, name);
                return requestRepresentativeDomains(url);
        }
        /**
         * Gets a list of all domain representatives
         */
        @Override
        public SortedSet<String> getRepresentativeDomains() {
                String url = base + "representativeDomains?cluster="+ cutoff;
                return requestRepresentativeDomains(url);
        }

        /**
         * Handles fetching and parsing XML from representativeDomains requests
         * @param url Eg "http://www.rcsb.org/pdb/rest/representativeDomains"
         * @return The names of all domain representatives
         */
        private SortedSet<String> requestRepresentativeDomains(String url) {
                try {

                        //System.out.println(url);

                        final SortedSet<String> results = new TreeSet<String>();
                        DefaultHandler handler = new DefaultHandler() {
                                @Override
                                public void startElement(String uri, String localName,String qName,
                                                Attributes attributes) throws SAXException {

                                        //System.out.println("Start Element :" + qName);

                                        if (qName.equalsIgnoreCase("representative")) {
                                                String name = attributes.getValue("name");
                                                results.add(name);
                                        }
                                }
                        };
                        handleRestRequest(url,handler);
                        return results;
                } catch (MalformedURLException e) {
                        e.printStackTrace();
                } catch (IOException e) {
                        e.printStackTrace();
                } catch (SAXException e) {
                        e.printStackTrace();
                } catch (ParserConfigurationException e) {
                        e.printStackTrace();
                }
                return null;
        }
        /**
         * Handles fetching and processing REST requests. The actual XML parsing is handled
         * by the handler, which is also in charge of storing interesting data.
         * @param url REST request
         * @param handler SAX XML parser
         * @throws SAXException
         * @throws IOException
         * @throws ParserConfigurationException
         */
        private static void handleRestRequest(String url, DefaultHandler handler) throws SAXException, IOException, ParserConfigurationException {
                // Fetch XML stream
                URL u = new URL(url);
                InputStream response = URLConnectionTools.getInputStream(u);
                InputSource xml = new InputSource(response);

                // Parse XML
                SAXParserFactory factory = SAXParserFactory.newInstance();
                SAXParser saxParser = factory.newSAXParser();
                saxParser.parse(xml, handler);

        }


        //TODO Add methods to access http://www.rcsb.org/pdb/rest/representatives

        public static void main(String[] args){
                PDBDomainProvider dom = new PDBDomainProvider();
                String name;
                name = "2CDG";

                SortedSet<String> domains = dom.getDomainNames(name);

                System.out.println("Domains for "+name+":");
                for(String s : domains) {
                        System.out.println(s);
                }

                SortedSet<String> reprs = dom.getRepresentativeDomains();
                System.out.format("%nFound %d clusters.%n",reprs.size());

                try {
                        File outfile  = new File("/Users/blivens/Downloads/representativeDomainsJava.xml");
                        Writer out = new BufferedWriter(new FileWriter(outfile));

                        for(String repr : reprs) {
                                out.write(String.format("  <representative name=\"%s\"/>%n", repr));
                        }
                        out.close();
                } catch (IOException e) {
                        e.printStackTrace();
                }

        }


}