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The protein structure modules of BioJava.
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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.structure.symmetry.utils;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.net.URL;
import java.util.*;


public class BlastClustReader implements Serializable {

	private static final long serialVersionUID = 1L;

	private int sequenceIdentity = 0;
	private List> clusters = new ArrayList>();
	private static final String coreUrl = "ftp://resources.rcsb.org/sequence/clusters/";
	private static List seqIdentities = Arrays.asList(30, 40, 50, 70, 90, 95, 100);

	public BlastClustReader(int sequenceIdentity)  {
		this.sequenceIdentity = sequenceIdentity;
	}

	public List> getPdbChainIdClusters() {
		loadClusters(sequenceIdentity);
		return clusters;
	}

	public Map getRepresentatives(String pdbId) {
		loadClusters(sequenceIdentity);
		String pdbIdUc = pdbId.toUpperCase();

		Map representatives = new LinkedHashMap();
		for (List cluster: clusters) {
			// map fist match to representative
			for (String chainId: cluster) {
				if (chainId.startsWith(pdbIdUc)) {
					representatives.put(chainId, cluster.get(0));
					break;
				}
			}
		}
		return representatives;
	}

	public String getRepresentativeChain(String pdbId, String chainId) {
		loadClusters(sequenceIdentity);

		String pdbChainId = pdbId.toUpperCase() + "." + chainId;

		for (List cluster: clusters) {
			if (cluster.contains(pdbChainId)) {
				return cluster.get(0);
			}
		}
		return "";
	}

	public int indexOf(String pdbId, String chainId) {
		loadClusters(sequenceIdentity);

		String pdbChainId = pdbId.toUpperCase() + "." + chainId;

		for (int i = 0; i < clusters.size(); i++) {
			List cluster = clusters.get(i);
			if (cluster.contains(pdbChainId)) {
				return i;
			}
		}
		return -1;
	}

	public List> getPdbChainIdClusters(String pdbId) {
		loadClusters(sequenceIdentity);
		String pdbIdUpper = pdbId.toUpperCase();

		List> matches = new ArrayList>();
		for (List cluster: clusters) {
			for (String chainId: cluster) {
				if (chainId.startsWith(pdbIdUpper)) {
					matches.add(cluster);
					break;
				}
			}
		}
		return matches;
	}

	public List> getChainIdsInEntry(String pdbId) {
		loadClusters(sequenceIdentity);

		List> matches = new ArrayList>();
		List match = null;

		for (List cluster: clusters) {
			for (String chainId: cluster) {
				if (chainId.startsWith(pdbId)) {
					if (match == null) {
						match = new ArrayList();
					}
					match.add(chainId.substring(5));
				}
			}
			if (match != null) {
				Collections.sort(match);
				matches.add(match);
				match = null;
			}
		}
		return matches;
	}

	private void loadClusters(int sequenceIdentity) {
		// load clusters only once
		if (clusters.size() > 0) {
			return;
		}

		if (!seqIdentities.contains(sequenceIdentity)) {
			System.err.println("Error: representative chains are not available for %sequence identity: "
					+ sequenceIdentity);
			return;
		}

		try {
			URL u = new URL(coreUrl + "bc-" + sequenceIdentity + ".out");
			InputStream stream = u.openStream();
	//		URLConnection connection = u.openConnection();
	//		connection.setConnectTimeout(60000);
	//		InputStream stream = connection.getInputStream();

			if (stream != null) {
				BufferedReader reader = new BufferedReader(new InputStreamReader(stream));

				String line = null;
				try {
					while ((line = reader.readLine()) != null) {
						line = line.replaceAll("_", ".");
						List cluster = Arrays.asList(line.split(" "));
						clusters.add(cluster);
					}
					reader.close();
					stream.close();
				} catch (IOException e) {
					//e.printStackTrace();
				} finally {
//					try {
//						System.out.println("closing reader");
//						reader.close();
//						stream.close();
//					} catch (IOException e) {
//						e.printStackTrace();
//					}
				}
			}

		} catch (Exception e) {
			e.printStackTrace();
		}

		return;
	}

}