/*--------------------------------------------------------------------------
 *  Copyright 2008 utgenome.org
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *--------------------------------------------------------------------------*/
//--------------------------------------
// utgb-shell Project
//
// BED2SilkReader.java
// Since: May 26, 2009
//
// $URL$ 
// $Author$
//--------------------------------------
package org.utgenome.shell.db.bed;

import java.io.IOException;
import java.io.PipedReader;
import java.io.PipedWriter;
import java.io.PrintWriter;
import java.io.Reader;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;

import org.utgenome.shell.UTGBShellException;
import org.xerial.util.log.Logger;

public class BED2SilkReader extends Reader {

	private static Logger _logger = Logger.getLogger(BED2SilkReader.class);

	private final Reader bedReader;
	private ExecutorService threadPool;

	private final PipedWriter pipeOut;
	private final PipedReader pipeIn;

	private boolean hasStarted = false;

	public BED2SilkReader(Reader bedReader) throws IOException {
		this.bedReader = bedReader;

		pipeOut = new PipedWriter();
		pipeIn = new PipedReader(pipeOut);

	}

	private static class PipeWorker implements Runnable {

		private final BED2Silk bed2silk;
		private final PrintWriter out;

		public PipeWorker(Reader in, PrintWriter out) throws IOException {
			bed2silk = new BED2Silk(in);
			this.out = out;
		}

		public void run() {
			if (out == null)
				return;
			try {
				bed2silk.toSilk(out);
				out.close();
			}
			catch (IOException e) {
				_logger.error(e);
			}
			catch (UTGBShellException e) {
				_logger.error(e);
			}
		}

	}

	@Override
	public void close() throws IOException {
		pipeIn.close();
		bedReader.close();
	}

	@Override
	public int read(char[] cbuf, int off, int len) throws IOException {

		if (!hasStarted) {
			threadPool = Executors.newFixedThreadPool(1);
			threadPool.submit(new PipeWorker(bedReader, new PrintWriter(pipeOut)));
			hasStarted = true;
		}

		int ret = pipeIn.read(cbuf, off, len);

		if (ret == -1) {
			threadPool.shutdownNow();
		}
		return ret;
	}

}