IgvSocket.java

/*
The MIT License (MIT)

Copyright (c) 2014 Pierre Lindenbaum

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.


History:
* 2015 creation

*/
package com.github.lindenb.jvarkit.util.igv;

import htsjdk.samtools.util.CloserUtil;
import htsjdk.variant.variantcontext.VariantContext;

import java.io.BufferedReader;
import java.io.Closeable;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.net.Socket;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Controlling IGV through a Port
 * 
 * http://www.broadinstitute.org/software/igv/PortCommands
 * @author lindenb
 *
 */
public class IgvSocket
	implements Closeable
	{
	public static final int DEFAULT_PORT=60151;
	public static final String DEFAULT_HOST="127.0.0.1";
	
	private String host=DEFAULT_HOST;
	private int port=DEFAULT_PORT;
	private Socket _socket=null;
	private PrintWriter _out=null;
	private BufferedReader _in=null;
	
	public IgvSocket()
		{
		
		}
	private IgvSocket(final IgvSocket src)
		{
		this.host = src.host;
		this.port = src.port;
		}
	
	public String getHost() {
		return host;
		}
	public int getPort() {
		return port;
		}
	public void setHost(final String host) {
		this.host = host;
		}
	public void setPort(int port) {
		this.port = port;
		}
	
	public Socket getSocket() throws IOException
		{
		if(_socket==null)
			{
			_socket=new Socket(getHost(), getPort());
			}
		return _socket;
		}
	
	public PrintWriter getWriter() throws IOException
		{
		if(_out==null)
			{
			_out= new PrintWriter(getSocket().getOutputStream(), true);
			}
		return _out;
		}

	public BufferedReader getReader() throws IOException
		{
		if(_in==null)
			{
			_in=  new BufferedReader(new InputStreamReader(getSocket().getInputStream()));
			}
		return _in;
		}
	
	
	@Override
	public void close() {
		CloserUtil.close(_in);
		_in=null;
		CloserUtil.close(_out);
		_out=null;
		CloserUtil.close(_socket);
		_socket=null;
		}
	
	public void show(final VariantContext ctx)
		{
		if( ctx ==null ) return ;
		show(ctx.getContig(),ctx.getStart());
		}	
	
	public void show(final String chrom,int chromStart)
		{
		if(chrom==null || chrom.trim().isEmpty() || chromStart<0) return;
		execute(Collections.singletonList("goto "+chrom+":"+chromStart));
		}
	
	public Runnable buildRunnable(final List<String> cmds) 
		{
		return new ShowRunner(this,cmds);
		}

	
	
	public void execute(final List<String> cmds) 
		{
		new Thread(buildRunnable(cmds)).start();
		}
	
	
	private static class ShowRunner implements Runnable
		{
		final IgvSocket copy;
		//String chrom;
		//int start;
		final List<String> commands;
		
		ShowRunner(final IgvSocket socket,final List<String> command) {
			this.commands = new ArrayList<>(command);
			this.copy =  new IgvSocket(socket);
			}
		@Override
		public void run() {

			PrintWriter out=null;
			try
				{
				out = this.copy.getWriter();
				this.copy.getReader();
				for(final String command:this.commands)
					{
					out.println(command);
					try{ Thread.sleep(5*1000);}
					catch(InterruptedException err2) {}
					 }
				}
			catch(final Exception err)
				{
				err.printStackTrace();
				}
			finally
				{
				CloserUtil.close(this.copy);
				}			
			}
		};
	

	}