content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   *
   * 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.
   */
  
  package juicebox;
  
  import juicebox.data.ChromosomeHandler;
  import org.broad.igv.ui.IGV;
  
  import java.io.BufferedReader;
  import java.io.IOException;
  import java.io.InputStreamReader;
  import java.io.PrintWriter;
  import java.net.Socket;
  import java.util.Arrays;
  import java.util.concurrent.ExecutorService;
  import java.util.concurrent.Executors;
  
  //import org.broad.igv.lists.GeneList;
  //import org.broad.igv.ui.WaitCursorManager;
  //import org.broad.igv.util.LongRunningTask;
  //import org.broad.igv.util.NamedRunnable;
  //import java.net.UnknownHostException;
  
  /**
   * @author Jim Robinson
   * @since 1/5/12
   */
  class IGVUtils {
  
      private static final ExecutorService threadExecutor = Executors.newFixedThreadPool(1);
  
      private static SocketHelper helper = null;
  
      private static void createSocketHelper() {
          if (helper == null) {
              Socket socket;
              PrintWriter out;
              BufferedReader in;
              try {
                  socket = new Socket("127.0.0.1", 60151);
                  out = new PrintWriter(socket.getOutputStream(), true);
                  in = new BufferedReader(new InputStreamReader(socket.getInputStream()), HiCGlobals.bufferSize);
                  helper = new SocketHelper(in, out, socket);
              } catch (IOException e) {
                  System.err.println("IOException" + e.getLocalizedMessage());
                  helper = null;
              }
  
          }
      }
  
      /**
       * Send instructions to IGV to open or adjust views on the 2 loci.
       *
       * @param locus1
       * @param locus2
       */
      public static void sendToIGV(final String locus1, final String locus2) {
  
          Runnable runnable = new Runnable() {
              public void run() {
  
                  if (ChromosomeHandler.isAllByAll(locus1)) {
                      return;
                  }
  
                  // Same JVM?
                  if (IGV.hasInstance()) {
                      IGV.getInstance().goToLociList(Arrays.asList(locus1, locus2));
  
                  } else {
  
                      if (helper == null) createSocketHelper();
  
                      if (helper != null) {
                          String cmd = "gotoimmediate " + locus1 + " " + locus2;
                          helper.out.println(cmd);
                          String response = null;
                          try {
                              response = helper.in.readLine();
                          } catch (IOException e) {
                              e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                          }
                          System.out.println(cmd + " " + response);
                      }
                  }
              }
          };
  
          threadExecutor.submit(runnable);
  
      }
  
      static class SocketHelper {
          Socket socket = null;
          PrintWriter out = null;
          BufferedReader in = null;
  
          SocketHelper(BufferedReader in, PrintWriter out, Socket socket) {
              this.in = in;
              this.out = out;
              this.socket = socket;
          }
      }
  
  }
  