content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.biointerpretation.networkanalysis;
  
  import com.act.jobs.FileChecker;
  import com.act.jobs.JavaRunnable;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.io.File;
  import java.io.IOException;
  import java.util.HashSet;
  import java.util.Set;
  
  /**
   * Runnable class to print out statistics about a metabolic network.
   * Very basic so far, but will be expanded as we are interested in more data.
   */
  public class NetworkStats implements JavaRunnable {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(NetworkStats.class);
  
    private final File inputFile;
  
    public NetworkStats(File inputFile) {
      this.inputFile = inputFile;
    }
  
    @Override
    public void run() throws IOException {
      // Check input file
      FileChecker.verifyInputFile(inputFile);
      LOGGER.info("Verified input file validity.");
  
      // Read in network from file
      MetabolismNetwork network = MetabolismNetwork.getNetworkFromJsonFile(inputFile);
  
      // Print stats on network
      LOGGER.info("Total nodes: %d", network.getNodes().size());
      LOGGER.info("Total edges: %d", network.getEdges().size());
  
      Set<String> orgs = new HashSet<String>();
      network.getEdges().forEach(e -> orgs.addAll(e.getOrgs()));
      LOGGER.info("Total organisms represented: %d", orgs.size());
  
      LOGGER.info("Complete!");
    }
  }
  