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 act.shared;
  
  import java.io.Serializable;
  import java.util.List;
  
  public class Configuration implements Serializable {
    private static final long serialVersionUID = 42L;
  
    public enum ReactionSimplification { HardCodedCoFactors, SimpleRarity, PairedRarity }
  
    public static class ConfigStructure {
      public static final String ConfigFile = "config.xml";
      public static final String actHost = "actHost";
      public static final String actPort = "actPort";
      public static final String actDB = "actDB";
      public static final String renderBadFlag = "renderBadRxnsForDebug";
      public static final String graphMatchingDiff = "graphMatchingDiff";
      public static final String rxnSimplifyUsing = "rxnSimplifyUsing";
      public static final String logLevel = "log-level";
      public static final String diffStart = "diff.start";
      public static final String diffEnd = "diff.end";
      public static final String diffDebugIDList = "diff.debug-dump";
      public static final String theoryROOutfile = "ROsFile";
      public static final String theoryROHierarchyFile = "ROsHierarchyFile";
      public static final String UIversion = "UIversion";
    }
  
    private static Configuration configInstance;
    public static Configuration getInstance() {
      if (configInstance == null)
        configInstance = new Configuration();
      return configInstance;
    }
  
    public String actHost;
    public int actPort;
    public String actDB;
  
    // flags and global params
    public boolean renderBadRxnsForDebug;
    public boolean graphMatchingDiff;
    public ReactionSimplification rxnSimplifyUsing;
    public int logLevel;
    public String theoryROOutfile, theoryROHierarchyFile;
    public int UIversion;
  
    // diff params
    public int diff_start;
    public int diff_end;
    public List<Integer> debug_dump_uuid;
  }
  