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.mechanisminspection;
  
  import chemaxon.reaction.ReactionException;
  import chemaxon.reaction.Reactor;
  import com.fasterxml.jackson.annotation.JsonIgnore;
  import com.fasterxml.jackson.annotation.JsonProperty;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.io.Serializable;
  
  public class Ero implements Serializable {
    private static final long serialVersionUID = 5679370596050943302L;
    private static final Logger LOGGER = LogManager.getLogger(Ero.class);
  
    @JsonProperty("id")
    private Integer id;
  
    @JsonProperty("category")
    private String category;
  
    @JsonProperty("is_trim")
    private Boolean is_trim = false;
  
    @JsonProperty("name")
    private String name = "";
  
    @JsonProperty("ro")
    private String ro;
  
    @JsonProperty("autotrim")
    private Boolean autotrim;
  
    @JsonProperty("note")
    private String note = "";
  
    @JsonProperty("confidence")
    private String confidence = "";
  
    @JsonProperty("manual_validation")
    private Boolean manual_validation = false;
  
    @JsonProperty("substrate_count")
    private Integer substrate_count;
  
    @JsonProperty("product_count")
    private Integer product_count;
  
    @JsonIgnore
    private transient ThreadLocal<Reactor> reactor = new ThreadLocal<Reactor>() {
      @Override
      protected Reactor initialValue() {
        Reactor r = new Reactor();
        try {
          r.setReactionString(getRo());
          return r;
        } catch (ReactionException e) {
          LOGGER.warn(String.format("Unable to set reaction string %s for RO %d.  " +
                  "Please verify validity of the reaction string for this RO.", getRo(), getId()));
          return null;
        }
      }
    };
  
    public Ero() {}
  
    public Integer getId() {
      return id;
    }
  
    public void setId(Integer id) {
      this.id = id;
    }
  
    public String getCategory() {
      return category;
    }
  
    public void setCategory(String category) {
      this.category = category;
    }
  
    public Boolean getIs_trim() {
      return is_trim;
    }
  
    public void setIs_trim(Boolean is_trim) {
      this.is_trim = is_trim;
    }
  
    public String getName() {
      return name;
    }
  
    public void setName(String name) {
      this.name = name;
    }
  
    public String getRo() {
      return ro;
    }
  
    public void setRo(String ro) {
      this.ro = ro;
    }
  
    public Boolean getAutotrim() {
      return autotrim;
    }
  
    public void setAutotrim(Boolean autotrim) {
      this.autotrim = autotrim;
    }
  
    public String getNote() {
      return note;
    }
  
    public void setNote(String note) {
      this.note = note;
    }
  
    public String getConfidence() {
      return confidence;
    }
  
    public void setConfidence(String confidence) {
      this.confidence = confidence;
    }
  
    public Boolean getManual_validation() {
      return manual_validation;
    }
  
    public void setManual_validation(Boolean manual_validation) {
      this.manual_validation = manual_validation;
    }
  
    public Integer getSubstrate_count() {
      return substrate_count;
    }
  
    public void setSubstrate_count(Integer substrate_count) {
      this.substrate_count = substrate_count;
    }
  
    public Integer getProduct_count() {
      return product_count;
    }
  
    public void setProduct_count(Integer product_count) {
      this.product_count = product_count;
    }
  
    @JsonIgnore
    public Reactor getReactor() throws ReactionException {
      // We don't cache the reactor every time as by caching
      // it we disallow concurrency operations on a single RO.
      // We also don't want to reconstruct it each time as this is an expensive operation.
      // Therefore, we only reconstruct it for each thread.
      return reactor.get();
    }
  }
  