L2Prediction.java

/*************************************************************************
*                                                                        *
*  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.l2expansion;

import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;

/**
 * Represents a single predicted reaction from the L2 expansion
 */
public class L2Prediction implements Serializable {
  private static final long serialVersionUID = -8781964186957158826L;

  @JsonProperty("_id")
  private Integer id;

  @JsonProperty("substrates")
  private List<L2PredictionChemical> substrates;

  // This field corresponds either to the RO id, in the case of an RO expansion, or the name of the characterized group,
  // in the case of a SAR expansion. This field replaced explicit fields that stored the SAR/RO used to generate this
  // prediction. Instead to find that info one must look up the name in the RO or SAR Corpus used in the predictions.
  @JsonProperty("projector_name")
  private String projectorName;

  @JsonProperty("products")
  private List<L2PredictionChemical> products;

  @JsonProperty("reactions_ro_match")
  private List<Long> reactionsRoMatch;

  @JsonProperty("reactions_no_ro_match")
  private List<Long> reactionsNoRoMatch;

  // Necessary for JSON reading
  private L2Prediction() {
  }

  public L2Prediction(L2Prediction template) {
    this.id = template.id;

    this.substrates = new ArrayList<>(template.substrates.size());
    for (L2PredictionChemical substrate : template.substrates) {
      this.substrates.add(new L2PredictionChemical(substrate));
    }

    this.projectorName = template.projectorName;

    this.products = new ArrayList<>(template.products.size());
    for (L2PredictionChemical product : template.products) {
      this.products.add(new L2PredictionChemical(product));
    }

    this.reactionsRoMatch = new ArrayList<Long>(template.reactionsRoMatch);
    this.reactionsNoRoMatch = new ArrayList<Long>(template.reactionsNoRoMatch);
  }

  public L2Prediction(Integer id,
                      List<L2PredictionChemical> substrates,
                      String projectorName,
                      List<L2PredictionChemical> products) {
    this.id = id;
    this.substrates = substrates;
    this.products = products;
    this.projectorName = projectorName;
    this.reactionsRoMatch = new ArrayList<Long>();
    this.reactionsNoRoMatch = new ArrayList<Long>();
  }

  @JsonIgnore
  public int getReactionCount() {
    return reactionsRoMatch.size() + reactionsNoRoMatch.size();
  }

  @JsonIgnore
  public List<String> getSubstrateInchis() {
    List<String> inchis = new ArrayList<>();
    for (L2PredictionChemical chemical : getSubstrates()) {
      inchis.add(chemical.getInchi());
    }
    return inchis;
  }

  @JsonIgnore
  public List<Long> getSubstrateIds() {
    List<Long> ids = new ArrayList<>();
    for (L2PredictionChemical chemical : getSubstrates()) {
      if (chemical.hasId()) {
        ids.add(chemical.getId());
      }
    }
    return ids;
  }

  @JsonIgnore
  public List<String> getSubstrateNames() {
    List<String> names = new ArrayList<>();
    for (L2PredictionChemical chemical : getSubstrates()) {
      if (chemical.hasName()) {
        names.add(chemical.getName());
      }
    }
    return names;
  }

  @JsonIgnore
  public List<String> getProductInchis() {
    List<String> inchis = new ArrayList<>();
    for (L2PredictionChemical chemical : getProducts()) {
      inchis.add(chemical.getInchi());
    }
    return inchis;
  }

  @JsonIgnore
  public List<Long> getProductIds() {
    List<Long> ids = new ArrayList<>();
    for (L2PredictionChemical chemical : getProducts()) {
      if (chemical.hasId()) {
        ids.add(chemical.getId());
      }
    }
    return ids;
  }

  @JsonIgnore
  public List<String> getProductNames() {
    List<String> names = new ArrayList<>();
    for (L2PredictionChemical chemical : getProducts()) {
      if (chemical.hasName()) {
        names.add(chemical.getName());
      }
    }
    return names;
  }

  public Integer getId() {
    return id;
  }

  public void setId(Integer id) {
    this.id = id;
  }

  public List<L2PredictionChemical> getSubstrates() {
    return substrates;
  }

  public void setSubstrates(List<L2PredictionChemical> substrates) {
    this.substrates = substrates;
  }

  public List<L2PredictionChemical> getProducts() {
    return products;
  }

  public void setProducts(List<L2PredictionChemical> products) {
    this.products = products;
  }

  public List<Long> getReactionsRoMatch() {
    return reactionsRoMatch;
  }

  public void setReactionsRoMatch(List<Long> reactionsRoMatch) {
    this.reactionsRoMatch = reactionsRoMatch;
  }

  public List<Long> getReactionsNoRoMatch() {
    return reactionsNoRoMatch;
  }

  public void setReactionsNoRoMatch(List<Long> reactionsNoRoMatch) {
    this.reactionsNoRoMatch = reactionsNoRoMatch;
  }

  public String getProjectorName() {
    return projectorName;
  }

  public void setProjectorName(String projectorName) {
    this.projectorName = projectorName;
  }
}