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.installer.pubchem;
  
  import act.shared.Chemical;
  import com.fasterxml.jackson.annotation.JsonProperty;
  import org.json.JSONArray;
  import org.json.JSONObject;
  
  import java.io.Serializable;
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  /**
   * This inner class exists as a serializable container for features extracted from PC-Compound documents.  We can go
   * directly to Chemical objects if this intermediate representation turns out to be unnecessary.
   */
  public class PubchemEntry implements Serializable {
    private static final long serialVersionUID = -6542683222963930035L;
  
    // TODO: use a builder for this instead of constructing and mutating.
  
    @JsonProperty("IUPAC_names")
    private Map<String, String> names = new HashMap<>(5); // There tend to be five name variants per chemical.
  
    @JsonProperty("pubchem_ids")
    private List<Long> pubchemIds = new ArrayList<>(1); // Hopefully there's only one id.
  
    @JsonProperty("InChI")
    private String inchi;
  
    /* Use a list for SMILES rather than a set to maintain order.  We could use a LinkedHashSet instead, but the
     * computational overhead of maintaining a set doesn't seem worth removing a few duplicated SMILES.
     * TODO: check that pubchem doesn't have many dupes. */
    @JsonProperty("SMILES")
    private List<String> smiles = new ArrayList<>(1); // Hopefully there's only one SMILES too!
  
    // For general use.
    public PubchemEntry(Long pubchemId) {
      this.pubchemIds.add(pubchemId);
    }
  
    // For deserialization.
    public PubchemEntry(Map<String, String> names, List<Long> pubchemIds, String inchi, List<String> smiles) {
      this.names = names;
      this.pubchemIds = pubchemIds;
      this.inchi = inchi;
      this.smiles = smiles;
    }
  
    public Map<String, String> getNames() {
      return names;
    }
  
    public void setNameByType(String type, String value) {
      names.put(type, value);
    }
  
    public List<Long> getPubchemIds() {
      return pubchemIds;
    }
  
    public void appendPubchemId(Long pubchemId) {
      pubchemIds.add(pubchemId);
    }
  
    public String getInchi() {
      return inchi;
    }
  
    public void setInchi(String inchi) {
      this.inchi = inchi;
    }
  
    public List<String> getSmiles() {
      return this.smiles;
    }
  
    public void appendSmiles(String smiles) {
      this.smiles.add(smiles);
    }
  
    public Chemical asChemical() {
      Chemical c = new Chemical(this.inchi);
      if (this.smiles.size() > 0) {
        c.setSmiles(this.smiles.get(0)); // Just use the first SMILES we find as the primary.
      }
      c.setPubchem(this.getPubchemIds().get(0)); // Assume we'll have at least one id to start with.
      for (Map.Entry<String, String> entry : names.entrySet()) {
        c.addNames(entry.getKey(), new String[] { entry.getValue() });
      }
      c.putRef(Chemical.REFS.ALT_PUBCHEM,
          new JSONObject().
              put("ids", new JSONArray(pubchemIds.toArray(new Long[pubchemIds.size()]))).
              put("smiles", new JSONArray(smiles.toArray(new String[smiles.size()])))
      );
      return c;
    }
  }
  