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.fasterxml.jackson.annotation.JsonCreator;
  import com.fasterxml.jackson.annotation.JsonProperty;
  import org.apache.commons.collections4.CollectionUtils;
  
  import java.util.Collections;
  import java.util.HashSet;
  import java.util.List;
  import java.util.Set;
  
  /**
   * Represents an edge, or reaction, in the metabolism network
   */
  public class NetworkEdge {
  
    @JsonProperty("substrates")
    private List<Integer> substrates;
  
    @JsonProperty("products")
    private List<Integer> products;
  
    @JsonProperty("reaction_ids")
    Set<Integer> reactionIds;
  
    @JsonProperty("projector_names")
    Set<String> projectorNames;
  
    @JsonProperty("orgs")
    Set<String> orgs;
  
    @JsonCreator
    public NetworkEdge(
        @JsonProperty("substrates") List<Integer> substrates,
        @JsonProperty("products") List<Integer> products,
        @JsonProperty("reaction_ids") Set<Integer> reactionIds,
        @JsonProperty("projector_names") Set<String> projectorNames,
        @JsonProperty("orgs") Set<String> orgs) {
      if (substrates == null || products == null) {
        throw new IllegalArgumentException("Cannot create network edge with null substrates or products.");
      }
      this.substrates = substrates;
      this.products = products;
      this.reactionIds = reactionIds;
      this.projectorNames = projectorNames;
      this.orgs = orgs;
    }
  
    public NetworkEdge(List<Integer> substrates, List<Integer> products) {
      this(substrates, products, new HashSet<Integer>(), new HashSet<String>(), new HashSet<String>());
    }
  
    /**
     * Merges another edge into this one by adding the auxiliary data from the other edge to this edge.
     * This includes reaction IDs and projector names associated with the other edge.
     * Ensures that the edges have the same chemicals; throws IllegalArgumentException otherwise.
     *
     * @param edge The edge whose data should be added.
     * @return This edge for chaining.
     * @throws IllegalArgumentException if the other edge has different chemicals from this one.
     */
    public NetworkEdge merge(NetworkEdge edge) {
      if (!hasSameSubstratesAndProducts(edge)) {
        throw new IllegalArgumentException("Can only merge two edges with the same chemicals.");
      }
      this.reactionIds.addAll(edge.getReactionIds());
      this.projectorNames.addAll(edge.getProjectorNames());
      return this;
    }
  
    /**
     * Tests if this edge should be considered the same as another. Returns true if substrate and product are the same,
     * regardless of auxiliary data. This takes into account both the identity and cardinality of each chemical in the lists.
     *
     * @param edge The edge to compare to.
     * @return True if same.
     */
    public boolean hasSameSubstratesAndProducts(NetworkEdge edge) {
      return CollectionUtils.isEqualCollection(this.getSubstrates(), edge.getSubstrates())
          && CollectionUtils.isEqualCollection(this.getProducts(), edge.getProducts());
    }
  
    public List<Integer> getSubstrates() {
      return substrates;
    }
  
    public List<Integer> getProducts() {
      return products;
    }
  
    public Set<Integer> getReactionIds() {
      return Collections.unmodifiableSet(reactionIds);
    }
  
    public NetworkEdge addReactionId(Integer reactionId) {
      this.reactionIds.add(reactionId);
      return this;
    }
  
    public Set<String> getProjectorNames() {
      return Collections.unmodifiableSet(projectorNames);
    }
  
    public NetworkEdge addProjectorName(String projectorName) {
      this.projectorNames.add(projectorName);
      return this;
    }
  
    public Set<String> getOrgs() {
      return this.orgs;
    }
  
    public void addOrg(String org) {
      this.orgs.add(org);
    }
  }
  
  