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.act.lcms.v2.Metabolite;
  import com.fasterxml.jackson.annotation.JsonCreator;
  import com.fasterxml.jackson.annotation.JsonIgnore;
  import com.fasterxml.jackson.annotation.JsonProperty;
  
  import java.util.Collection;
  import java.util.Collections;
  import java.util.HashSet;
  import java.util.Set;
  import java.util.concurrent.atomic.AtomicInteger;
  
  /**
   * Represents a node, or chemical, in the metabolism network
   */
  public class NetworkNode {
  
    private static AtomicInteger uidCounter = new AtomicInteger(0);
  
    @JsonProperty("uid")
    private final Integer UID;
  
    @JsonProperty("metabolite")
    private Metabolite metabolite;
  
    private Set<NetworkEdge> outEdges;
  
    private Set<NetworkEdge> inEdges;
  
    @JsonCreator
    private NetworkNode(@JsonProperty("metabolite") Metabolite metabolite,
                        @JsonProperty("uid") Integer UID) {
      this.outEdges = new HashSet<>();
      this.inEdges = new HashSet<>();
      this.metabolite = metabolite;
      this.UID = UID;
      uidCounter.set(Math.max(UID + 1, uidCounter.get()));
    }
  
    public NetworkNode(Metabolite metabolite) {
      this.outEdges = new HashSet<>();
      this.inEdges = new HashSet<>();
      this.metabolite = metabolite;
      this.UID = uidCounter.getAndIncrement();
    }
  
    public Metabolite getMetabolite() {
      return metabolite;
    }
  
    public Integer getUID() {
      return UID;
    }
  
    /**
     * Get out edges.
     * Don't need to explicitly serialize these because connectivity information is all contained in the edge -> node pointers.
     * The node -> edge pointers can thus be reconstructed on deserialization.
     */
    @JsonIgnore
    public Collection<NetworkEdge> getOutEdges() {
      return Collections.unmodifiableSet(outEdges);
    }
  
    public void addOutEdge(NetworkEdge edge) {
      this.outEdges.add(edge);
    }
  
    /**
     * Get in edges.
     * Don't need to explicitly serialize these because connectivity information is all contained in the edge -> node pointers.
     * The node -> edge pointers can thus be reconstructed on deserialization.
     */
    @JsonIgnore
    public Collection<NetworkEdge> getInEdges() {
      return Collections.unmodifiableSet(inEdges);
    }
  
    public void addInEdge(NetworkEdge edge) {
      this.inEdges.add(edge);
    }
  }
  