/*************************************************************************
*                                                                        *
*  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.JsonSubTypes;
import com.fasterxml.jackson.annotation.JsonTypeInfo;

import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.Set;

@JsonTypeInfo(
    use = JsonTypeInfo.Id.NAME,
    include = JsonTypeInfo.As.PROPERTY,
    property = "type")
@JsonSubTypes({
    @JsonSubTypes.Type(value = MetabolismNetwork.class, name = "MetabolismNetwork")
})
public interface ImmutableNetwork {

  public NetworkNode getNodeByUID(Integer uid);

  public Optional<NetworkNode> getNodeOptionByUID(Integer uid);

  public NetworkNode getNodeByInchi(String inchi);

  public Optional<NetworkNode> getNodeOptionByInchi(String inchi);

  public List<NetworkNode> getNodesByMass(Double mass, Double massTolerance);

  public Collection<NetworkNode> getNodes();

  /**
   * Get all edges from the graph.
   *
   * @return An unmodifiable collection of the graph's edges.
   */
  public Collection<NetworkEdge> getEdges();

  public Set<NetworkNode> getSubstrates(NetworkEdge edge);

  public Set<NetworkNode> getProducts(NetworkEdge edge);

  /**
   * Get all nodes that are one step forward from this node. These are predicted products of reactions that have this
   * node as a substrate.
   *
   * @param node The starting node.
   * @return The list of potential product nodes.
   */
  public List<NetworkNode> getDerivatives(NetworkNode node);

  /**
   * Get all nodes that are one step before this node. These are substrates of reactions that are predicted to produce
   * this node as a product.
   *
   * @param node The starting node.
   * @return The list of potential substrate nodes.
   */
  public List<NetworkNode> getPrecursors(NetworkNode node);
}