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.GraphViz;
  
  import java.io.BufferedWriter;
  import java.io.File;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Represents a GraphViz graph.
   * See user manual for format here: http://graphviz.org/Documentation/dotguide.pdf
   */
  public class DotGraph {
  
    List<DotEdge> edges;
    List<DotNode> nodes;
  
    public DotGraph() {
      edges = new ArrayList<>();
      nodes = new ArrayList<>();
    }
  
    public void addEdge(DotEdge edge) {
      edges.add(edge);
    }
  
    public void addNode(DotNode node) {
      nodes.add(node);
    }
  
    /**
     * Writes this graph to a given stream in DOT format, so it can be processed by GraphViz.
     * @param outputFile The file to write to.
     * @throws IOException
     */
    public void writeGraphToFile(File outputFile) throws IOException {
      try (BufferedWriter writer = new BufferedWriter(new FileWriter(outputFile))) {
        writer.write("digraph G {\n");
        for (DotNode node : nodes) {
          writer.write(node.getDotString());
        }
        for (DotEdge edge : edges) {
          writer.write(edge.getDotString());
        }
        writer.write("}\n");
      }
    }
  }
  