mcode.h

/**************************************************************************
 * Copyright (c) 2002-2011 T. M. Murali                                   *
 * Copyright (c) 2007-2011 Naveed Massjouni                               *
 *                                                                        *
 * This file is part of Biorithm.                                         *
 *                                                                        *
 * Biorithm 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.                                    *
 *                                                                        *
 * Biorithm 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 Biorithm.  If not, see <http://www.gnu.org/licenses/>.      *
 *                                                                        *
 **************************************************************************/

#ifndef MCODE_H
#define MCODE_H

//#define DEBUG 0

#include <algorithm>
#include <iostream>
#include <list>
#include <map>
#include <set>
#include <string>
#include <vector>

#define WITH_GTEST 0
#if WITH_GTEST
#include "gtest/gtest_prod.h"
#endif //WITH_GTEST

#include "graph.h"
using namespace  std;

typedef MyNode Node;
typedef MyNode::EdgeIterator EdgeIterator;
typedef MyEdge Edge;
typedef MyGraph Graph;
typedef MyGraph::MyConstNodeIterator ConstNodeIterator;
typedef MyNodeId NodeId; // string

// Class: MCODE
// This class implements the MCODE clustering algorithm.
// G. D. Bader and C. W. Hogue, "An automated method for finding molecular complexes in large protein interaction networks." BMC Bioinformatics, vol. 4, no. 1, January 2003.
class MCODE {

#if WITH_GTEST
  // Declare friends so we can unit test private methods.
  FRIEND_TEST(MCODETest, TestDensity);
  FRIEND_TEST(MCODETest, TestMaxKCore);
  FRIEND_TEST(MCODETest, TestWeighNode);
#endif // WITH_GTEST

private:
        map<NodeId, double> nodeWeightsMap;
        list<NodeId> sortedNodes;
        set<NodeId> seenNodesSet;

  void maxKCore(const Graph& graph, int &k, Graph &kcore);

  void maxKCoreFaster(const Graph &graph, int &k, Graph &kcore);

        double weighNode(const Graph&, NodeId nodeId);

        void weighNodes(const Graph&);

        double computeDensity(const Graph&);

        set<NodeId> getNeighbours(const Graph& graph, NodeId nodeId);

        void findComplex(const Graph& graph, double vwp, NodeId nodeId,
                set<NodeId>& complexNodes, double seedWeight);


public:

  double computeGraphScore(const MyGraph &graph);

  vector<Graph> findComplexes(const Graph& graph, double vwp,
                              map< string, double> *nodeWeights = NULL);
};

#endif // MCODE_H

// vim:fdm=indent:fdn=1