BioGraph.h

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#ifndef BIOGRAPH_H
#define BIOGRAPH_H

#include <limits.h>
#include "BioUtilities.h"

using namespace std;

class BioGraph
{
  vector<string> node_ids;
  int **adj_matrix_;
  int minDistance(int dist[],bool sptSet[]);
  //vector<int> dijkstra(int** graph,int src, int V);
public:
  BioGraph();
  BioGraph(vector<string> nids, int **adj);
  BioGraph& operator =(BioGraph& g);
  void setGraph(vector<string> nids, int **adj);
  void setNodeIds(vector<string> nids);
  void setNodeId(int index, string s);
  void setAdjacencyMatrix(int **adj);
  int ** getAdjacencyMatrix();
  vector<string> getNodeIds();
  string getNodeId(int i);
  long getNodeIdIndex(string s);
  int getNumberOfEdges();//return total number of edges in the graph
  long getNumberOfNodes();  
  bool isNeighbor(string n1,string n2); //Given node ids returns if they have an edge or not
  bool isNeighbor(long n1in,long n2in); //Same as above but in case indices are given
  int getNumberOfNodeEdges(string nid); //returns number of edges given a node id.
  void showAdjacencyMatrix(ostream& = cout);
  vector<string> getNeighborNodeIds(string n);
  float getClusteringCoefficient(string nid);
  float getAverageClusteringCoefficient();
  //Network manipulation methods
  void addEdge(string n1, string n2);
  void deleteEdge(string n1, string n2);
  void addNode(string n1);
  void deleteNode(string n1);
  //To be tested
  int getNumberOfSharedNeighbors(string n1, string n2);
  vector<string> getSharedNeighborIds(string n1, string n2);
  float getTopologicalCoefficient(string ni);
  vector<int> getNodeDistances(string n1);
  //Returns distance betweein n1 and all the nodes in the graph
  //In the same order as node_ids, if distance==INT_MAX, ~ not connected
  int getNodeDistance(string n1,string n2);
  
};

#endif