scorepair.h

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#ifndef SCOREPAIR_H
#define SCOREPAIR_H
//#define HAVE_NAMESPACE_STD

#include <string>
#include <map>
#include <vector>
#include <set>
//#include "forest.h"
#include "hatrees.h"
//#include "libpq++.h"
#include <pqxx>

using namespace std;
using namespace pqxx;

//enum pairquality { good, bad, modify };
//void deleteCluster(PgDatabase &pgdb, const string &clusterid);
void deleteCluster(connection &pgdb, const string &clusterid);

class scorepair {
        public:
                void read(istream &in, int cut);
                void clear() { names.clear(); seqlens.clear(); rel.clear(); }

                // 1=good, 9=bad, 5=modify; reading subclstr
                int quality();
                void showcluster(ostream &ou);

                /* return all those that are not included in any cluster */
                set<string> badMembers() const;
                //void loadTable(PgDatabase &pgdb);
                void clusterArray(vector<set<string> > &clar);
                vector<set<string> > getClusters();  // too expensive don't call

                void addNewCluster(connection &pgdb, const string &clusterid, 
                                int &clusterIdCnt);

        private:
                multimap<string, string> rel;  // use integer for speed
                vector<string> names;  // name -> identifier
                vector<int> seqlens;
                hatrees<string> subclstr;
};

#endif