trapper: acewriteralgo.h Source File

00001 #include "R_algo.h"
00002 #include <vector>
00003 
00004 class AceWriter : public RAlgo
00005 {
00006 public:
00007   AceWriter(TrapperDoc * pDoc_, std::set< db_recno_t >& recnoList, AlgoParam* param) : 
00008     RAlgo(pDoc_, recnoList, param) {}
00009   
00010   void start();
00011 
00012 private:
00013   
00014   void write_ace_file();
00015   int get_consensus(std::vector<char> &cons, std::vector<int> &rowVec, int &num);
00016   int get_realignment_row(const int row, std::vector<char> &aligned_read, int &row_start);
00017   
00018 
00019 };