BGI/SOAPsnp/Call_winManager.h

   1 /*
   2  ******************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-8-10
   8  *CLASS NAME: Call_winManager, Call_win_Task
   9  *FUNCTION : a class that can control Call_win vector.
  10  *FILE NAME : Call_winManager.h
  11  *UPDATE DATE : 2010-9-15
  12  *UPDATE BY : Bill Tang
  13  *UPDATE: 2010-10-13 add struct CALL_WIN_ARGS and Class Call_win_Task.
  14  *******************************************************************************
  15  */
  16
  17 #pragma once
  18 #include "soap_snp.h"
  19 #include "CThreadPool.h"
  20
  21 #define CRE_WIN_FAILED -1       // create Call_win object failed.
  22 #define INDEX_EXCEED    -2      // m_cw_vec index exceed
  23 #define SOAP2CNS_SUCCESS 1      // soap2cns successful.
  24
  25 class Call_winManager
  26 {
  27         // Call_win objects vector
  28         vector<Call_win*> m_cw_vec;
  29         Call_winManager(void);
  30
  31 public:
  32         Call_winManager(ubit64_t read_len, int file_num, Genome* genome);
  33         virtual ~Call_winManager(void);
  34         // add a Call_win object to the Call_win vector
  35         virtual int addCallwin(ubit64_t read_len);
  36         // soap to consensus
  37         virtual int soap2cns(vector<Soap_format>& alignment_vec, gzoutstream * consensus, my_ofstream& baseinfo, Genome* genome, Prob_matrix* mat, Parameter* para, int index, int ali_index, SfsMethod &sfsMethod);
  38         // deal the tail of sample
  39         virtual int dealTail(gzoutstream * consensus, my_ofstream& baseinfo, Genome* genome, Prob_matrix* mat, Parameter* para, int index, SfsMethod &sfsMethod);
  40         // set call win's last_start
  41         void setLast_start(int start_pos);
  42 };
  43
  44 /**
  45  * DATE: 2010-10-13
  46  * FUNCTION: a parameter structure that about Call_win.
  47  * PARAMETER:
  48  * RETURN:
  49  */
  50 typedef struct _call_win_args
  51 {
  52         Call_winManager * call_winManager_p;
  53         vector<Soap_format> * alignment_vec_p;
  54         gzoutstream * consensus_p;
  55         my_ofstream * baseinfo_p;
  56         Genome * genome;
  57         Prob_matrix * mat;
  58         Parameter *para;
  59         int index;
  60         int ali_index;
  61         SfsMethod * sfsMethod_p;
  62
  63         // initialize
  64         inline _call_win_args(Call_winManager* a, vector<Soap_format> * b,gzoutstream * c,my_ofstream* d,Genome* e,Prob_matrix* f,Parameter* g,int h, int i, SfsMethod *j)
  65         {
  66                 call_winManager_p = a;
  67                 alignment_vec_p = b;
  68                 consensus_p = c;
  69                 baseinfo_p = d;
  70                 genome = e;
  71                 mat = f;
  72                 para = g;
  73                 index = h;
  74                 ali_index = i;
  75                 sfsMethod_p = j;
  76         };
  77         inline _call_win_args()
  78         {
  79                 call_winManager_p = NULL;
  80                 alignment_vec_p = NULL;
  81                 consensus_p = NULL;
  82                 baseinfo_p = NULL;
  83                 genome = NULL;
  84                 mat = NULL;
  85                 para = NULL;
  86                 index = 0;
  87                 ali_index = 0;
  88                 sfsMethod_p = NULL;
  89         };
  90 }CALL_WIN_ARGS;
  91
  92 //void* _call_winManager_soap2cns_norm(void * __args);
  93
  94 class Call_win_Task : public CTask
  95 {
  96 public:
  97         // overload the function Run().
  98         int Run();
  99         /*{
 100                 _call_winManager_soap2cns_norm(this->m_ptrData);
 101                 return 1;
 102         }*/
 103 };