BGI/SOAPsnp/MatrixManager.h

   1 /*
   2  ******************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-8-9
   8  *CLASS NAME: FileListManager
   9  *FUNCTION : a class that can control Prob_matrix vector. support add, change, get
  10  *                       Matrix ect functions.
  11  *FILE NAME : MatrixManager.h
  12  *UPDATE DATE : 2010-8-25
  13  *UPDATE BY : Bill Tang
  14  *UPDATE: 2010-11-2 change the interface which is related to soap file.
  15  *UPDATA BY :BIll Tang
  16  *******************************************************************************
  17  */
  18
  19 #pragma once
  20 #include <fstream>
  21 #include <vector>
  22 #include "soap_snp.h"
  23
  24 #define INDEX_OVER_FLOW NULL
  25 #define CREATE_MAT_FAILED -1
  26
  27 using namespace std;
  28 class MatrixManager
  29 {
  30 public:
  31         MatrixManager(void);
  32         virtual ~MatrixManager(void);
  33 private:
  34         // a Prob_matrix vectior point
  35         vector<Prob_matrix*> m_mat_vec;
  36 public:
  37         // add Matrix to the vector
  38         virtual int addMatrix(SamCtrl &alignment, Parameter* para, Genome* genome, fstream *outFile, int index);
  39         // add a matrix from the prior matrixfile.
  40         virtual int addMatrix(igzstream &alignment, Parameter* para, Genome* genome, fstream *outFile, int index);
  41         // change the Prob_matrix with new soap_vec
  42         virtual int changeMatrix(vector<Soap_format>& soap_vec, Parameter* para, Genome* genome, int index);
  43         // get a Prob_matrix point that point to the m_mat_vec[index]
  44         virtual Prob_matrix* getMatrix(int index);
  45         // add a matrix from the prior matrixfile.
  46         virtual int addMatrix(std::fstream& matrix_file, Parameter *para);
  47         // set the m_mat_vec's size
  48         virtual void setMatrixNum(const int number);
  49 };
  50
  51
  52 void *_matrixManager_addMatrix(void * __args);
  53
  54 /**
  55  * DATE: 2010-10-12
  56  * FUNCTION: a parameter structure that about matrix.
  57  * PARAMETER:
  58  * RETURN:
  59  */
  60 typedef struct _matrix_args
  61 {
  62         MatrixManager * matrixManager;
  63         //FileListManager * fileListManager;
  64         Parameter * para;
  65         Genome* genome;
  66         igzstream *soap_alignment;
  67         std::fstream *outFile;
  68         SamCtrl *sam_alignment;
  69         int index;
  70
  71         /**
  72          * DATE: 2010-10-12
  73          * FUNCTION: initialize the struct.
  74          * PARAMETER:
  75          * RETURN:
  76          */
  77         inline _matrix_args(MatrixManager * a, Parameter * b, Genome* c,
  78                         igzstream * d, std::fstream * e, SamCtrl * f, int g)
  79         {
  80                 matrixManager = a;
  81                 para = b;
  82                 genome = c;
  83                 soap_alignment = d;
  84                 outFile = e;
  85                 sam_alignment = f;
  86                 index = g;
  87         }
  88         ;
  89         /**
  90          * DATE: 2010-10-12
  91          * FUNCTION: initialize the struct.
  92          * PARAMETER:
  93          * RETURN:
  94          */
  95         inline _matrix_args()
  96         {
  97                 matrixManager = 0;
  98                 para = 0;
  99                 genome = 0;
 100                 soap_alignment = 0;
 101                 outFile = 0;
 102                 sam_alignment = 0;
 103         }
 104         ;
 105
 106 }MATRIX_ARGS;
 107