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#pragma once
/*
* This function is a base clase for CGenome_Index_Table
* It has an array of genome index, which is binned and sorted into buckets.
* It has a CHashIndex, which is a hash index array pointing to the first reacord of each bin
*/
#include "HashIndexT.h"
#include "boolFlagArray.h"
#include "chdir.h"
#include "stdafx.h"
#include "seedOptions.h"
#include <string>
#include <iostream>
using std::string;
typedef unsigned int CIndex_Type;
class CIndex_Table
{
public:
CIndex_Table(void);
~CIndex_Table(void);
void delete_index_table(void);
// A index array represent the substring of a genome
CIndex_Type* pIndexTable;
// A hash index array pointing to the first reacord of each bin
CHashIndexT* pHashIndexTable;
// A bit array object indicating the neighborhood seed-pattern record are the same.
CboolFlagArray* pbaMaskedFlag;
// Flag array which mark the index as the representative copy of the mathmatical repeats.
CboolFlagArray* pbaRepeatRepresentativeFlag;
unsigned int size;
// unsigned int capacity;
unsigned int chosenSeedId;
unsigned int uiSubDiffThreshold;
unsigned int uiRead_Length;
bool bMapReadInColors;
protected:
string indexFileName;
bool save_Hash_Table(FILE* fp) const;
bool read_Hash_Table(FILE* fp);
private:
int initialization(void);
void printInfo(void) const;
};
string default_index_path(string filePostfix, bool colorReads,\
unsigned int seedOption, unsigned int uiReadLength);
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