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#ifndef DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
#define DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
#include <algorithm>
#include <cassert>
#include <iostream>
#include <map>
#include <string>
#include <vector>
#include <pbdata/Enumerations.h>
#include <pbdata/Types.h>
class CmpAlignmentBase
{
public:
//
// For use in referencing alignment sets. TODO: subclass.
//
PlatformId platformId;
int Z;
unsigned int index, readGroupId, movieId, refSeqId;
unsigned int expId, runId, panel;
unsigned int x, y;
unsigned int rcRefStrand;
unsigned int holeNumber;
unsigned int offsetBegin, offsetEnd;
unsigned int setNumber, strobeNumber, mapQV, nBackRead, nReadOverlap;
unsigned int subreadId;
unsigned int nMatch, nMismatch, nIns, nDel;
std::vector<unsigned char> alignmentArray;
std::vector<unsigned int> alignmentIndex;
static std::map<std::string, int> columnNameToIndex;
static bool initializedColumnNameToIndex;
std::map<std::string, std::vector<UChar> > fields;
unsigned int *GetAlignmentIndex();
int GetAlignmentIndexSize();
unsigned int GetAlignedStrand();
unsigned int GetRCRefStrand();
// synonym
unsigned int GetTStrand();
bool GetX(int &xp);
unsigned int GetAlignmentId();
unsigned int GetX();
unsigned int GetY();
unsigned int GetMovieId();
unsigned int GetAlnGroupId();
unsigned int GetReadGroupId();
unsigned int LookupColumnValue(const char *columnName);
void InitializeColumnNameToIndex(std::vector<std::string> &columnNames);
unsigned int GetHoleNumber();
unsigned int GetRefGroupId();
unsigned int GetRefSeqId();
unsigned int GetOffsetBegin();
unsigned int GetOffsetEnd();
unsigned int GetQueryStart();
unsigned int GetQueryEnd();
unsigned int GetRefStart();
unsigned int GetRefEnd();
unsigned int GetNMatch();
unsigned int GetNMismatch();
unsigned int GetNInsertions();
unsigned int GetNDeletions();
unsigned int GetMapQV();
unsigned int GetSubreadId();
unsigned int GetStrobeNumber();
unsigned int GetSetNumber();
CmpAlignmentBase(PlatformId platformIdP = Springfield);
void SetPlatformId(PlatformId platformIdP);
};
class CmpAlignment : public CmpAlignmentBase
{
public:
int qStrand, tStrand;
DNALength qStart, qLength;
DNALength tStart, tLength;
//
// Default constructor just calls the base constructor to initialize platoformType
CmpAlignment(PlatformId pid = Springfield);
void StoreAlignmentIndex(unsigned int *alignmentIndexPtr, DSLength alignmentIndexLength);
void StoreAlignmentArray(unsigned char *alignmentArrayPtr, DSLength alignmentArrayLength);
template <typename T_Field>
void StoreField(std::string fieldName, T_Field *fieldValues, DSLength length);
CmpAlignment &operator=(const CmpAlignment &rhs);
int operator<(const CmpAlignment &rhs) const;
};
#include "CmpAlignmentImpl.hpp"
#endif
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