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// Author: Mark Chaisson
#ifndef DATASTRUCTURES_READS_SCAN_DATA_H_
#define DATASTRUCTURES_READS_SCAN_DATA_H_
#include <map>
#include <string>
#include <pbdata/Enumerations.h>
#include <pbdata/PacBioDefs.h>
#include <pbdata/reads/AcqParams.hpp>
class HDFScanDataReader;
class HDFScanDataWriter;
class ScanData
{
friend class HDFScanDataReader;
friend class HDFScanDataWriter;
public:
// Convert base map from a std::map<char, size_t> to a std::string.
// e.g., {{'A', 2}, {'C', 1}, {'T', 0}, {'G', 3}} --> TCAG
static std::string BaseMapToStr(const std::map<char, size_t>& baseMap);
// Convert base map from a std::string to a std::map<char, size_t>.
// e.g., TCAG --> {{'A', 2}, {'C', 1}, {'T', 0}, {'G', 3}}
static std::map<char, size_t> StrToBaseMap(const std::string& baseMapStr);
// A baseMap must contain maps from bases (e.g., ACGT) to indices (e.g., 0, 1, 2, 3).
static bool IsValidBaseMap(const std::map<char, size_t>& baseMap);
public:
PlatformId platformId;
float frameRate;
unsigned int numFrames;
std::string movieName, runCode;
std::string whenStarted;
std::map<char, size_t> baseMap;
ScanData(const AcqParams& acqParams = AcqParams());
std::string GetMovieName();
ScanData& PlatformID(const PlatformId& id);
ScanData& FrameRate(const float& rate);
ScanData& NumFrames(const unsigned int& num);
ScanData& MovieName(const std::string& name);
ScanData& RunCode(const std::string& code);
ScanData& WhenStarted(const std::string& when);
ScanData& BaseMap(const std::map<char, size_t>& bmp);
ScanData& BaseMap(const std::string& baseMapStr);
ScanData& SequencingKit(const std::string sequencingKit);
ScanData& BindingKit(const std::string bindingKit);
ScanData& SetAcqParams(const AcqParams& acqParams);
PlatformId PlatformID(void) const;
float FrameRate(void) const;
unsigned int NumFrames(void) const;
std::string MovieName(void) const;
std::string RunCode(void) const;
std::string WhenStarted(void) const;
std::map<char, size_t> BaseMap(void) const;
std::string BaseMapStr(void) const;
std::string SequencingKit(void) const;
std::string BindingKit(void) const;
AcqParams GetAcqParams(void) const;
private:
std::string sequencingKit_;
std::string bindingKit_;
AcqParams acqParams_;
};
#endif
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