/usr/include/pbseq/pbdata/reads/ScanData.hpp is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#ifndef DATASTRUCTURES_READS_SCAN_DATA_H_
#define DATASTRUCTURES_READS_SCAN_DATA_H_
#include <string>
#include <map>
#include "AcqParams.hpp"
#include "../Enumerations.h"
#include "../PacBioDefs.h"
class HDFScanDataReader;
class HDFScanDataWriter;
class ScanData {
friend class HDFScanDataReader;
friend class HDFScanDataWriter;
public:
// Convert base map from a map<char, size_t> to a 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 string to a 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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