Class SequenceParser

• Defined in File SequenceParser.h

Class Documentation

class SequenceParser

Public Functions

SequenceParser() = delete

~SequenceParser() = delete

SequenceParser(const SequenceParser&) = delete

SequenceParser &operator=(const SequenceParser&) = delete

SequenceParser(SequenceParser&&) = delete

SequenceParser &operator=(SequenceParser&&) = delete

Public Static Functions

static void readSequenceFile(SequenceHandler &sequenceHandler, const std::filesystem::path &pathname, const std::string &delimiter)

static void makeSequenceFileSmartPeak(SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out)

static void writeSequenceFileSmartPeak(SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::string &delimiter = ",")

static void makeSequenceFileAnalyst(SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out)

static void writeSequenceFileAnalyst(SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::string &delimiter = "\)

static void makeSequenceFileMasshunter(SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out)

static void writeSequenceFileMasshunter(SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::string &delimiter = "\)

static void makeSequenceFileXcalibur(SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out)

static void writeSequenceFileXcalibur(SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::string &delimiter = "\)

static void makeDataTableFromMetaValue(const SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out, const std::vector<std::string> &meta_data, const std::set<SampleType> &sample_types, const std::set<std::string> &sample_names, const std::set<std::string> &component_group_names, const std::set<std::string> &component_names)

static bool writeDataTableFromMetaValue(const SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::vector<FeatureMetadata> &meta_data, const std::set<SampleType> &sample_types)

static void makeGroupDataTableFromMetaValue(const SequenceHandler &sequenceHandler, std::vector<std::vector<std::string>> &rows_out, std::vector<std::string> &headers_out, const std::vector<std::string> &meta_data, const std::set<SampleType> &sample_types, const std::set<std::string> &sample_names, const std::set<std::string> &component_group_names, const std::set<std::string> &component_names)

static bool writeGroupDataTableFromMetaValue(const SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::vector<FeatureMetadata> &meta_data, const std::set<SampleType> &sample_types)

static void makeDataMatrixFromMetaValue(const SequenceHandler &sequenceHandler, Eigen::Tensor<float, 2> &data_out, Eigen::Tensor<std::string, 1> &columns_out, Eigen::Tensor<std::string, 2> &rows_out, const std::vector<std::string> &meta_data, const std::set<SampleType> &sample_types, const std::set<std::string> &sample_names, const std::set<std::string> &component_group_names, const std::set<std::string> &component_names)

static bool writeDataMatrixFromMetaValue(const SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::vector<FeatureMetadata> &meta_data, const std::set<SampleType> &sample_types)

static void makeGroupDataMatrixFromMetaValue(const SequenceHandler &sequenceHandler, Eigen::Tensor<float, 2> &data_out, Eigen::Tensor<std::string, 1> &columns_out, Eigen::Tensor<std::string, 2> &rows_out, const std::vector<std::string> &meta_data, const std::set<SampleType> &sample_types, const std::set<std::string> &sample_names, const std::set<std::string> &component_group_names, const std::set<std::string> &component_names)

static bool writeGroupDataMatrixFromMetaValue(const SequenceHandler &sequenceHandler, const std::filesystem::path &filename, const std::vector<FeatureMetadata> &meta_data, const std::set<SampleType> &sample_types)

Public Static Attributes

static constexpr char const *const s_PeptideRef = {"PeptideRef"}

static constexpr char const *const s_native_id = {"native_id"}