C++ API Reference

Class Hierarchy

• • Namespace noLZSS
    • Struct Factor
    • Struct FactorFileFooter
    • Struct FastaFactorizationResult
    • Struct FastaParseResult
    • Struct FastaPerSequenceCountResult
    • Struct FastaPerSequenceFactorizationResult
    • Struct FastaReferenceTargetResult
    • Struct PreparedSequenceResult
    • Struct ThreadContext
    • Class ParallelFactorizer
    • Enum FastaDnaSanitizationMode

File Hierarchy

• • Directory src
    • Directory cpp
      • File bindings.cpp
      • File factorizer.cpp
      • File factorizer.hpp
      • File factorizer_core.hpp
      • File factorizer_helpers.hpp
      • File factorizer_templates.hpp
      • File fasta_processor.cpp
      • File fasta_processor.hpp
      • File parallel_factorizer.cpp
      • File parallel_factorizer.hpp
      • File parallel_fasta_processor.cpp
      • File parallel_fasta_processor.hpp

Full API

Namespaces

• Namespace noLZSS
  • Namespaces
  • Classes
  • Enums
  • Functions
  • Typedefs
  • Variables

• Namespace noLZSS::detail
  • Functions

Classes and Structs

• Struct Factor
  • Struct Documentation
    • noLZSS::Factor
      • start
      • length
      • ref

• Struct FactorFileFooter
  • Struct Documentation
    • noLZSS::FactorFileFooter
      • FactorFileFooter()
      • magic
      • num_factors
      • num_sequences
      • num_sentinels
      • footer_size
      • total_length

• Struct FastaFactorizationResult
  • Struct Documentation
    • noLZSS::FastaFactorizationResult
      • factors
      • sentinel_factor_indices
      • sequence_ids

• Struct FastaParseResult
  • Struct Documentation
    • noLZSS::FastaParseResult
      • sequences
      • sequence_ids

• Struct FastaPerSequenceCountResult
  • Struct Documentation
    • noLZSS::FastaPerSequenceCountResult
      • sequence_ids
      • factor_counts
      • total_factors

• Struct FastaPerSequenceFactorizationResult
  • Struct Documentation
    • noLZSS::FastaPerSequenceFactorizationResult
      • per_sequence_factors
      • sequence_ids

• Struct FastaReferenceTargetResult
  • Struct Documentation
    • noLZSS::FastaReferenceTargetResult
      • concatinated_sequences
      • sequence_ids
      • num_ref_sequences
      • num_target_sequences
      • target_start_index

• Struct PreparedSequenceResult
  • Struct Documentation
    • noLZSS::PreparedSequenceResult
      • prepared_string
      • original_length
      • sentinel_positions

• Struct ThreadContext
  • Struct Documentation
    • noLZSS::ThreadContext
      • thread_id
      • start_pos
      • end_pos
      • text_length
      • temp_file_path
      • is_last_thread
      • next_thread_factor_index
      • last_read_factor

• Class ParallelFactorizer
  • Class Documentation
    • noLZSS::ParallelFactorizer
      • ParallelFactorizer()
      • ~ParallelFactorizer()
      • parallel_factorize()
      • parallel_factorize_file()
      • parallel_factorize_dna_w_rc()
      • parallel_factorize_multiple_dna_w_rc()
      • parallel_factorize_file_dna_w_rc()
      • create_temp_file_path()
      • merge_temp_files()
      • cleanup_temp_files()
      • factorize_dna_w_rc_thread()
      • MIN_CHARS_PER_THREAD

Enums

• Enum FastaDnaSanitizationMode
  • Enum Documentation
    • FastaDnaSanitizationMode
      • RemoveAmbiguous
      • Strict

Functions

• Function noLZSS::complement
  • Function Documentation
    • complement()

• Function noLZSS::count_factors
  • Function Documentation
    • count_factors()

• Function noLZSS::count_factors_dna_w_rc
  • Function Documentation
    • count_factors_dna_w_rc()

• Function noLZSS::count_factors_fasta_dna_no_rc_per_sequence
  • Function Documentation
    • count_factors_fasta_dna_no_rc_per_sequence()

• Function noLZSS::count_factors_fasta_dna_w_rc_per_sequence
  • Function Documentation
    • count_factors_fasta_dna_w_rc_per_sequence()

• Function noLZSS::count_factors_file
  • Function Documentation
    • count_factors_file()

• Function noLZSS::count_factors_file_dna_w_rc
  • Function Documentation
    • count_factors_file_dna_w_rc()

• Function noLZSS::count_factors_file_multiple_dna_w_rc
  • Function Documentation
    • count_factors_file_multiple_dna_w_rc()

• Function noLZSS::count_factors_multiple_dna_w_rc
  • Function Documentation
    • count_factors_multiple_dna_w_rc()

• Template Function noLZSS::detail::nolzss
  • Function Documentation
    • nolzss()

• Template Function noLZSS::detail::nolzss_dna_w_rc
  • Function Documentation
    • nolzss_dna_w_rc()

• Template Function noLZSS::detail::nolzss_multiple_dna_w_rc
  • Function Documentation
    • nolzss_multiple_dna_w_rc()

• Function noLZSS::factorize
  • Function Documentation
    • factorize()

• Function noLZSS::factorize_dna_rc_w_ref_fasta_files
  • Function Documentation
    • factorize_dna_rc_w_ref_fasta_files()

• Function noLZSS::factorize_dna_w_rc
  • Function Documentation
    • factorize_dna_w_rc()

• Function noLZSS::factorize_dna_w_reference_seq
  • Function Documentation
    • factorize_dna_w_reference_seq()

• Function noLZSS::factorize_dna_w_reference_seq_file
  • Function Documentation
    • factorize_dna_w_reference_seq_file()

• Function noLZSS::factorize_fasta_dna_no_rc_per_sequence
  • Function Documentation
    • factorize_fasta_dna_no_rc_per_sequence()

• Function noLZSS::factorize_fasta_dna_w_rc_per_sequence
  • Function Documentation
    • factorize_fasta_dna_w_rc_per_sequence()

• Function noLZSS::factorize_fasta_multiple_dna_no_rc
  • Function Documentation
    • factorize_fasta_multiple_dna_no_rc()

• Function noLZSS::factorize_fasta_multiple_dna_w_rc
  • Function Documentation
    • factorize_fasta_multiple_dna_w_rc()

• Function noLZSS::factorize_file
  • Function Documentation
    • factorize_file()

• Function noLZSS::factorize_file_dna_w_rc
  • Function Documentation
    • factorize_file_dna_w_rc()

• Function noLZSS::factorize_file_multiple_dna_w_rc
  • Function Documentation
    • factorize_file_multiple_dna_w_rc()

• Template Function noLZSS::factorize_file_stream
  • Function Documentation
    • factorize_file_stream()

• Template Function noLZSS::factorize_file_stream_dna_w_rc
  • Function Documentation
    • factorize_file_stream_dna_w_rc()

• Template Function noLZSS::factorize_file_stream_multiple_dna_w_rc
  • Function Documentation
    • factorize_file_stream_multiple_dna_w_rc()

• Function noLZSS::factorize_multiple_dna_w_rc
  • Function Documentation
    • factorize_multiple_dna_w_rc()

• Template Function noLZSS::factorize_stream
  • Function Documentation
    • factorize_stream()

• Template Function noLZSS::factorize_stream_dna_w_rc
  • Function Documentation
    • factorize_stream_dna_w_rc()

• Template Function noLZSS::factorize_stream_multiple_dna_w_rc
  • Function Documentation
    • factorize_stream_multiple_dna_w_rc()

• Function noLZSS::factorize_w_reference
  • Function Documentation
    • factorize_w_reference()

• Function noLZSS::factorize_w_reference_file
  • Function Documentation
    • factorize_w_reference_file()

• Function noLZSS::identify_sentinel_factors
  • Function Documentation
    • identify_sentinel_factors()

• Function noLZSS::is_canonical_dna
  • Function Documentation
    • is_canonical_dna()

• Function noLZSS::is_rc
  • Function Documentation
    • is_rc()

• Function noLZSS::lcp
  • Function Documentation
    • lcp()

• Function noLZSS::next_leaf
  • Function Documentation
    • next_leaf()

• Function noLZSS::parallel_factorize_dna_w_rc_to_file(::std::string_view, const ::std::string&, size_t)
  • Function Documentation
    • parallel_factorize_dna_w_rc_to_file()

• Function noLZSS::parallel_factorize_dna_w_rc_to_file(std::string_view, const std::string&, size_t)
  • Function Documentation
    • parallel_factorize_dna_w_rc_to_file()

• Function noLZSS::parallel_factorize_file_dna_w_rc_to_file(const ::std::string&, const ::std::string&, size_t)
  • Function Documentation
    • parallel_factorize_file_dna_w_rc_to_file()

• Function noLZSS::parallel_factorize_file_dna_w_rc_to_file(const std::string&, const std::string&, size_t)
  • Function Documentation
    • parallel_factorize_file_dna_w_rc_to_file()

• Function noLZSS::parallel_factorize_file_to_file(const ::std::string&, const ::std::string&, size_t, size_t)
  • Function Documentation
    • parallel_factorize_file_to_file()

• Function noLZSS::parallel_factorize_file_to_file(const std::string&, const std::string&, size_t, size_t)
  • Function Documentation
    • parallel_factorize_file_to_file()

• Function noLZSS::parallel_factorize_to_file(::std::string_view, const ::std::string&, size_t, size_t)
  • Function Documentation
    • parallel_factorize_to_file()

• Function noLZSS::parallel_factorize_to_file(std::string_view, const std::string&, size_t, size_t)
  • Function Documentation
    • parallel_factorize_to_file()

• Function noLZSS::parallel_write_factors_binary_file_fasta_dna_no_rc_per_sequence
  • Function Documentation
    • parallel_write_factors_binary_file_fasta_dna_no_rc_per_sequence()

• Function noLZSS::parallel_write_factors_binary_file_fasta_dna_w_rc_per_sequence
  • Function Documentation
    • parallel_write_factors_binary_file_fasta_dna_w_rc_per_sequence()

• Function noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_no_rc
  • Function Documentation
    • parallel_write_factors_binary_file_fasta_multiple_dna_no_rc()

• Function noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_w_rc
  • Function Documentation
    • parallel_write_factors_binary_file_fasta_multiple_dna_w_rc()

• Function noLZSS::parallel_write_factors_dna_w_reference_fasta_files_to_binary
  • Function Documentation
    • parallel_write_factors_dna_w_reference_fasta_files_to_binary()

• Function noLZSS::parse_fasta_sequences_and_ids
  • Function Documentation
    • parse_fasta_sequences_and_ids()

• Function noLZSS::prepare_multiple_dna_sequences_no_rc
  • Function Documentation
    • prepare_multiple_dna_sequences_no_rc()

• Function noLZSS::prepare_multiple_dna_sequences_w_rc
  • Function Documentation
    • prepare_multiple_dna_sequences_w_rc()

• Function noLZSS::prepare_ref_target_dna_no_rc_from_fasta
  • Function Documentation
    • prepare_ref_target_dna_no_rc_from_fasta()

• Function noLZSS::prepare_ref_target_dna_w_rc_from_fasta
  • Function Documentation
    • prepare_ref_target_dna_w_rc_from_fasta()

• Function noLZSS::rc_end
  • Function Documentation
    • rc_end()

• Function noLZSS::revcomp
  • Function Documentation
    • revcomp()

• Function noLZSS::sanitize_filename
  • Function Documentation
    • sanitize_filename()

• Function noLZSS::to_upper_ascii
  • Function Documentation
    • to_upper_ascii()

• Function noLZSS::write_factors_binary_file
  • Function Documentation
    • write_factors_binary_file()

• Function noLZSS::write_factors_binary_file_dna_w_rc
  • Function Documentation
    • write_factors_binary_file_dna_w_rc()

• Function noLZSS::write_factors_binary_file_fasta_dna_no_rc_per_sequence
  • Function Documentation
    • write_factors_binary_file_fasta_dna_no_rc_per_sequence()

• Function noLZSS::write_factors_binary_file_fasta_dna_w_rc_per_sequence
  • Function Documentation
    • write_factors_binary_file_fasta_dna_w_rc_per_sequence()

• Function noLZSS::write_factors_binary_file_fasta_multiple_dna_no_rc
  • Function Documentation
    • write_factors_binary_file_fasta_multiple_dna_no_rc()

• Function noLZSS::write_factors_binary_file_fasta_multiple_dna_w_rc
  • Function Documentation
    • write_factors_binary_file_fasta_multiple_dna_w_rc()

• Function noLZSS::write_factors_binary_file_multiple_dna_w_rc
  • Function Documentation
    • write_factors_binary_file_multiple_dna_w_rc()

• Function noLZSS::write_factors_dna_w_reference_fasta_files_to_binary
  • Function Documentation
    • write_factors_dna_w_reference_fasta_files_to_binary()

• Function noLZSS::write_fasta_metadata
  • Function Documentation
    • write_fasta_metadata()

• Function noLZSS::write_single_sequence_factors
  • Function Documentation
    • write_single_sequence_factors()

• Function parse_fasta_sanitization_mode
  • Function Documentation

• Function PYBIND11_MODULE
  • Function Documentation

Variables

• Variable noLZSS::RC_MASK
  • Variable Documentation
    • RC_MASK

Typedefs

• Typedef noLZSS::cst_t
  • Typedef Documentation
    • cst_t