C++ API Reference

Class Hierarchy

• • Namespace noLZSS
    • Struct Factor
    • Struct FactorFileHeader
    • Struct FastaFactorizationResult
    • Struct FastaParseResult
    • Struct FastaProcessResult
    • Struct PreparedSequenceResult

File Hierarchy

• • Directory src
    • Directory cpp
      • File bindings.cpp
      • File factorizer.cpp
      • File factorizer.hpp
      • File fasta_processor.cpp
      • File fasta_processor.hpp
      • File version.hpp

Full API

Namespaces

• Namespace noLZSS
  • Classes
  • Functions
  • Typedefs
  • Variables

Classes and Structs

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

• Struct FactorFileHeader
  • Struct Documentation
    • noLZSS::FactorFileHeader
      • magic
      • num_factors
      • num_sequences
      • num_sentinels
      • header_size

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

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

• Struct FastaProcessResult
  • Struct Documentation
    • noLZSS::FastaProcessResult
      • sequence
      • num_sequences
      • sequence_ids
      • sequence_lengths
      • sequence_positions

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

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_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()

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

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

• 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::identify_sentinel_factors
  • Function Documentation
    • identify_sentinel_factors()

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

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

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

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

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

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

• Function noLZSS::parse_fasta_sequences
  • Function Documentation
    • parse_fasta_sequences()

• 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::process_amino_acid_fasta
  • Function Documentation
    • process_amino_acid_fasta()

• Function noLZSS::process_nucleotide_fasta
  • Function Documentation
    • process_nucleotide_fasta()

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

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

• 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_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 PYBIND11_MODULE
  • Function Documentation

Variables

• Variable noLZSS::RC_MASK
  • Variable Documentation
    • RC_MASK

• Variable noLZSS::VERSION_MAJOR
  • Variable Documentation
    • VERSION_MAJOR

• Variable noLZSS::VERSION_MINOR
  • Variable Documentation
    • VERSION_MINOR

• Variable noLZSS::VERSION_PATCH
  • Variable Documentation
    • VERSION_PATCH

Typedefs

• Typedef noLZSS::cst_t
  • Typedef Documentation
    • cst_t