Index

A

analyze_alphabet() (in module noLZSS.utils)

C

count_factors() (in module noLZSS.core)

count_factors_file() (in module noLZSS.core)

D

detect_sequence_type() (in module noLZSS.genomics.sequences)

F

factorize() (in module noLZSS.core) factorize_file() (in module noLZSS.core)

factorize_with_info() (in module noLZSS.core) FASTAError

I

InvalidInputError (class in noLZSS)

is_dna_sequence() (in module noLZSS.genomics.sequences) is_protein_sequence() (in module noLZSS.genomics.sequences)

M

module noLZSS noLZSS.core noLZSS.genomics noLZSS.genomics.fasta noLZSS.genomics.plots noLZSS.genomics.sequences noLZSS.utils

N

noLZSS module noLZSS.core module noLZSS.genomics module noLZSS.genomics.fasta module noLZSS.genomics.plots module noLZSS.genomics.sequences module noLZSS.utils module noLZSS::complement (C++ function) noLZSS::count_factors (C++ function) noLZSS::count_factors_dna_w_rc (C++ function) noLZSS::count_factors_file (C++ function) noLZSS::count_factors_file_dna_w_rc (C++ function) noLZSS::count_factors_file_multiple_dna_w_rc (C++ function) noLZSS::count_factors_multiple_dna_w_rc (C++ function) noLZSS::cst_t (C++ type) noLZSS::Factor (C++ struct) noLZSS::Factor::length (C++ member) noLZSS::Factor::ref (C++ member) noLZSS::Factor::start (C++ member) noLZSS::FactorFileHeader (C++ struct) noLZSS::FactorFileHeader::header_size (C++ member) noLZSS::FactorFileHeader::magic (C++ member) noLZSS::FactorFileHeader::num_factors (C++ member) noLZSS::FactorFileHeader::num_sentinels (C++ member) noLZSS::FactorFileHeader::num_sequences (C++ member) noLZSS::factorize (C++ function) noLZSS::factorize_dna_w_rc (C++ function) noLZSS::factorize_fasta_multiple_dna_no_rc (C++ function) noLZSS::factorize_fasta_multiple_dna_w_rc (C++ function) noLZSS::factorize_file (C++ function) noLZSS::factorize_file_dna_w_rc (C++ function) noLZSS::factorize_file_multiple_dna_w_rc (C++ function) noLZSS::factorize_file_stream (C++ function) noLZSS::factorize_file_stream_dna_w_rc (C++ function) noLZSS::factorize_file_stream_multiple_dna_w_rc (C++ function) noLZSS::factorize_multiple_dna_w_rc (C++ function) noLZSS::factorize_stream (C++ function)

noLZSS::factorize_stream_dna_w_rc (C++ function) noLZSS::factorize_stream_multiple_dna_w_rc (C++ function) noLZSS::FastaFactorizationResult (C++ struct) noLZSS::FastaFactorizationResult::factors (C++ member) noLZSS::FastaFactorizationResult::sentinel_factor_indices (C++ member) noLZSS::FastaParseResult (C++ struct) noLZSS::FastaParseResult::sequence_ids (C++ member) noLZSS::FastaParseResult::sequences (C++ member) noLZSS::FastaProcessResult (C++ struct) noLZSS::FastaProcessResult::num_sequences (C++ member) noLZSS::FastaProcessResult::sequence (C++ member) noLZSS::FastaProcessResult::sequence_ids (C++ member) noLZSS::FastaProcessResult::sequence_lengths (C++ member) noLZSS::FastaProcessResult::sequence_positions (C++ member) noLZSS::identify_sentinel_factors (C++ function) noLZSS::is_rc (C++ function) noLZSS::lcp (C++ function) noLZSS::next_leaf (C++ function) noLZSS::nolzss (C++ function) noLZSS::nolzss_dna_w_rc (C++ function) noLZSS::nolzss_multiple_dna_w_rc (C++ function) noLZSS::parse_fasta_sequences (C++ function) noLZSS::parse_fasta_sequences_and_ids (C++ function) noLZSS::prepare_multiple_dna_sequences_no_rc (C++ function) noLZSS::prepare_multiple_dna_sequences_w_rc (C++ function) noLZSS::PreparedSequenceResult (C++ struct) noLZSS::PreparedSequenceResult::original_length (C++ member) noLZSS::PreparedSequenceResult::prepared_string (C++ member) noLZSS::PreparedSequenceResult::sentinel_positions (C++ member) noLZSS::process_amino_acid_fasta (C++ function) noLZSS::process_nucleotide_fasta (C++ function) noLZSS::rc_end (C++ function) noLZSS::RC_MASK (C++ member) noLZSS::revcomp (C++ function) noLZSS::VERSION_MAJOR (C++ member) noLZSS::VERSION_MINOR (C++ member) noLZSS::VERSION_PATCH (C++ member) noLZSS::write_factors_binary_file (C++ function) noLZSS::write_factors_binary_file_dna_w_rc (C++ function) noLZSS::write_factors_binary_file_fasta_multiple_dna_no_rc (C++ function) noLZSS::write_factors_binary_file_fasta_multiple_dna_w_rc (C++ function) noLZSS::write_factors_binary_file_multiple_dna_w_rc (C++ function) NoLZSSError (class in noLZSS)

P

plot_factor_lengths() (in module noLZSS.utils) plot_multiple_seq_self_lz_factor_plot_from_fasta() (in module noLZSS.genomics.plots)

plot_multiple_seq_self_weizmann_factor_plot_from_fasta() (in module noLZSS.genomics.plots) plot_single_seq_accum_factors_from_fasta() (in module noLZSS.genomics.plots) PlotError

R

read_factors_binary_file() (in module noLZSS.utils) read_fasta_auto() (in module noLZSS.genomics.fasta)

read_nucleotide_fasta() (in module noLZSS.genomics.fasta) read_protein_fasta() (in module noLZSS.genomics.fasta)

V

validate_input() (in module noLZSS.utils)

W

write_factors_binary_file() (in module noLZSS.core)