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_dna_w_reference_seq() (in module noLZSS.genomics.sequences) factorize_dna_w_reference_seq_file() (in module noLZSS.genomics.sequences) factorize_file() (in module noLZSS.core)

factorize_w_reference() (in module noLZSS.core) factorize_w_reference_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.fasta noLZSS.genomics.plots noLZSS.genomics.sequences noLZSS.utils

N

noLZSS module noLZSS.core 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_fasta_dna_no_rc_per_sequence (C++ function) noLZSS::count_factors_fasta_dna_w_rc_per_sequence (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::detail::nolzss (C++ function) noLZSS::detail::nolzss_dna_w_rc (C++ function) noLZSS::detail::nolzss_multiple_dna_w_rc (C++ function) noLZSS::Factor (C++ struct) noLZSS::Factor::length (C++ member) noLZSS::Factor::ref (C++ member) noLZSS::Factor::start (C++ member) noLZSS::FactorFileFooter (C++ struct) noLZSS::FactorFileFooter::FactorFileFooter (C++ function) noLZSS::FactorFileFooter::footer_size (C++ member) noLZSS::FactorFileFooter::magic (C++ member) noLZSS::FactorFileFooter::num_factors (C++ member) noLZSS::FactorFileFooter::num_sentinels (C++ member) noLZSS::FactorFileFooter::num_sequences (C++ member) noLZSS::FactorFileFooter::total_length (C++ member) noLZSS::factorize (C++ function) noLZSS::factorize_dna_rc_w_ref_fasta_files (C++ function) noLZSS::factorize_dna_w_rc (C++ function) noLZSS::factorize_dna_w_reference_seq (C++ function) noLZSS::factorize_dna_w_reference_seq_file (C++ function) noLZSS::factorize_fasta_dna_no_rc_per_sequence (C++ function) noLZSS::factorize_fasta_dna_w_rc_per_sequence (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::factorize_w_reference (C++ function) noLZSS::factorize_w_reference_file (C++ function) noLZSS::FastaDnaSanitizationMode (C++ enum) noLZSS::FastaDnaSanitizationMode::RemoveAmbiguous (C++ enumerator) noLZSS::FastaDnaSanitizationMode::Strict (C++ enumerator) noLZSS::FastaFactorizationResult (C++ struct) noLZSS::FastaFactorizationResult::factors (C++ member) noLZSS::FastaFactorizationResult::sentinel_factor_indices (C++ member) noLZSS::FastaFactorizationResult::sequence_ids (C++ member) noLZSS::FastaParseResult (C++ struct) noLZSS::FastaParseResult::sequence_ids (C++ member) noLZSS::FastaParseResult::sequences (C++ member) noLZSS::FastaPerSequenceCountResult (C++ struct) noLZSS::FastaPerSequenceCountResult::factor_counts (C++ member) noLZSS::FastaPerSequenceCountResult::sequence_ids (C++ member)

noLZSS::FastaPerSequenceCountResult::total_factors (C++ member) noLZSS::FastaPerSequenceFactorizationResult (C++ struct) noLZSS::FastaPerSequenceFactorizationResult::per_sequence_factors (C++ member) noLZSS::FastaPerSequenceFactorizationResult::sequence_ids (C++ member) noLZSS::FastaReferenceTargetResult (C++ struct) noLZSS::FastaReferenceTargetResult::concatinated_sequences (C++ member) noLZSS::FastaReferenceTargetResult::num_ref_sequences (C++ member) noLZSS::FastaReferenceTargetResult::num_target_sequences (C++ member) noLZSS::FastaReferenceTargetResult::sequence_ids (C++ member) noLZSS::FastaReferenceTargetResult::target_start_index (C++ member) noLZSS::identify_sentinel_factors (C++ function) noLZSS::is_canonical_dna (C++ function) noLZSS::is_rc (C++ function) noLZSS::lcp (C++ function) noLZSS::next_leaf (C++ function) noLZSS::parallel_factorize_dna_w_rc_to_file (C++ function), [1] noLZSS::parallel_factorize_file_dna_w_rc_to_file (C++ function), [1] noLZSS::parallel_factorize_file_to_file (C++ function), [1] noLZSS::parallel_factorize_to_file (C++ function), [1] noLZSS::parallel_write_factors_binary_file_fasta_dna_no_rc_per_sequence (C++ function) noLZSS::parallel_write_factors_binary_file_fasta_dna_w_rc_per_sequence (C++ function) noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_no_rc (C++ function) noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_w_rc (C++ function) noLZSS::parallel_write_factors_dna_w_reference_fasta_files_to_binary (C++ function) noLZSS::ParallelFactorizer (C++ class) noLZSS::ParallelFactorizer::cleanup_temp_files (C++ function) noLZSS::ParallelFactorizer::create_temp_file_path (C++ function) noLZSS::ParallelFactorizer::factorize_dna_w_rc_thread (C++ function) noLZSS::ParallelFactorizer::merge_temp_files (C++ function) noLZSS::ParallelFactorizer::MIN_CHARS_PER_THREAD (C++ member) noLZSS::ParallelFactorizer::parallel_factorize (C++ function) noLZSS::ParallelFactorizer::parallel_factorize_dna_w_rc (C++ function) noLZSS::ParallelFactorizer::parallel_factorize_file (C++ function) noLZSS::ParallelFactorizer::parallel_factorize_file_dna_w_rc (C++ function) noLZSS::ParallelFactorizer::parallel_factorize_multiple_dna_w_rc (C++ function) noLZSS::ParallelFactorizer::ParallelFactorizer (C++ function) noLZSS::ParallelFactorizer::~ParallelFactorizer (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::prepare_ref_target_dna_no_rc_from_fasta (C++ function) noLZSS::prepare_ref_target_dna_w_rc_from_fasta (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::rc_end (C++ function) noLZSS::RC_MASK (C++ member) noLZSS::revcomp (C++ function) noLZSS::sanitize_filename (C++ function) noLZSS::ThreadContext (C++ struct) noLZSS::ThreadContext::end_pos (C++ member) noLZSS::ThreadContext::is_last_thread (C++ member) noLZSS::ThreadContext::last_read_factor (C++ member) noLZSS::ThreadContext::next_thread_factor_index (C++ member) noLZSS::ThreadContext::start_pos (C++ member) noLZSS::ThreadContext::temp_file_path (C++ member) noLZSS::ThreadContext::text_length (C++ member) noLZSS::ThreadContext::thread_id (C++ member) noLZSS::to_upper_ascii (C++ function) noLZSS::write_factors_binary_file (C++ function) noLZSS::write_factors_binary_file_dna_w_rc (C++ function) noLZSS::write_factors_binary_file_fasta_dna_no_rc_per_sequence (C++ function) noLZSS::write_factors_binary_file_fasta_dna_w_rc_per_sequence (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) noLZSS::write_factors_dna_w_reference_fasta_files_to_binary (C++ function) noLZSS::write_fasta_metadata (C++ function) noLZSS::write_single_sequence_factors (C++ function) NoLZSSError (class in noLZSS)

P

plot_factor_length_ccdf() (in module noLZSS.genomics.plots) plot_factor_lengths() (in module noLZSS.utils) plot_multiple_seq_self_lz_factor_plot_from_file() (in module noLZSS.genomics.plots) plot_multiple_seq_self_lz_factor_plot_simple() (in module noLZSS.genomics.plots) plot_reference_seq_lz_factor_plot() (in module noLZSS.genomics.plots)

plot_reference_seq_lz_factor_plot_simple() (in module noLZSS.genomics.plots) plot_single_seq_accum_factors_from_file() (in module noLZSS.genomics.plots) plot_space_scale_heatmap() (in module noLZSS.genomics.plots) plot_strand_bias_heatmap() (in module noLZSS.genomics.plots) PlotError

R

read_binary_file_metadata() (in module noLZSS.utils) read_factors_binary_file() (in module noLZSS.utils) read_factors_binary_file_with_metadata() (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)

write_factors_dna_w_reference_fasta_files_to_binary() (in module noLZSS.genomics.fasta)