List of all items

Structs

• algorithms::gene_finding::optimization::GeneBuilder
• algorithms::gene_finding::scoring::ScoredAlternative
• config::OrphosConfig
• engine::Orphos
• engine::OrphosAnalyzer
• engine::Trained
• engine::Untrained
• metagenomic::MetagenomicBin
• results::OrphosResults
• results::SequenceInfo
• sequence::encoded::EncodedSequence
• types::Gene
• types::GeneAnnotation
• types::GeneCoordinates
• types::GeneScore
• types::Mask
• types::Motif
• types::Node
• types::NodeMotifInfo
• types::NodePosition
• types::NodeScores
• types::NodeState
• types::Training

Enums

• algorithms::dynamic_programming::scoring::connection_types::ConnectionType
• config::OutputFormat
• types::CodonType
• types::OrphosError
• types::StartType

Traits

• engine::TrainingState
• types::NodeSliceExtension

Functions

• algorithms::dynamic_programming::gene_prediction::predict_genes
• algorithms::dynamic_programming::overlap_resolution::resolve_simple_overlaps
• algorithms::dynamic_programming::overlap_resolution::resolve_triple_overlaps
• algorithms::dynamic_programming::path_optimization::eliminate_bad_genes
• algorithms::dynamic_programming::scoring::connection_types::determine_connection_type
• algorithms::dynamic_programming::scoring::connection_types::has_edge_artifacts
• algorithms::dynamic_programming::scoring::handlers::score_connection
• algorithms::gene_finding::annotation::record_gene_annotation_and_score
• algorithms::gene_finding::creation::add_genes
• algorithms::gene_finding::scoring::calculate_intergenic_score
• bitmap::clear_bit
• bitmap::set_bit
• bitmap::test_bit
• bitmap::toggle_bit
• metagenomic::bins
• metagenomic::presets::get_preset_training
• metagenomic::presets::get_preset_training_ref
• node::add_nodes
• node::calc_orf_gc
• node::calculate_dicodon_gene
• node::find_best_upstream_motif
• node::intergenic_mod
• node::raw_coding_score
• node::rbs_score
• node::record_gc_bias
• node::record_overlapping_starts
• node::reset_node_scores
• node::score_nodes
• node::sort_nodes_by_position
• output::write_results
• sequence::calculate_background_mer_frequencies
• sequence::calculate_kmer_index
• sequence::char_to_nuc
• sequence::create_reverse_complement_sequence
• sequence::encode_sequence
• sequence::encode_sequence_simd_wide
• sequence::encode_sequence_simd_wide_packed
• sequence::find_max_reading_frame
• sequence::gc_content
• sequence::io::read_fasta_sequences
• sequence::is_a
• sequence::is_atg
• sequence::is_c
• sequence::is_g
• sequence::is_gc
• sequence::is_gtg
• sequence::is_n
• sequence::is_start
• sequence::is_stop
• sequence::is_t
• sequence::is_ttg
• sequence::mer_text
• sequence::min_of_two_integers
• sequence::processing::calc_most_gc_frame
• sequence::processing::shine_dalgarno_exact
• sequence::processing::shine_dalgarno_mm
• sequence::reverse_strand_reading_frame
• training::common::normalize_and_log_transform
• training::load_training_file
• training::non_sd_training::train_starts_nonsd
• training::sd_training::train_starts_sd
• training::should_use_sd
• training::write_training_file

Type Aliases

• engine::TrainedOrphos
• engine::UntrainedOrphos
• sequence::io::FastaRecord
• types::DicodonTable
• types::GcBias
• types::GcFrameScores
• types::MotifWeights
• types::RbsWeights
• types::StarPointers
• types::StartWeights
• types::UpstreamComposition

Constants

• constants::CHUNK_SIZE
• constants::CODING_SCORE_SENTINEL
• constants::CODING_SCORE_THRESHOLD
• constants::CODON_LENGTH
• constants::DEFAULT_START_WEIGHT_FACTOR
• constants::DICODON_SIZE
• constants::EDGE_BONUS
• constants::EDGE_POSITION_OFFSET
• constants::EDGE_POSITION_THRESHOLD
• constants::EDGE_UPSTREAM
• constants::EXPECTED_NO_STOP_PROB
• constants::GC_HIGH_AT_FREQ
• constants::GC_HIGH_GC_FREQ
• constants::GC_LOW_AT_FREQ
• constants::GC_LOW_GC_FREQ
• constants::GENE_RATIO_THRESHOLD
• constants::GENE_SIZE_SCALING_FACTOR
• constants::HIGH_GC_FREQ
• constants::INITIAL_MAX_SCORE
• constants::INITIAL_SCORE_THRESHOLD
• constants::LENGTH_FACTOR_MULTIPLIER
• constants::LENGTH_FACTOR_THRESHOLD
• constants::LOWER_BITS
• constants::LOW_GC_FREQ
• constants::MASK_SIZE
• constants::MAXIMUM_GENES
• constants::MAXIMUM_OPPOSITE_OVERLAP
• constants::MAXIMUM_OVERLAP
• constants::MAXIMUM_SAME_OVERLAP
• constants::MAX_CONFIDENCE_SCORE
• constants::MAX_GC_CONTENT
• constants::MAX_GENES
• constants::MAX_GENE_SIZE_CODONS
• constants::MAX_LINE_LENGTH
• constants::MAX_LOG_LIKELIHOOD
• constants::MAX_MOTIF_INDEX
• constants::MAX_MOTIF_LENGTH
• constants::MAX_NODE_DIST
• constants::MAX_RIBOSOME_DISTANCE
• constants::MAX_SEQUENCE_LENGTH
• constants::MAX_TRAINING_ITERATIONS_NONSD
• constants::MAX_TRAINING_ITERATIONS_SD
• constants::METAGENOMIC_LENGTH_THRESHOLD
• constants::METAGENOMIC_MIN_LENGTH_FACTOR
• constants::METAGENOMIC_PENALTY
• constants::METAGENOMIC_PENALTY_DIVISOR
• constants::MINIMUM_EDGE_GENE_LENGTH
• constants::MINIMUM_GENE_LENGTH
• constants::MIN_CUMULATIVE_SCORE
• constants::MIN_DISTANCE_FROM_START
• constants::MIN_GC_CONTENT
• constants::MIN_GENE_SIZE_CODONS
• constants::MIN_LOG_LIKELIHOOD
• constants::MIN_META_GENE_LENGTH
• constants::MIN_MOTIF_LENGTH
• constants::MIN_MOTIF_SCORE
• constants::MIN_SEQUENCE_LENGTH
• constants::MOTIF_THRESHOLD_OFFSET
• constants::NEGATIVE_SCORE_PENALTY
• constants::NODE_SEARCH_WINDOW
• constants::NO_MOTIF_THRESHOLD
• constants::NUCLEOTIDE_LETTERS
• constants::NUCLEOTIDE_LOOKUP
• constants::NUM_BASES
• constants::NUM_CODON_TYPES
• constants::NUM_DICODONS
• constants::NUM_MOTIF_SIZES
• constants::NUM_RBS_WEIGHTS
• constants::OPERON_DISTANCE
• constants::OVERLAP_PENALTY_FACTOR
• constants::RBS_DESCRIPTIONS
• constants::RBS_DOWNSTREAM_DISTANCE
• constants::RBS_UPSTREAM_DISTANCE
• constants::RBS_WEIGHT_STRONG_THRESHOLD
• constants::RBS_WEIGHT_THRESHOLD_HIGH
• constants::RBS_WEIGHT_THRESHOLD_LOW
• constants::READING_FRAMES
• constants::SEARCH_WINDOW
• constants::SHORT_GENE_THRESHOLD
• constants::SLIDING_WINDOW_SIZE
• constants::STOP_CODON_OFFSET
• constants::STT_NOD
• constants::TEST_SEQUENCE_REPEAT_FACTOR
• constants::THRESHOLD_DIVISOR
• constants::UPPER_BITS
• constants::UPSTREAM_COMPOSITION_WEIGHT
• constants::UPSTREAM_END_POS
• constants::UPSTREAM_MOTIF_COVERAGE_THRESHOLD
• constants::UPSTREAM_POSITIONS
• constants::UPSTREAM_SCAN_RANGE
• constants::UPSTREAM_SKIP_END
• constants::UPSTREAM_SKIP_START
• constants::UPSTREAM_START_POS
• constants::VERSION
• constants::WEIGHT_CLAMP_MAX
• constants::WEIGHT_CLAMP_MIN