List of all items

Structs

• align::bounded::structs::CloudBound
• align::bounded::structs::CloudBoundGroup
• align::bounded::structs::CloudMatrixLinear
• align::bounded::structs::CloudSearchParams
• align::bounded::structs::DpMatrixSparse
• align::bounded::structs::RowBounds
• align::bounded::structs::Seed
• structs::DpMatrixFlat
• structs::alignment::Alignment
• structs::alignment::ScoreParams
• structs::dp_matrix::DpMatrix3D
• structs::hmm::Header
• structs::hmm::Hmm
• structs::hmm::Model
• structs::hmm::Stats
• structs::profile::Profile
• structs::sequence::Sequence
• structs::sequence::UnknownDigitalSequenceByteError
• structs::sequence::UnknownUtf8SequenceByteError
• structs::trace::Trace

Enums

• align::needleman_wunsch::SimpleTraceStep
• structs::hmm::Alphabet

Traits

• output::path_buf_ext::PathBufExt
• structs::dp_matrix::DpMatrix

Macros

• log_sum
• max_f32

Functions

• align::bounded::backward_bounded
• align::bounded::cloud_search_backward
• align::bounded::cloud_search_forward
• align::bounded::forward_bounded
• align::bounded::null1_score
• align::bounded::null2_score_bounded
• align::bounded::optimal_accuracy_bounded
• align::bounded::posterior_bounded
• align::bounded::prune_and_scrub
• align::bounded::scrub_co_located
• align::bounded::traceback_bounded
• align::naive::backward::backward
• align::naive::forward::forward
• align::naive::null2::null2_score
• align::naive::optimal_accuracy::optimal_accuracy
• align::naive::posterior::posterior
• align::needleman_wunsch::needleman_wunsch
• align::needleman_wunsch::print_alignment
• align::needleman_wunsch::print_trace
• output::output_standard::write_standard_output
• output::output_tabular::write_tabular_output
• structs::hmm::parse_hmms_from_p7hmm_file

Type Aliases

• align::needleman_wunsch::SimpleTrace
• viz::JsonVec

Constants

• alphabet::AMINO_ALPHABET
• alphabet::AMINO_ALPHABET_WITH_DEGENERATE
• alphabet::AMINO_BACKGROUND_FREQUENCIES
• alphabet::AMINO_INVERSE_MAP
• alphabet::AMINO_INVERSE_MAP_LOWER
• alphabet::UTF8_DASH
• alphabet::UTF8_DOT
• alphabet::UTF8_NUMERIC
• alphabet::UTF8_PIPE
• alphabet::UTF8_PLUS
• alphabet::UTF8_SPACE
• alphabet::UTF8_STAR
• alphabet::UTF8_TO_DIGITAL_AMINO
• structs::hmm::constants::HMM_DELETE_TO_DELETE
• structs::hmm::constants::HMM_DELETE_TO_MATCH
• structs::hmm::constants::HMM_INSERT_TO_INSERT
• structs::hmm::constants::HMM_INSERT_TO_MATCH
• structs::hmm::constants::HMM_MATCH_TO_DELETE
• structs::hmm::constants::HMM_MATCH_TO_INSERT
• structs::hmm::constants::HMM_MATCH_TO_MATCH
• structs::trace::constants::TRACE_B
• structs::trace::constants::TRACE_BOGUS
• structs::trace::constants::TRACE_C
• structs::trace::constants::TRACE_D
• structs::trace::constants::TRACE_E
• structs::trace::constants::TRACE_I
• structs::trace::constants::TRACE_IDX_TO_NAME
• structs::trace::constants::TRACE_J
• structs::trace::constants::TRACE_M
• structs::trace::constants::TRACE_N
• structs::trace::constants::TRACE_S
• structs::trace::constants::TRACE_T
• structs::trace::constants::TRACE_X