List of all items

Structs

• Feature
• FeatureFindingOutput
• Hill
• IsolationWindow
• PipelineOptions
• ScoredFeature
• Spectrum
• alignment::AlignmentConfig
• alignment::AlignmentResult
• alignment::RtSigmaModel
• alignment::RunAlignment
• alignment::RunInput
• alignment::anchors::AnchorPair
• alignment::drift::DriftFit
• alignment::warp::RtWarp
• config::AlignConfig
• config::AlignOutputConfig
• config::FeaturesConfig
• config::FileConfig
• config::HillsConfig
• config::HillsMs2Overrides
• config::KothConfig
• config::OutputConfig
• config::ScoringConfig
• features::recalibration::MzRecalBuilder
• features::recalibration::MzRecalModel
• hills::active::ActiveHill
• hills::detector::HillDetector
• input::RunMobility
• input::RunPaths
• io::prefetch::Prefetch
• io::tims_calibration::ScanToMobility
• io::tims_calibration::TimsCalibrationModel
• lfq::IntensityMatrix
• lfq::LfqConfig
• lfq::LfqEntry
• lfq::consensus::ConsensusConfig
• lfq::consensus::ConsensusFeature
• lfq::consensus::EvidenceAudit
• lfq::consensus::PermutationAudit
• lfq::grid::GridSample
• lfq::grid::HillKey
• lfq::grid::SortedHills
• lfq::grid::XicGrid
• lfq::integrate::PeakResult
• lfq::score::ColumnScores
• lfq::targets::Identification
• lfq::targets::ImportSummary
• lfq::targets::InferredCharge
• lfq::targets::RejectedTarget
• lfq::targets::RtRescue
• lfq::targets::SearchGuidance
• lfq::targets::SearchTarget
• models::Feature
• models::Hill
• models::IsolationWindow
• models::Peak
• models::ScoredFeature
• models::Spectrum
• output::align_report::AlignReport
• output::align_report::AlignmentDiagnostics
• output::align_report::AnchorRecord
• output::align_report::LfqRunSummary
• output::align_report::QvaluePercentiles
• output::align_report::ResidualStats
• output::align_report::ResidualSummary
• output::align_report::RunAlignReport
• output::align_report::Timing
• output::report::CalibrationRow
• output::report::FeaturesReport
• output::report::HillsReport
• output::report::MobilityReport
• output::report::RunReport
• output::report::StatSummary
• pipeline::FeatureFindingOutput
• pipeline::PipelineOptions
• scoring::elements::ElementCache
• scoring::model::IsotopeModel

Enums

• Polarity
• alignment::WarpKind
• config::CosineAnchor
• config::ImToleranceType
• config::MobilityScale
• config::OutputFormat
• config::ToleranceType
• error::KothError
• hills::tic_norm::RefMode
• io::InputFormat
• io::tims_calibration::MobilityScale
• lfq::ScoreMode
• lfq::rescore::search::SearchScoring
• lfq::targets::TargetFormat
• models::Polarity
• scoring::model::IsotopeClass
• scoring::model::IsotopeModelSpec

Traits

• PipelineSink
• pipeline::PipelineSink

Functions

• alignment::align_runs
• alignment::anchors::find_anchors
• alignment::anchors::normalize_rt
• alignment::drift::fit_im_drift
• alignment::drift::fit_mass_drift
• alignment::warp::fit_ransac_warp
• alignment::warp::identity_warp
• alignment::warp::piecewise_linear
• features::cosine::cosine_similarity
• features::detect_features
• features::detect_features_with_recal
• features::learn_recal_model
• group_ms2_hills_by_window
• hills::assign_hill_ids
• hills::detect_hills
• hills::detect_hills_from_iter
• hills::detect_ms2_hills_from_iter
• hills::filter::filter_large_baseline_hills
• hills::noise::filter_spectrum
• hills::smooth::apply_intensity_filters
• hills::smooth::compute_hill_score
• hills::smooth::fill_gaps
• hills::smooth::running_average
• hills::split::split_coeluting
• hills::split::split_hill_persistence
• hills::tic_norm::normalize_tic_in_place
• input::check_batch_mobility_scales
• input::check_mobility_scales
• input::discover_runs
• input::read_features
• input::read_features_parquet
• input::read_features_tsv
• input::read_hills
• input::read_hills_parquet
• input::read_hills_tsv
• input::recorded_mobility_scale
• input::run_mobility
• io::bruker::inner::read_bruker
• io::bruker::inner::read_bruker_ms2
• io::bruker::inner::stream_bruker
• io::detect_format
• io::mzml::read_mzml
• io::mzml::stream_mzml
• io::mzml::stream_mzml_ms2
• io::prefetch::prefetch
• io::prefetch::try_prefetch
• io::read_spectra
• io::stream_spectra
• io::thermo::read_thermo
• io::thermo::read_thermo_ms2
• io::thermo::stream_thermo
• io::tims_calibration::dnoise_scale
• io::tims_calibration::load
• lfq::consensus::audit_consensus
• lfq::consensus::audit_permutation_consensus
• lfq::consensus::build_consensus
• lfq::consensus::build_consensus_candidates
• lfq::grid::build_grid
• lfq::grid::build_grid_excluding
• lfq::integrate::integrate
• lfq::quantify
• lfq::quantify_consensus
• lfq::quantify_guided
• lfq::rescore::compute_qvalues_qda
• lfq::rescore::search::compute
• lfq::rescore::search::peptide_fold
• lfq::score::score_grid
• lfq::targets::build_targets
• lfq::targets::read_identifications
• lfq::targets::write_search_outputs
• lfq::tdc::compute_qvalues
• mem::log_mem
• mem::rss_mb
• output::align_report::build_align_report
• output::align_report::write_align_report
• output::long_matrix::sha256
• output::long_matrix::write_bundle
• output::report::build_features_report
• output::report::build_hills_report
• output::report::write_report
• output::write_features_parquet
• output::write_features_tsv
• output::write_hills_parquet
• output::write_hills_tsv
• output::write_ms2_hills_parquet
• output::write_ms2_hills_tsv
• pipeline::group_ms2_hills_by_window
• pipeline::run_pipeline
• pipeline::run_pipeline_from_hills
• pipeline::run_pipeline_from_spectra
• pipeline::run_pipeline_streaming
• pipeline::run_pipeline_streaming_from_spectra
• pipeline::run_pipeline_with_ms2
• read_spectra
• run_features
• run_hills
• run_hills_streaming
• run_ms2_hills_streaming
• run_pipeline_from_spectra
• run_pipeline_streaming_from_spectra
• run_scoring
• scoring::averagine::bhattacharyya_score
• scoring::averagine::bhattacharyya_score_best_sulfur
• scoring::averagine::resolve_sulfur_counts
• scoring::elements::cache
• scoring::score_features
• stats::median
• stats::std_dev

Type Aliases

• io::SpectrumStream
• lfq::grid::SampleId

Constants

• VERSION
• config::SCALE_CALIBRATED
• config::SCALE_LINEAR
• input::SCALE_AS_READ
• input::SCALE_CALIBRATED
• input::SCALE_LINEAR
• io::tims_calibration::SUPPORTED_MODEL_TYPE
• lfq::consensus::VARIANT_NAMES
• lfq::grid::C13_NEUTRON
• models::PROTON_MASS
• scoring::elements::K_PATTERN
• scoring::model::DNA
• scoring::model::PEPTIDE
• scoring::model::RNA