Struct TimsTofSyntheticsDataHandle 

pub struct TimsTofSyntheticsDataHandle {
    pub connection: Connection,
}

Fields

connection: Connection

Implementations

impl TimsTofSyntheticsDataHandle

pub fn new(path: &Path) -> Result<Self>

pub fn read_frames(&self) -> Result<Vec<FramesSim>>

pub fn read_scans(&self) -> Result<Vec<ScansSim>>

pub fn read_peptides(&self) -> Result<Vec<PeptidesSim>>

pub fn read_ions(&self) -> Result<Vec<IonSim>>

pub fn read_mobility_env(&self) -> Result<MobilityEnv>

Read the run’s mobility environment from experiment_conditions, falling back to timsTOF defaults when the table/columns are absent (pre-P1 DB). Requires all three env columns; a partially-migrated table falls back to defaults rather than erroring on a missing column.

pub fn read_peptides_scalar(&self) -> Result<Vec<PeptideScalar>>

pub fn read_peptides_scalar_for_ids( &self, peptide_ids: &[u32], ) -> Result<Vec<PeptideScalar>>

Read scalar peptides for a specific set of ids (chunked IN query), so the lazy projector path loads only the batch’s candidates instead of the whole table. Order matches read_peptides_scalar (ORDER BY peptide_id).

pub fn read_ions_scalar(&self, env: &MobilityEnv) -> Result<Vec<IonScalar>>

Read ions as scalar-native trunk entities (no scan-occurrence vectors). CCS is read directly if a ccs column exists, otherwise derived from the legacy inv_mobility_gru_predictor (1/K0) under env.

pub fn read_ions_scalar_for_peptides( &self, peptide_ids: &[u32], env: &MobilityEnv, ) -> Result<Vec<IonScalar>>

Read scalar ions for a specific set of peptide ids (chunked IN query). The lazy projector path uses this so it does NOT load + JSON-deserialize every ion’s simulated spectrum per batch (that would restore eager-scale memory). Within a peptide, ions are ordered by ion_id (chunking is by peptide_id, so a peptide’s ions all live in one chunk).

pub fn read_peptides_with_source( &self, source: &DistributionSource, ) -> Result<Vec<PeptidesSim>>

Read peptides with their frame distribution from source.

pub fn read_ions_with_source( &self, source: &DistributionSource, ) -> Result<Vec<IonSim>>

Read ions with their scan distribution from source.

pub fn read_prediction_set(&self) -> Result<PredictionSet>

Read the fragment prediction set (P5). Returns the single registered set, or PredictionSet::legacy_bruker() for pre-P5 DBs that have no prediction_sets table (so existing data keeps rendering as the implicit Bruker set). Distinguishes “verified provenance” from “assumed legacy” by virtue of the table’s presence.

pub fn read_peptides_for_frame_range_with_source( &self, frame_min: u32, frame_max: u32, source: &DistributionSource, ) -> Result<Vec<PeptidesSim>>

Lazy per-batch peptide read, source-aware. Columns returns the legacy column-fed read_peptides_for_frame_range; Projector selects candidates for the range, reads their scalars, and projects (same entities the eager projector reader produces, restricted to the batch).

pub fn read_ions_for_peptides_with_source( &self, peptide_ids: &[u32], source: &DistributionSource, ) -> Result<Vec<IonSim>>

Lazy per-batch ion read, source-aware. Columns returns the legacy read_ions_for_peptides; Projector reads the scalars for these peptides and projects their scan distributions.

pub fn read_window_group_settings(&self) -> Result<Vec<WindowGroupSettingsSim>>

pub fn read_frame_to_window_group(&self) -> Result<Vec<FrameToWindowGroupSim>>

pub fn read_pasef_meta(&self) -> Result<Vec<PASEFMeta>>

pub fn read_peptides_for_frame_range( &self, frame_min: u32, frame_max: u32, ) -> Result<Vec<PeptidesSim>>

Read peptides that are present in the given frame range. A peptide is included if its frame range overlaps with [frame_min, frame_max].

pub fn read_ions_for_peptides(&self, peptide_ids: &[u32]) -> Result<Vec<IonSim>>

Read ions for specific peptide IDs. Uses batched queries for efficiency with large peptide ID lists.

pub fn read_fragment_ions_for_peptides( &self, peptide_ids: &[u32], ) -> Result<Vec<FragmentIonSim>>

Read fragment ions for specific peptide IDs. Uses batched queries for efficiency with large peptide ID lists.

pub fn read_fragment_ions(&self) -> Result<Vec<FragmentIonSim>>

pub fn get_transmission_dia(&self) -> TimsTransmissionDIA

pub fn get_transmission_dda(&self) -> TimsTransmissionDDA

pub fn get_collision_energy_dia(&self) -> TimsTofCollisionEnergyDIA

pub fn get_transmitted_ions( &self, num_threads: usize, dda_mode: bool, ) -> (Vec<i32>, Vec<i32>, Vec<String>, Vec<i8>, Vec<f32>)

pub fn get_transmitted_ions_for_frame_range( &self, frame_min: u32, frame_max: u32, num_threads: usize, dda_mode: bool, ) -> (Vec<i32>, Vec<i32>, Vec<String>, Vec<i8>, Vec<f32>)

Lazy version of get_transmitted_ions that only loads data for a specific frame range. This reduces memory usage by only loading peptides and ions that are relevant to the specified frame range instead of all data from the database.

Arguments

• frame_min - Minimum frame ID to include (inclusive)
• frame_max - Maximum frame ID to include (inclusive)
• num_threads - Number of threads to use for parallel processing
• dda_mode - If true, use DDA transmission; if false, use DIA transmission

Returns

Tuple of (peptide_ids, ion_ids, sequences, charges, collision_energies) for transmitted ions

pub fn build_peptide_to_ion_map( ions: &Vec<IonSim>, ) -> BTreeMap<u32, Vec<IonSim>>

Method to build a map from peptide id to ions

pub fn build_peptide_map( peptides: &Vec<PeptidesSim>, ) -> BTreeMap<u32, PeptidesSim>

Method to build a map from peptide id to events (absolute number of events in the simulation)

pub fn build_precursor_frame_id_set(frames: &Vec<FramesSim>) -> HashSet<u32>

Method to build a set of precursor frame ids, can be used to check if a frame is a precursor frame

pub fn build_peptide_to_events( peptides: &Vec<PeptidesSim>, ) -> BTreeMap<u32, f32>

pub fn build_frame_to_rt(frames: &Vec<FramesSim>) -> BTreeMap<u32, f32>

pub fn build_scan_to_mobility(scans: &Vec<ScansSim>) -> BTreeMap<u32, f32>

pub fn build_frame_to_abundances( peptides: &Vec<PeptidesSim>, ) -> BTreeMap<u32, (Vec<u32>, Vec<f32>)>

pub fn build_peptide_to_ions( ions: &Vec<IonSim>, ) -> BTreeMap<u32, (Vec<f32>, Vec<Vec<u32>>, Vec<Vec<f32>>, Vec<i8>, Vec<MzSpectrum>)>

pub fn build_fragment_ions( peptides_sim: &BTreeMap<u32, PeptidesSim>, fragment_ions: &Vec<FragmentIonSim>, num_threads: usize, ) -> BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrum>)>

pub fn build_fragment_ions_annotated( peptides_sim: &BTreeMap<u32, PeptidesSim>, fragment_ions: &Vec<FragmentIonSim>, num_threads: usize, ) -> BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrumAnnotated>)>

pub fn build_fragment_ions_with_transmission_data( peptides_sim: &BTreeMap<u32, PeptidesSim>, fragment_ions: &Vec<FragmentIonSim>, num_threads: usize, ) -> BTreeMap<(u32, i8, i32), FragmentIonsWithComplementary>

Build fragment ions with complementary isotope distribution data.

This variant calculates both the fragment isotope distribution and the complementary fragment isotope distribution, which are needed for quad-selection dependent isotope transmission calculations.

Arguments

• peptides_sim - Map of peptide_id to PeptidesSim
• fragment_ions - Vector of FragmentIonSim
• num_threads - Number of threads for parallel processing

Returns

• BTreeMap mapping (peptide_id, charge, collision_energy) to (PeptideProductIonSeriesCollection, fragment spectra, fragment distributions, complementary distributions) Build fragment ions with transmission data for both precursor scaling and per-fragment modes.

This function calculates:

• Precursor isotope distribution (for PrecursorScaling mode)
• Per-fragment isotope distributions with their complementary distributions (for PerFragment mode)

Trait Implementations

impl Debug for TimsTofSyntheticsDataHandle

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.