Struct TimsTofSyntheticsPrecursorFrameBuilder 

pub struct TimsTofSyntheticsPrecursorFrameBuilder {
    pub ions: BTreeMap<u32, Vec<IonSim>>,
    pub peptides: BTreeMap<u32, PeptidesSim>,
    pub scans: Vec<ScansSim>,
    pub frames: Vec<FramesSim>,
    pub precursor_frame_id_set: HashSet<u32>,
    pub frame_to_abundances: BTreeMap<u32, (Vec<u32>, Vec<f32>)>,
    pub peptide_to_ions: BTreeMap<u32, (Vec<f32>, Vec<Vec<u32>>, Vec<Vec<f32>>, Vec<i8>, Vec<MzSpectrum>)>,
    pub frame_to_rt: BTreeMap<u32, f32>,
    pub scan_to_mobility: BTreeMap<u32, f32>,
    pub peptide_to_events: BTreeMap<u32, f32>,
    pub ion_id_to_peptide_charge: BTreeMap<u32, (u32, i8)>,
}

Fields

ions: BTreeMap<u32, Vec<IonSim>>

peptides: BTreeMap<u32, PeptidesSim>

scans: Vec<ScansSim>

frames: Vec<FramesSim>

precursor_frame_id_set: HashSet<u32>

frame_to_abundances: BTreeMap<u32, (Vec<u32>, Vec<f32>)>

peptide_to_ions: BTreeMap<u32, (Vec<f32>, Vec<Vec<u32>>, Vec<Vec<f32>>, Vec<i8>, Vec<MzSpectrum>)>

frame_to_rt: BTreeMap<u32, f32>

scan_to_mobility: BTreeMap<u32, f32>

peptide_to_events: BTreeMap<u32, f32>

ion_id_to_peptide_charge: BTreeMap<u32, (u32, i8)>

Mapping from ion_id to (peptide_id, charge) for DDA precursor lookup

Implementations

impl TimsTofSyntheticsPrecursorFrameBuilder

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

Create a new instance of TimsTofSynthetics

Arguments

• path - A reference to a Path

Returns

• A Result containing the TimsTofSynthetics instance

pub fn from_source(path: &Path, source: &DistributionSource) -> Result<Self>

Construct the builder with occurrence/abundance distributions sourced from source (P4): Columns (legacy JSON, the default — byte-unchanged) or the render-time Projector. Identical-shape PeptidesSim/IonSim either way, so the maps + all downstream consumers are untouched.

pub fn from_entities( ions: Vec<IonSim>, peptides: Vec<PeptidesSim>, scans: Vec<ScansSim>, frames: Vec<FramesSim>, ) -> Self

Construct the builder from already-loaded, in-memory entities instead of reading the database. Used by the lazy builders, which load only a per-batch slice of peptides/ions (the scans/frames metadata is full). All lookup maps are derived identically to from_source, so a builder constructed here behaves exactly like an eager one restricted to the supplied entities.

pub fn precursor_frame_contributions( &self, frame_id: u32, ) -> Vec<(i32, MzSpectrum)>

Vendor-neutral MS1 spectral-contribution kernel (P6a): the ordered (scan, scaled_spectrum) contributions for a precursor frame — for each (peptide, ion, scan) the isotope spectrum scaled by its abundance factor, PRE m/z-noise, in builder order (peptide → ion → scan). Bruker aggregates these per scan into a TimsFrame (see build_precursor_frame); a non-IMS instrument sums them into a single MS1 Scan. Factoring this out lets both vendors share the exact same physics without duplicating it.

pub fn precursor_scan_spectrum(&self, frame_id: u32) -> MzSpectrum

Faithful sum of the per-scan contributions for a frame into ONE spectrum: Σ_scans (scaled_spectrum). The scan coordinate is discarded; peaks at the same m/z merge (from_collection’s deterministic m/z binning).

NOTE — this is not the correct non-IMS MS1 physics. It reproduces what the TIMS scan grid captured, whose total mobility mass is Σ scan_abundance ≲ target_p (grid truncation) and can be far less for ions whose mobility sits at/outside the grid edge (those are under-counted, or dropped entirely when no scan captured them). A real no-mobility instrument has no such grid, so it sees the FULL mobility marginal — use Self::precursor_scan_marginal_spectrum for the Astral render. This captured-grid collapse is kept as a diagnostic / exact-equivalent of the Bruker per-scan contributions.

pub fn precursor_scan_marginal_spectrum(&self, frame_id: u32) -> MzSpectrum

Non-IMS (e.g. Astral) MS1 spectrum: the full mobility marginal (P6c).

A no-mobility instrument integrates the entire ion-mobility distribution (marginal = 1.0 by construction) — it cannot lose ions to TIMS-grid truncation. So each (peptide, ion) in the frame contributes its isotope spectrum scaled by frame_abundance × ion_abundance × total_events, with the per-scan mobility split (scan_abundance, summing to ≲ target_p) replaced by the full marginal 1.0. Crucially, ions are included by frame membership (frame_abundance > 0), NOT by whether the TIMS grid captured any of their mobility — so grid-edge ions [precursor_scan_spectrum] would under-count or drop are recorded at full abundance. PRE m/z-noise; peaks at the same m/z merge deterministically.

pub fn render_precursor_scan( &self, frame_id: u32, data_mode: DataMode, ) -> RenderedEvent

Render a precursor (MS1) frame as a vendor-neutral RenderedEvent::Scan for a non-IMS instrument (P6c). This is the scan-based render core’s MS1 path: it collapses the mobility axis via Self::precursor_scan_marginal_spectrum (the full mobility marginal, the correct non-IMS physics — NOT the captured-grid sum) into the single MS1 spectrum an Astral/Orbitrap records.

The spectrum is tagged as physical-m/z, NOT detector-applied, at the IntensityStage::Mobility stage — the marginal already carries the yield (events), time (frame abundance) and mobility (fully integrated) factors, but no quadrupole transmission (MS1 is unisolated) and no detector response; the writer / detector model applies those downstream without double- counting. data_mode is the instrument’s MS1 acquisition mode (Astral MS1 = Profile). Returns an empty-spectrum Scan for a frame with no contributions (the caller decides whether to emit it).

pub fn build_precursor_frame( &self, frame_id: u32, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, right_drag: bool, ) -> TimsFrame

Build a precursor frame

Arguments

• frame_id - A u32 representing the frame id

Returns

• A TimsFrame instance

pub fn build_precursor_frames( &self, frame_ids: Vec<u32>, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, right_drag: bool, num_threads: usize, ) -> Vec<TimsFrame>

Build a collection of precursor frames in parallel

Arguments

• frame_ids - A vector of u32 representing the frame ids
• num_threads - A usize representing the number of threads

Returns

• A vector of TimsFrame instances

pub fn build_precursor_frame_annotated( &self, frame_id: u32, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, right_drag: bool, ) -> TimsFrameAnnotated

pub fn build_precursor_frames_annotated( &self, frame_ids: Vec<u32>, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, right_drag: bool, num_threads: usize, ) -> Vec<TimsFrameAnnotated>