Struct PipelineOptions 

pub struct PipelineOptions {
    pub scoring: bool,
    pub emit_ms2: bool,
}

Knobs that mirror the koth_ff binary’s optional stages. Everything else is taken from the KothConfig passed in explicitly.

Fields

scoring: bool

Run the averagine isotope-pattern scoring stage. true mirrors the binary’s default; false mirrors --no-scoring (features are still emitted, wrapped as ScoredFeature with zeroed scores).

emit_ms2: bool

Also run MS2 hill detection (DIA, partitioned by precursor isolation window) over the same input, and deliver the finalized MS2 hill set via PipelineSink::on_ms2_hills (and FeatureFindingOutput::ms2_hills).

Default false. When false, the MS1 feature path is byte-for-byte unchanged — no MS2 reader is opened and no MS2 hook fires; this exactly reproduces the historic MS1-only behavior.

On koth-ms’s file path, MS2 detection mirrors its run_ms2_hills_streaming: mzML, Bruker diaPASEF .d and Thermo DIA .raw are supported; DDA acquisitions (ddaPASEF .d, DDA .raw) yield an empty MS2 set plus a warning (the MS1 result is unaffected). Over in-memory spectra, the ms_level == 2 spectra are used. MS2 detection is independent of MS1 feature finding — they share only the input.

Trait Implementations

impl Clone for PipelineOptions

fn clone(&self) -> PipelineOptions

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for PipelineOptions

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

Formats the value using the given formatter.

impl Default for PipelineOptions

fn default() -> PipelineOptions

Returns the “default value” for a type.