Struct FragmentIndex 

pub struct FragmentIndex { /* private fields */ }

Implementations

impl FragmentIndex

pub fn ms2_slice(&self) -> &[ClusterResult1D]

pub fn get_ms2_by_index(&self, idx: usize) -> Option<&ClusterResult1D>

pub fn get_ms2_by_cluster_id(&self, cid: u64) -> Option<&ClusterResult1D>

pub fn metadata(&self) -> FragmentMetadata

Get pre-computed MS2 metadata.

pub fn storage(&self) -> FragmentStorage

Get storage wrapper for cluster access.

pub fn dia_index(&self) -> &Arc<DiaIndex>

Get the DIA index reference.

pub fn group_index(&self, group: u32) -> Option<&FragmentGroupIndex>

Get group index for a specific window group.

pub fn groups(&self) -> Vec<u32>

Get all window groups.

pub fn count_valid(&self) -> usize

Count valid (kept) MS2 clusters.

pub fn len(&self) -> usize

Count total MS2 clusters.

pub fn is_empty(&self) -> bool

Check if empty.

pub fn from_parquet_file( dia_index: Arc<DiaIndex>, parquet_path: impl AsRef<Path>, opts: &CandidateOpts, ) -> Result<Self>

pub fn from_parquet_dir( dia_index: Arc<DiaIndex>, dir: impl AsRef<Path>, opts: &CandidateOpts, ) -> Result<Self>

Your requested builder: read all .parquet files in a directory and merge.

pub fn from_slice( dia_index: Arc<DiaIndex>, ms2: &[ClusterResult1D], opts: &CandidateOpts, ) -> Self

Backwards-compatible: build from a borrowed slice (one copy into Arc).

pub fn from_owned( dia_index: Arc<DiaIndex>, ms2: Vec<ClusterResult1D>, opts: &CandidateOpts, ) -> Self

Preferred: build from an owned Vec.

pub fn query_precursor( &self, prec: &ClusterResult1D, groups: Option<&[u32]>, opts: &FragmentQueryOpts, ) -> Vec<u64>

pub fn query_precursors_par( &self, precursors: &[ClusterResult1D], opts: &FragmentQueryOpts, num_threads: usize, ) -> Vec<Vec<u64>>

Parallel batch query: for each precursor, return a Vec of MS2 cluster_ids.

pub fn enumerate_candidates_for_precursor_thin( &self, prec: &ThinPrecursor, window_groups: Option<&[u32]>, opts: &FragmentQueryOpts, ) -> Vec<usize>

Enumerate candidate MS2 indices for a thin precursor.

Returns indices into self.ms2.

pub fn enumerate_candidates_for_feature( &self, feat: &SimpleFeature, opts: &FragmentQueryOpts, ) -> Vec<usize>

Enumerate candidate MS2 indices for a given SimpleFeature.

Uses the representative member cluster (highest raw_sum) of the feature and reuses the standard precursor enumeration logic.

Returns indices into self.ms2.

pub fn query_precursor_scored( &self, prec: &ClusterResult1D, window_groups: Option<&[u32]>, opts: &FragmentQueryOpts, mode: MatchScoreMode, geom_opts: &ScoreOpts, xic_opts: &XicScoreOpts, min_score: f32, ) -> Vec<ScoredHit>

pub fn query_precursors_scored_par( &self, precs: &[ClusterResult1D], opts: &FragmentQueryOpts, mode: MatchScoreMode, geom_opts: &ScoreOpts, xic_opts: &XicScoreOpts, min_score: f32, ) -> Vec<Vec<ScoredHit>>

pub fn query_feature_scored( &self, feat: &SimpleFeature, opts: &FragmentQueryOpts, mode: MatchScoreMode, geom_opts: &ScoreOpts, xic_opts: &XicScoreOpts, min_score: f32, ) -> Vec<ScoredHit>

Score a single SimpleFeature precursor against all physically plausible fragment candidates, as determined internally by the FragmentIndex.

This is the feature twin of query_precursor_scored, but it does not require the caller to pass window groups or candidate indices.

pub fn query_features_scored_par( &self, feats: &[SimpleFeature], opts: &FragmentQueryOpts, mode: MatchScoreMode, geom_opts: &ScoreOpts, xic_opts: &XicScoreOpts, min_score: f32, ) -> Vec<Vec<ScoredHit>>

Parallel scoring for many SimpleFeatures.

• Candidate enumeration is done inside the index.
• feats[i] is scored against the MS2 candidates inferred for feat i.

pub fn make_thin_precursor( &self, prec: &ClusterResult1D, ) -> Option<ThinPrecursor>

Build a thin precursor representation used for candidate enumeration.

This folds all the “how do we get RT apex / m/z apex / IM apex?” logic into one place and drops everything else (raw points, axes, …).

Trait Implementations

impl Clone for FragmentIndex

fn clone(&self) -> FragmentIndex

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FragmentIndex

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

Formats the value using the given formatter.