Struct AnnotationIndex 

pub struct AnnotationIndex { /* private fields */ }

Fast interval index using interval trees for O(log n + k) overlap queries

This implementation uses a centered interval tree per chromosome, providing logarithmic query time instead of linear scanning.

Implementations

impl AnnotationIndex

pub fn new() -> Self

Create an empty annotation index

pub fn build_trees(&mut self, annotations: HashMap<String, Vec<Annotation>>)

Build interval trees from collected annotations

This should be called after all insertions are complete. For efficiency, batch all insertions then call this once.

pub fn from_bed<P, F>(path: P, extractor: F) -> Result<Self>

where P: AsRef<Path>, F: Fn(&BedRecord) -> String,

Build annotation index from BED file

The extractor function converts each BED record into annotation data. Typically this extracts the “name” field, but can be customized.

Examples

use genomicframe_core::interval::annotation::AnnotationIndex;

// Extract gene names from BED name field
let index = AnnotationIndex::from_bed("genes.bed", |record| {
    record.name.clone().unwrap_or_default()
})?;

// Custom extraction: combine name and score
let index = AnnotationIndex::from_bed("features.bed", |record| {
    format!("{}:{}",
        record.name.as_deref().unwrap_or("unknown"),
        record.score.unwrap_or(0))
})?;

pub fn from_records<'a, I, F>(records: I, extractor: F) -> Self

where I: IntoIterator<Item = &'a BedRecord>, F: Fn(&BedRecord) -> String,

Build annotation index from an iterator of BED records

pub fn from_reader<I, F>(reader: I, extractor: F) -> Result<Self>

where I: GenomicRecordIterator<Record = BedRecord>, F: Fn(&BedRecord) -> String,

Build annotation index from a reader (possibly filtered)

pub fn query(&self, interval: &GenomicInterval) -> Vec<&str>

Query for all annotations overlapping the given interval

Returns references to annotation data strings.

Performance

O(log n + k) where n = number of annotations on the chromosome, k = number of overlapping annotations

pub fn query_annotations(&self, interval: &GenomicInterval) -> Vec<&Annotation>

Query for all annotations overlapping the given interval

Returns full Annotation structs (includes intervals).

pub fn len(&self) -> usize

Count total annotations in the index

pub fn is_empty(&self) -> bool

Check if the index is empty

pub fn chromosomes(&self) -> Vec<&str>

Get chromosomes present in the index

Trait Implementations

impl Clone for AnnotationIndex

fn clone(&self) -> AnnotationIndex

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AnnotationIndex

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

Formats the value using the given formatter.

impl Default for AnnotationIndex

fn default() -> Self

Returns the “default value” for a type.