Struct AnnotationTypeView 

pub struct AnnotationTypeView<'a> { /* private fields */ }

View over a specific annotation type, providing the column-oriented surface fibertools historically got from FiberAnnotations while delegating per-annotation iteration to the library’s AnnotationInfo.

Stays valid when the type is absent: every accessor returns an empty Vec / zero count, so call sites avoid Option plumbing.

All accessors and the per-annotation iterator yield results in BAM-orient ascending order. The spec stores annotations in molecular order; for reverse-aligned reads we reverse so consumers (BED12 blocks, pileup intervals, TSV columns) get ascending output.

Implementations

impl<'a> AnnotationTypeView<'a>

pub fn len(&self) -> usize

pub fn is_empty(&self) -> bool

pub fn infos(&self) -> &[AnnotationInfo<'a>]

Borrow the memoized infos directly, BAM-orient ascending. Lets hot loops scan query coordinates without the per-call Vec allocation that the column accessors incur.

pub fn count_query_in(&self, start: i64, end: i64) -> usize

Count annotations whose BAM-orient query_start falls in [start, end). Allocation-free over the memoized infos.

pub fn starts(&self) -> Vec<i64>

pub fn ends(&self) -> Vec<i64>

pub fn option_starts(&self) -> Vec<Option<i64>>

pub fn option_ends(&self) -> Vec<Option<i64>>

pub fn option_lengths(&self) -> Vec<Option<i64>>

pub fn lengths(&self) -> Vec<i64>

pub fn qual(&self) -> Vec<u8>

Convenience over Self::qual_at for the common case where the annotation type carries at most one quality per annotation. Returns 0 for annotations with no qualities.

All fibertools-rs annotation types (nuc, msp+ / msp+Q, fire+P, m6a+Q, cpg+Q) are single-quality; this method debug- asserts that invariant. If you add a multi-quality type, call Self::qual_at with an explicit index instead — qual() silently dropping quality columns would be a footgun.

pub fn qual_at(&self, idx: usize) -> Vec<u8>

Per-annotation quality at the given index, BAM-orient ascending. Returns 0 when the annotation has fewer than idx + 1 qualities.

qual_at(0) is the canonical single-quality accessor and debug-asserts that the type has at most one quality. Other indices skip the assertion — the caller is presumed to know the type’s QualitySpec.

pub fn reference_starts(&self) -> Vec<Option<i64>>

pub fn reference_ends(&self) -> Vec<Option<i64>>

pub fn reference_lengths(&self) -> Vec<Option<i64>>

pub fn iter(&self) -> IntoIter<AnnotationInfo<'a>>

Iterate per-annotation in BAM-orient ascending order, yielding the library’s AnnotationInfo view directly. Call sites read fields like info.query_start, info.ref_start, info.qualities.

Trait Implementations

impl<'a> Debug for AnnotationTypeView<'a>

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

Formats the value using the given formatter.

impl<'a> IntoIterator for &AnnotationTypeView<'a>

type Item = AnnotationInfo<'a>

The type of the elements being iterated over.

type IntoIter = IntoIter<AnnotationInfo<'a>>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.