Struct gfa::gfa::GFA

pub struct GFA<N, T: OptFields> {
    pub header: Header<T>,
    pub segments: Vec<Segment<N, T>>,
    pub links: Vec<Link<N, T>>,
    pub containments: Vec<Containment<N, T>>,
    pub paths: Vec<Path<N, T>>,
}

This module defines the various GFA line types, the GFA object, and some utility functions and types. Simple representation of a parsed GFA file, using a Vec to store each separate GFA line type.

Fields

header: Header<T>

segments: Vec<Segment<N, T>>

links: Vec<Link<N, T>>

containments: Vec<Containment<N, T>>

paths: Vec<Path<N, T>>

Implementations

impl<N, T: OptFields> GFA<N, T>

pub fn insert_line(&mut self, line: Line<N, T>)

Insert a GFA line (wrapped in the Line enum) into an existing GFA. Simply pushes it into the corresponding Vec in the GFA, or replaces the header, so there's no deduplication or sorting taking place.

pub fn lines_into_iter(self) -> impl Iterator<Item = Line<N, T>>

Consume a GFA object to produce an iterator over all the lines contained within. The iterator first produces all segments, then links, then containments, and finally paths.

pub fn lines_iter(&self) -> impl Iterator<Item = LineRef<'_, N, T>>

Return an iterator over references to the lines in the GFA

impl<N: SegmentId, T: OptFields> GFA<N, T>

pub fn new() -> Self

Trait Implementations

impl<N: Clone, T: Clone + OptFields> Clone for GFA<N, T>

fn clone(&self) -> GFA<N, T>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<N: Debug, T: Debug + OptFields> Debug for GFA<N, T>

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

Formats the value using the given formatter.

impl<N: Default, T: Default + OptFields> Default for GFA<N, T>

fn default() -> GFA<N, T>

Returns the "default value" for a type.

impl<N: PartialEq, T: PartialEq + OptFields> PartialEq<GFA<N, T>> for GFA<N, T>

fn eq(&self, other: &GFA<N, T>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &GFA<N, T>) -> bool

This method tests for !=.

impl<N: PartialOrd, T: PartialOrd + OptFields> PartialOrd<GFA<N, T>> for GFA<N, T>

fn partial_cmp(&self, other: &GFA<N, T>) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &GFA<N, T>) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &GFA<N, T>) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &GFA<N, T>) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &GFA<N, T>) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl<N, T: OptFields> StructuralPartialEq for GFA<N, T>