Enum atglib::models::Frame

pub enum Frame {
    None,
    Zero,
    One,
    Two,
}

Frame indicates the reading frame offset of an Exon

It is based on GTF nomenclature:

• 0 indicates that the feature begins with a whole codon at the 5’ most base.
• 1 means that there is one extra base (the third base of a codon) before the first whole codon
• 2 means that there are two extra bases (the second and third bases of the codon) before the first codon.

Important: The reading-frame offset is handled differently in RefGene

Examples

use std::str::FromStr;
use atglib::models::Frame;

let frame_str = Frame::from_str("1").unwrap();
let frame_int = Frame::from_int(1).unwrap();

assert_eq!(frame_str, frame_int);

Variants

None

Zero

One

Two

Implementations

impl Frame

pub fn from_int(s: u32) -> Result<Self, String>

Returns a Frame based on the integer frame offset

pub fn from_gtf(s: &str) -> Result<Self, String>

Returns Frame from a GTF value

This method is the same as Frame::from_str but is present for consistency reasons

Examples

use atglib::models::Frame;
let frame = Frame::from_gtf("1").unwrap();

assert_eq!(frame, Frame::One);

pub fn from_refgene(s: &str) -> Result<Self, String>

Returns Frame from a RefGene value

RefGene uses a different specification than GTF when it comes to specifying 1 or 2. RefGene specifies how many nucleotides of the first codon are present on the previous exon.

Examples

use atglib::models::Frame;
let frame = Frame::from_refgene("1").unwrap();

assert_eq!(frame, Frame::Two);

pub fn to_gtf(&self) -> String

Returns the GTF String for Frame

This method is the same as the fmt::Display trait but is present for consistency reasons

Examples

use atglib::models::Frame;
let frame = Frame::One.to_gtf();

assert_eq!(frame, "1".to_string());

pub fn to_refgene(&self) -> String

Returns the RefGene String for Frame

RefGene uses a different specification than GTF when it comes to specifying 1 or 2. RefGene specifies how many nucleotides of the first codon are present on the previous exon.

Examples

use atglib::models::Frame;
let frame = Frame::One.to_refgene();

assert_eq!(frame, "2".to_string());

pub fn is_known(&self) -> bool

Returns true if the Frame is 0, 1 or 2

Trait Implementations

impl Add<Frame> for Frame

fn add(self, other: Self) -> Result<Self, String>

Calculates the next resulting Frame offset

type Output = Result<Frame, String>

The resulting type after applying the + operator.

impl Clone for Frame

fn clone(&self) -> Frame

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Frame

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Frame

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl Display for Frame

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

Formats the value using the given formatter.

impl FromStr for Frame

fn from_str(s: &str) -> Result<Self, String>

Creates a Frame from a string (as in GTF format)

Only accepts the following options:

• -1
• 0
• 1
• 2
• .

type Err = String

The associated error which can be returned from parsing.

impl PartialEq<Frame> for Frame

fn eq(&self, other: &Frame) -> bool

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

fn ne(&self, other: &Rhs) -> bool

This method tests for !=.

impl Serialize for Frame

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl Copy for Frame

impl Eq for Frame

impl StructuralEq for Frame

impl StructuralPartialEq for Frame