Struct ModChar 

pub struct ModChar(/* private fields */);

Our struct to hold a modification tag. The BAM file format uses the syntax base+mod_code in its ML tag to show which modification is represented e.g. C+m, A+a, T+T, … This can be a letter or a number e.g. T+472232 represents BrdU as that is its CheBI code. As we rely on a fibertools-rs data structure to store mod information (BaseMod), which uses a char datatype to represent the mod code, representing a one letter mod code is easy, but numbers need to be converted to char first. Fortunately, rust’s char datatype is almost equivalent to u32, so we just convert numbers to char before storing. NOTE: the above conversion has some problems e.g. A+a is equivalent to A+97 etc. (as 97 is the ascii code of a), and the rust char datatype does not allow a set of u32s somewhere between 55000 and 59000. We have chosen to live with this problem. I think the probability of having a DNA modification with a CheBI code overlapping with ASCII values or within this narrow range of values near 59000 is very small.

Implementations

impl ModChar

pub fn new(val: char) -> Self

We initialize with a character

pub fn val(&self) -> char

Returns the character

use nanalogue_core::ModChar;
for y in vec!['a','b','c','\u{D000}']{
    let x = ModChar::new(y.clone());
    assert_eq!(x.val(), y);
}

Trait Implementations

impl Clone for ModChar

fn clone(&self) -> ModChar

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ModChar

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

Formats the value using the given formatter.

impl Default for ModChar

Defaults to mod tag ‘N’

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for ModChar

fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>

where D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Display for ModChar

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

converts to string for display. If the value is in the alphabet, display it. Otherwise, display the equivalent number.

impl From<char> for ModChar

fn from(value: char) -> Self

Converts to this type from the input type.

impl From<u8> for ModChar

fn from(value: u8) -> Self

Converts to this type from the input type.

impl FromStr for ModChar

fn from_str(mod_type: &str) -> Result<Self, Self::Err>

process the modification type from a string, returning the first character if it is a letter, or converting it to a character if the first character is a number

use nanalogue_core::ModChar;
use std::str::FromStr;

// Single letter modification codes
let mod_char = ModChar::from_str("m")?;
assert_eq!(mod_char.val(), 'm');

// CheBI code for BrdU (5-bromo-2'-deoxyuridine)
let mod_char = ModChar::from_str("472232")?;

// Small numeric codes
let mod_char = ModChar::from_str("123")?;

// Invalid: starts with special character
let mod_char = ModChar::from_str("@123")?;

type Err = Error

The associated error which can be returned from parsing.

impl Hash for ModChar

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for ModChar

fn cmp(&self, other: &ModChar) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for ModChar

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

Tests for self and other values to be equal, and is used by ==.

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

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for ModChar

fn partial_cmp(&self, other: &ModChar) -> Option<Ordering>

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

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

Tests less than (for self and other) and is used by the < operator.

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

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

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

Tests greater than (for self and other) and is used by the > operator.

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

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

impl Serialize for ModChar

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 ModChar

impl Eq for ModChar

impl StructuralPartialEq for ModChar