Struct consalign::Record

pub struct Record { /* private fields */ }

A FASTA record.

Implementations

impl Record

pub fn new() -> Record

Create a new instance.

pub fn with_attrs(id: &str, desc: Option<&str>, seq: &[u8]) -> Record

Create a new Record from given attributes.

Examples

use bio::io::fasta::Record;

let read_id = "read1";
let description = Some("sampleid=foobar");
let sequence = b"ACGT";
let record = Record::with_attrs(read_id, description, sequence);

assert_eq!(">read1 sampleid=foobar\nACGT\n", record.to_string())

pub fn is_empty(&self) -> bool

Check if record is empty.

pub fn check(&self) -> Result<(), &str>

Check validity of Fasta record.

pub fn id(&self) -> &str

Return the id of the record.

pub fn desc(&self) -> Option<&str>

Return descriptions if present.

pub fn seq(&self) -> &[u8]

Return the sequence of the record.

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

fn default() -> Record

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for Record

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

Deserialize this value from the given Serde deserializer.

impl Display for Record

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

Allows for using Record in a given formatter f. In general this is for creating a String representation of a Record and, optionally, writing it to a file.

Errors

Returns std::fmt::Error if there is an issue formatting to the stream.

Examples

Read in a Fasta Record and create a String representation of it.

use bio::io::fasta::Reader;
use std::fmt::Write;
// create a "fake" fasta file
let fasta: &'static [u8] = b">id comment1 comment2\nACGT\n";
let mut records = Reader::new(fasta).records().map(|r| r.unwrap());
let record = records.next().unwrap();

let mut actual = String::new();
// populate `actual` with a string representation of our record
write!(actual, "{}", record).unwrap();

let expected = std::str::from_utf8(fasta).unwrap();

assert_eq!(actual, expected)

impl Hash for Record

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

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 Record

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

This method returns an Ordering between self and other.

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

Compares and returns the maximum of two values.

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

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Selfwhere Self: Sized + PartialOrd<Self>,

Restrict a value to a certain interval.

impl PartialEq<Record> for Record

fn eq(&self, other: &Record) -> 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 !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd<Record> for Record

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

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

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

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

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

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

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

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

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

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

impl Serialize for Record

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

Serialize this value into the given Serde serializer.

impl Eq for Record

impl StructuralEq for Record

impl StructuralPartialEq for Record