pub struct Reader<B> { /* private fields */ }
Expand description
A FASTA reader.
Implementations§
§impl Reader<BufReader<File>>
impl Reader<BufReader<File>>
§impl<R> Reader<BufReader<R>>where
R: Read,
impl<R> Reader<BufReader<R>>where R: Read,
pub fn new(reader: R) -> Reader<BufReader<R>>
pub fn new(reader: R) -> Reader<BufReader<R>>
Create a new Fasta reader given an instance of io::Read
.
Example
let reader = Reader::new(fasta_file);
pub fn with_capacity(capacity: usize, reader: R) -> Reader<BufReader<R>>
pub fn with_capacity(capacity: usize, reader: R) -> Reader<BufReader<R>>
Create a new Fasta reader given a capacity and an instance of io::Read
.
Example
let reader = Reader::with_capacity(16384, fasta_file);
Trait Implementations§
§impl<'de, B> Deserialize<'de> for Reader<B>where
B: Deserialize<'de>,
impl<'de, B> Deserialize<'de> for Reader<B>where B: Deserialize<'de>,
§fn deserialize<__D>(
__deserializer: __D
) -> Result<Reader<B>, <__D as Deserializer<'de>>::Error>where
__D: Deserializer<'de>,
fn deserialize<__D>( __deserializer: __D ) -> Result<Reader<B>, <__D as Deserializer<'de>>::Error>where __D: Deserializer<'de>,
Deserialize this value from the given Serde deserializer. Read more
§impl<B> FastaRead for Reader<B>where
B: BufRead,
impl<B> FastaRead for Reader<B>where B: BufRead,
§fn read(&mut self, record: &mut Record) -> Result<(), Error>
fn read(&mut self, record: &mut Record) -> Result<(), Error>
Read the next FASTA record into the given Record
.
An empty record indicates that no more records can be read.
Use this method when you want to read records as fast as
possible because it allows the reuse of a Record
allocation.
The records iterator provides a more ergonomic approach to accessing FASTA records.
Errors
This function will return an error if the record is incomplete, syntax is violated or any form of I/O error is encountered.
Example
use bio::io::fasta::Record;
use bio::io::fasta::{FastaRead, Reader};
const fasta_file: &'static [u8] = b">id desc
AAAA
";
let mut reader = Reader::new(fasta_file);
let mut record = Record::new();
// Check for errors parsing the record
reader
.read(&mut record)
.expect("fasta reader: got an io::Error or could not read_line()");
assert_eq!(record.id(), "id");
assert_eq!(record.desc().unwrap(), "desc");
assert_eq!(record.seq().to_vec(), b"AAAA");
§impl<B> Ord for Reader<B>where
B: Ord,
impl<B> Ord for Reader<B>where B: Ord,
§impl<B> PartialOrd<Reader<B>> for Reader<B>where
B: PartialOrd<B>,
impl<B> PartialOrd<Reader<B>> for Reader<B>where B: PartialOrd<B>,
§fn partial_cmp(&self, other: &Reader<B>) -> Option<Ordering>
fn partial_cmp(&self, other: &Reader<B>) -> Option<Ordering>
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for
self
and other
) and is used by the <=
operator. Read more§impl<B> Serialize for Reader<B>where
B: Serialize,
impl<B> Serialize for Reader<B>where B: Serialize,
§fn serialize<__S>(
&self,
__serializer: __S
) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::Error>where
__S: Serializer,
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. Read more
impl<B> Eq for Reader<B>where B: Eq,
impl<B> StructuralEq for Reader<B>
impl<B> StructuralPartialEq for Reader<B>
Auto Trait Implementations§
impl<B> RefUnwindSafe for Reader<B>where B: RefUnwindSafe,
impl<B> Send for Reader<B>where B: Send,
impl<B> Sync for Reader<B>where B: Sync,
impl<B> Unpin for Reader<B>where B: Unpin,
impl<B> UnwindSafe for Reader<B>where B: UnwindSafe,
Blanket Implementations§
source§impl<Q, K> Equivalent<K> for Qwhere
Q: Eq + ?Sized,
K: Borrow<Q> + ?Sized,
impl<Q, K> Equivalent<K> for Qwhere Q: Eq + ?Sized, K: Borrow<Q> + ?Sized,
source§fn equivalent(&self, key: &K) -> bool
fn equivalent(&self, key: &K) -> bool
Compare self to
key
and return true
if they are equal.§impl<Q, K> Equivalent<K> for Qwhere
Q: Eq + ?Sized,
K: Borrow<Q> + ?Sized,
impl<Q, K> Equivalent<K> for Qwhere Q: Eq + ?Sized, K: Borrow<Q> + ?Sized,
§fn equivalent(&self, key: &K) -> bool
fn equivalent(&self, key: &K) -> bool
Checks if this value is equivalent to the given key. Read more
§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere SS: SubsetOf<SP>,
§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
The inverse inclusion map: attempts to construct
self
from the equivalent element of its
superset. Read more§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
Checks if
self
is actually part of its subset T
(and can be converted to it).§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
Use with care! Same as
self.to_subset
but without any property checks. Always succeeds.§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
The inclusion map: converts
self
to the equivalent element of its superset.