pub struct Decoder<'z, R: BufRead + Seek> { /* private fields */ }
Expand description
A decoder for Nucleotide Archive Format files.
The internal reader is shared and accessed non-sequentially to read the
different block components of the archive. This means that the internal
file heavily make use of Seek::seek
, so make sure that the actual
type has a fast seeking implementation.
By default, the decoder will decode all available fields, which may not
be needed. Use a DecoderBuilder
to configure decoding of individual
fields.
§Thread safety
By default, Decoder
objects are not Send
because they use reference
counting to share the reader between the different block parsers. Compile
the crate with the arc feature to use Arc
instead of Rc
, making
the decoder Send
.
Implementations§
source§impl<R: BufRead + Seek> Decoder<'_, R>
impl<R: BufRead + Seek> Decoder<'_, R>
sourcepub fn new(reader: R) -> Result<Self, Error>
pub fn new(reader: R) -> Result<Self, Error>
Create a new decoder from the given reader.
This constructor is a shortcut for DecoderBuilder::new().with_reader(reader)
.
Use DecoderBuilder
to configure a
decoder with more options.
sourcepub fn header(&self) -> &Header
pub fn header(&self) -> &Header
Get the header extracted from the archive.
The NAF header contains useful metadata which are decoded before starting to decode the rest of the archive, such as the total number of sequences (useful for building a progress bar) or the line length (useful for writing the decoded sequences in FASTA format).
sourcepub fn sequence_type(&self) -> SequenceType
pub fn sequence_type(&self) -> SequenceType
Get the type of sequence in the archive being decoded.
This method is a shortcut for self.header().sequence_type()
.
sourcepub fn into_inner(self) -> R
pub fn into_inner(self) -> R
Extract the internal reader.
Note that the internal reader may have been advanced even if no records were obtained from the decoder yet, since at least the header needs to be decoded to obtain a working decoder.
Trait Implementations§
source§impl<R: BufRead + Seek> Iterator for Decoder<'_, R>
impl<R: BufRead + Seek> Iterator for Decoder<'_, R>
source§fn next(&mut self) -> Option<Self::Item>
fn next(&mut self) -> Option<Self::Item>
source§fn size_hint(&self) -> (usize, Option<usize>)
fn size_hint(&self) -> (usize, Option<usize>)
source§fn next_chunk<const N: usize>(
&mut self
) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where
Self: Sized,
fn next_chunk<const N: usize>(
&mut self
) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where
Self: Sized,
iter_next_chunk
)N
values. Read more1.0.0 · source§fn count(self) -> usizewhere
Self: Sized,
fn count(self) -> usizewhere
Self: Sized,
1.0.0 · source§fn last(self) -> Option<Self::Item>where
Self: Sized,
fn last(self) -> Option<Self::Item>where
Self: Sized,
source§fn advance_by(&mut self, n: usize) -> Result<(), NonZero<usize>>
fn advance_by(&mut self, n: usize) -> Result<(), NonZero<usize>>
iter_advance_by
)n
elements. Read more1.0.0 · source§fn nth(&mut self, n: usize) -> Option<Self::Item>
fn nth(&mut self, n: usize) -> Option<Self::Item>
n
th element of the iterator. Read more1.28.0 · source§fn step_by(self, step: usize) -> StepBy<Self>where
Self: Sized,
fn step_by(self, step: usize) -> StepBy<Self>where
Self: Sized,
1.0.0 · source§fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>
1.0.0 · source§fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where
Self: Sized,
U: IntoIterator,
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where
Self: Sized,
U: IntoIterator,
source§fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>
iter_intersperse
)separator
between adjacent items of the original iterator. Read more1.0.0 · source§fn map<B, F>(self, f: F) -> Map<Self, F>
fn map<B, F>(self, f: F) -> Map<Self, F>
1.0.0 · source§fn filter<P>(self, predicate: P) -> Filter<Self, P>
fn filter<P>(self, predicate: P) -> Filter<Self, P>
1.0.0 · source§fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>
fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>
1.0.0 · source§fn enumerate(self) -> Enumerate<Self>where
Self: Sized,
fn enumerate(self) -> Enumerate<Self>where
Self: Sized,
1.0.0 · source§fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>
fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>
1.0.0 · source§fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>
fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>
1.57.0 · source§fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>
fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>
1.0.0 · source§fn skip(self, n: usize) -> Skip<Self>where
Self: Sized,
fn skip(self, n: usize) -> Skip<Self>where
Self: Sized,
n
elements. Read more1.0.0 · source§fn take(self, n: usize) -> Take<Self>where
Self: Sized,
fn take(self, n: usize) -> Take<Self>where
Self: Sized,
n
elements, or fewer
if the underlying iterator ends sooner. Read more1.0.0 · source§fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>
fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>
source§fn map_windows<F, R, const N: usize>(self, f: F) -> MapWindows<Self, F, N>
fn map_windows<F, R, const N: usize>(self, f: F) -> MapWindows<Self, F, N>
iter_map_windows
)f
for each contiguous window of size N
over
self
and returns an iterator over the outputs of f
. Like slice::windows()
,
the windows during mapping overlap as well. Read more1.0.0 · source§fn inspect<F>(self, f: F) -> Inspect<Self, F>
fn inspect<F>(self, f: F) -> Inspect<Self, F>
1.0.0 · source§fn by_ref(&mut self) -> &mut Selfwhere
Self: Sized,
fn by_ref(&mut self) -> &mut Selfwhere
Self: Sized,
source§fn collect_into<E>(self, collection: &mut E) -> &mut E
fn collect_into<E>(self, collection: &mut E) -> &mut E
iter_collect_into
)1.0.0 · source§fn partition<B, F>(self, f: F) -> (B, B)
fn partition<B, F>(self, f: F) -> (B, B)
source§fn is_partitioned<P>(self, predicate: P) -> bool
fn is_partitioned<P>(self, predicate: P) -> bool
iter_is_partitioned
)true
precede all those that return false
. Read more1.27.0 · source§fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R
fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R
1.27.0 · source§fn try_for_each<F, R>(&mut self, f: F) -> R
fn try_for_each<F, R>(&mut self, f: F) -> R
1.0.0 · source§fn fold<B, F>(self, init: B, f: F) -> B
fn fold<B, F>(self, init: B, f: F) -> B
1.51.0 · source§fn reduce<F>(self, f: F) -> Option<Self::Item>
fn reduce<F>(self, f: F) -> Option<Self::Item>
source§fn try_reduce<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType
fn try_reduce<F, R>( &mut self, f: F ) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType
iterator_try_reduce
)1.0.0 · source§fn all<F>(&mut self, f: F) -> bool
fn all<F>(&mut self, f: F) -> bool
1.0.0 · source§fn any<F>(&mut self, f: F) -> bool
fn any<F>(&mut self, f: F) -> bool
1.0.0 · source§fn find<P>(&mut self, predicate: P) -> Option<Self::Item>
fn find<P>(&mut self, predicate: P) -> Option<Self::Item>
1.30.0 · source§fn find_map<B, F>(&mut self, f: F) -> Option<B>
fn find_map<B, F>(&mut self, f: F) -> Option<B>
source§fn try_find<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType
fn try_find<F, R>( &mut self, f: F ) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType
try_find
)1.0.0 · source§fn position<P>(&mut self, predicate: P) -> Option<usize>
fn position<P>(&mut self, predicate: P) -> Option<usize>
1.6.0 · source§fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>
fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>
1.15.0 · source§fn max_by<F>(self, compare: F) -> Option<Self::Item>
fn max_by<F>(self, compare: F) -> Option<Self::Item>
1.6.0 · source§fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>
fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>
1.15.0 · source§fn min_by<F>(self, compare: F) -> Option<Self::Item>
fn min_by<F>(self, compare: F) -> Option<Self::Item>
1.0.0 · source§fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)
fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)
1.36.0 · source§fn copied<'a, T>(self) -> Copied<Self>
fn copied<'a, T>(self) -> Copied<Self>
source§fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where
Self: Sized,
fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where
Self: Sized,
iter_array_chunks
)N
elements of the iterator at a time. Read more1.11.0 · source§fn product<P>(self) -> P
fn product<P>(self) -> P
source§fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering
iter_order_by
)Iterator
with those
of another with respect to the specified comparison function. Read more1.5.0 · source§fn partial_cmp<I>(self, other: I) -> Option<Ordering>
fn partial_cmp<I>(self, other: I) -> Option<Ordering>
PartialOrd
elements of
this Iterator
with those of another. The comparison works like short-circuit
evaluation, returning a result without comparing the remaining elements.
As soon as an order can be determined, the evaluation stops and a result is returned. Read moresource§fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where
Self: Sized,
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where
Self: Sized,
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
iter_order_by
)Iterator
with those
of another with respect to the specified comparison function. Read moresource§fn eq_by<I, F>(self, other: I, eq: F) -> bool
fn eq_by<I, F>(self, other: I, eq: F) -> bool
iter_order_by
)1.5.0 · source§fn lt<I>(self, other: I) -> bool
fn lt<I>(self, other: I) -> bool
Iterator
are lexicographically
less than those of another. Read more1.5.0 · source§fn le<I>(self, other: I) -> bool
fn le<I>(self, other: I) -> bool
Iterator
are lexicographically
less or equal to those of another. Read more1.5.0 · source§fn gt<I>(self, other: I) -> bool
fn gt<I>(self, other: I) -> bool
Iterator
are lexicographically
greater than those of another. Read more1.5.0 · source§fn ge<I>(self, other: I) -> bool
fn ge<I>(self, other: I) -> bool
Iterator
are lexicographically
greater than or equal to those of another. Read moresource§fn is_sorted_by<F>(self, compare: F) -> bool
fn is_sorted_by<F>(self, compare: F) -> bool
is_sorted
)source§fn is_sorted_by_key<F, K>(self, f: F) -> bool
fn is_sorted_by_key<F, K>(self, f: F) -> bool
is_sorted
)