Struct bio::pattern_matching::myers::FullMatches
source · pub struct FullMatches<'a, T, C, I>{ /* private fields */ }
Expand description
Iterator over tuples of starting position, end position and distance of matches. In addition, methods for obtaining the hit alignment path are provided.
Implementations§
source§impl<'a, T, C, I> FullMatches<'a, T, C, I>
impl<'a, T, C, I> FullMatches<'a, T, C, I>
sourcepub fn next_end(&mut self) -> Option<(usize, T::DistType)>
pub fn next_end(&mut self) -> Option<(usize, T::DistType)>
Searches the next match and returns a tuple of end position and distance
if found. This involves no searching for a starting position and is thus
faster than just iterating over FullMatches
sourcepub fn next_path(
&mut self,
ops: &mut Vec<AlignmentOperation>
) -> Option<(usize, usize, T::DistType)>
pub fn next_path( &mut self, ops: &mut Vec<AlignmentOperation> ) -> Option<(usize, usize, T::DistType)>
Searches the next match and returns a tuple of starting position, end position and
distance, or None
if no match was found. In addition, the alignment path is added to
ops
. Existing data in the vector will be cleared beforehand.
sourcepub fn next_path_reverse(
&mut self,
ops: &mut Vec<AlignmentOperation>
) -> Option<(usize, usize, T::DistType)>
pub fn next_path_reverse( &mut self, ops: &mut Vec<AlignmentOperation> ) -> Option<(usize, usize, T::DistType)>
Like FullMatches::path_reverse()
, but the operations will be in reverse order. This
is slightly faster, as the traceback algorithm adds them in reverse order,
and path()
needs to reverse them. Existing data in the vector will be cleared
beforehand.
sourcepub fn next_alignment(&mut self, aln: &mut Alignment) -> bool
pub fn next_alignment(&mut self, aln: &mut Alignment) -> bool
Searches the next match and updates the given Alignment
with its position
and alignment path if found. The distance is stored in Alignment::score
.
If no next hit is found, false
is returned and aln
remains unchanged.
sourcepub fn start(&self) -> Option<usize>
pub fn start(&self) -> Option<usize>
Returns the starting position of the current hit. If the search is finished and no hit was
found, None
is returned.
sourcepub fn path(&self, ops: &mut Vec<AlignmentOperation>) -> Option<usize>
pub fn path(&self, ops: &mut Vec<AlignmentOperation>) -> Option<usize>
Adds the path of the current hit alignment to ops
and returns the starting position of
the current hit. If the search is finished and no hit was found, None
is returned.
Adds the path of the current hit alignment to ops
and returns the starting position of
the current hit. If the search is finished and no hit was found, None
is returned.
Existing data in the vector will be cleared beforehand.
sourcepub fn path_reverse(&self, ops: &mut Vec<AlignmentOperation>) -> Option<usize>
pub fn path_reverse(&self, ops: &mut Vec<AlignmentOperation>) -> Option<usize>
Like FullMatches::path()
, but the operations will be in reverse order. This
is slightly faster, as the traceback algorithm adds them in reverse order,
and path()
needs to reverse them.
Existing data in the vector will be cleared beforehand.
Trait Implementations§
source§impl<'a, T, C, I> Debug for FullMatches<'a, T, C, I>
impl<'a, T, C, I> Debug for FullMatches<'a, T, C, I>
source§impl<'a, T, C, I> Iterator for FullMatches<'a, T, C, I>
impl<'a, T, C, I> Iterator for FullMatches<'a, T, C, I>
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PartialOrd
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)Auto Trait Implementations§
impl<'a, T, C, I> Freeze for FullMatches<'a, T, C, I>
impl<'a, T, C, I> RefUnwindSafe for FullMatches<'a, T, C, I>
impl<'a, T, C, I> Send for FullMatches<'a, T, C, I>
impl<'a, T, C, I> Sync for FullMatches<'a, T, C, I>
impl<'a, T, C, I> Unpin for FullMatches<'a, T, C, I>
impl<'a, T, C, I> !UnwindSafe for FullMatches<'a, T, C, I>
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returns true
. Read moresource§fn take_while_ref<F>(&mut self, accept: F) -> TakeWhileRef<'_, Self, F>
fn take_while_ref<F>(&mut self, accept: F) -> TakeWhileRef<'_, Self, F>
Clone
-able iterator
to only pick off elements while the predicate accept
returns true
. Read moresource§fn take_while_inclusive<F>(
&mut self,
accept: F
) -> TakeWhileInclusive<'_, Self, F>
fn take_while_inclusive<F>( &mut self, accept: F ) -> TakeWhileInclusive<'_, Self, F>
true
, including the element for which the predicate
first returned false
. Read moresource§fn while_some<A>(self) -> WhileSome<Self>
fn while_some<A>(self) -> WhileSome<Self>
Option<A>
iterator elements
and produces A
. Stops on the first None
encountered. Read moresource§fn tuple_combinations<T>(self) -> TupleCombinations<Self, T>
fn tuple_combinations<T>(self) -> TupleCombinations<Self, T>
source§fn combinations(self, k: usize) -> Combinations<Self>
fn combinations(self, k: usize) -> Combinations<Self>
k
-length combinations of
the elements from an iterator. Read moresource§fn combinations_with_replacement(
self,
k: usize
) -> CombinationsWithReplacement<Self>
fn combinations_with_replacement( self, k: usize ) -> CombinationsWithReplacement<Self>
k
-length combinations of
the elements from an iterator, with replacement. Read moresource§fn permutations(self, k: usize) -> Permutations<Self>
fn permutations(self, k: usize) -> Permutations<Self>
source§fn powerset(self) -> Powerset<Self>
fn powerset(self) -> Powerset<Self>
source§fn pad_using<F>(self, min: usize, f: F) -> PadUsing<Self, F>
fn pad_using<F>(self, min: usize, f: F) -> PadUsing<Self, F>
min
by filling missing elements using a closure f
. Read moresource§fn with_position(self) -> WithPosition<Self>where
Self: Sized,
fn with_position(self) -> WithPosition<Self>where
Self: Sized,
Position
to
ease special-case handling of the first or last elements. Read moresource§fn positions<P>(self, predicate: P) -> Positions<Self, P>
fn positions<P>(self, predicate: P) -> Positions<Self, P>
source§fn update<F>(self, updater: F) -> Update<Self, F>
fn update<F>(self, updater: F) -> Update<Self, F>
source§fn next_tuple<T>(&mut self) -> Option<T>
fn next_tuple<T>(&mut self) -> Option<T>
source§fn collect_tuple<T>(self) -> Option<T>
fn collect_tuple<T>(self) -> Option<T>
source§fn find_position<P>(&mut self, pred: P) -> Option<(usize, Self::Item)>
fn find_position<P>(&mut self, pred: P) -> Option<(usize, Self::Item)>
source§fn find_or_last<P>(self, predicate: P) -> Option<Self::Item>
fn find_or_last<P>(self, predicate: P) -> Option<Self::Item>
source§fn find_or_first<P>(self, predicate: P) -> Option<Self::Item>
fn find_or_first<P>(self, predicate: P) -> Option<Self::Item>
source§fn contains<Q>(&mut self, query: &Q) -> bool
fn contains<Q>(&mut self, query: &Q) -> bool
true
if the given item is present in this iterator. Read moresource§fn all_equal_value(
&mut self
) -> Result<Self::Item, Option<(Self::Item, Self::Item)>>
fn all_equal_value( &mut self ) -> Result<Self::Item, Option<(Self::Item, Self::Item)>>
source§fn all_unique(&mut self) -> bool
fn all_unique(&mut self) -> bool
source§fn dropping(self, n: usize) -> Selfwhere
Self: Sized,
fn dropping(self, n: usize) -> Selfwhere
Self: Sized,
n
elements from the iterator eagerly,
and return the same iterator again. Read moresource§fn dropping_back(self, n: usize) -> Selfwhere
Self: Sized + DoubleEndedIterator,
fn dropping_back(self, n: usize) -> Selfwhere
Self: Sized + DoubleEndedIterator,
n
elements from the iterator eagerly,
and return the same iterator again. Read moresource§fn foreach<F>(self, f: F)
fn foreach<F>(self, f: F)
f
eagerly on each element of the iterator. Read moresource§fn collect_vec(self) -> Vec<Self::Item>where
Self: Sized,
fn collect_vec(self) -> Vec<Self::Item>where
Self: Sized,
.collect_vec()
is simply a type specialization of Iterator::collect
,
for convenience.source§fn try_collect<T, U, E>(self) -> Result<U, E>
fn try_collect<T, U, E>(self) -> Result<U, E>
source§fn set_from<'a, A, J>(&mut self, from: J) -> usize
fn set_from<'a, A, J>(&mut self, from: J) -> usize
self
from the from
iterator,
stopping at the shortest of the two iterators. Read moresource§fn join(&mut self, sep: &str) -> String
fn join(&mut self, sep: &str) -> String
sep
. Read moresource§fn format(self, sep: &str) -> Format<'_, Self>where
Self: Sized,
fn format(self, sep: &str) -> Format<'_, Self>where
Self: Sized,
sep
. Read moresource§fn format_with<F>(self, sep: &str, format: F) -> FormatWith<'_, Self, F>
fn format_with<F>(self, sep: &str, format: F) -> FormatWith<'_, Self, F>
sep
. Read moresource§fn fold_results<A, E, B, F>(&mut self, start: B, f: F) -> Result<B, E>
fn fold_results<A, E, B, F>(&mut self, start: B, f: F) -> Result<B, E>
.fold_ok()
.source§fn fold_ok<A, E, B, F>(&mut self, start: B, f: F) -> Result<B, E>
fn fold_ok<A, E, B, F>(&mut self, start: B, f: F) -> Result<B, E>
Result
values from an iterator. Read moresource§fn fold_options<A, B, F>(&mut self, start: B, f: F) -> Option<B>
fn fold_options<A, B, F>(&mut self, start: B, f: F) -> Option<B>
Option
values from an iterator. Read moresource§fn fold1<F>(self, f: F) -> Option<Self::Item>
fn fold1<F>(self, f: F) -> Option<Self::Item>
Iterator::reduce
insteadsource§fn tree_fold1<F>(self, f: F) -> Option<Self::Item>
fn tree_fold1<F>(self, f: F) -> Option<Self::Item>
source§fn fold_while<B, F>(&mut self, init: B, f: F) -> FoldWhile<B>
fn fold_while<B, F>(&mut self, init: B, f: F) -> FoldWhile<B>
source§fn sum1<S>(self) -> Option<S>
fn sum1<S>(self) -> Option<S>
source§fn product1<P>(self) -> Option<P>
fn product1<P>(self) -> Option<P>
source§fn sorted_unstable(self) -> IntoIter<Self::Item>
fn sorted_unstable(self) -> IntoIter<Self::Item>
source§fn sorted_unstable_by<F>(self, cmp: F) -> IntoIter<Self::Item>
fn sorted_unstable_by<F>(self, cmp: F) -> IntoIter<Self::Item>
source§fn sorted_unstable_by_key<K, F>(self, f: F) -> IntoIter<Self::Item>
fn sorted_unstable_by_key<K, F>(self, f: F) -> IntoIter<Self::Item>
source§fn sorted(self) -> IntoIter<Self::Item>
fn sorted(self) -> IntoIter<Self::Item>
source§fn sorted_by<F>(self, cmp: F) -> IntoIter<Self::Item>
fn sorted_by<F>(self, cmp: F) -> IntoIter<Self::Item>
source§fn sorted_by_key<K, F>(self, f: F) -> IntoIter<Self::Item>
fn sorted_by_key<K, F>(self, f: F) -> IntoIter<Self::Item>
source§fn sorted_by_cached_key<K, F>(self, f: F) -> IntoIter<Self::Item>
fn sorted_by_cached_key<K, F>(self, f: F) -> IntoIter<Self::Item>
source§fn k_smallest(self, k: usize) -> IntoIter<Self::Item>
fn k_smallest(self, k: usize) -> IntoIter<Self::Item>
source§fn partition_map<A, B, F, L, R>(self, predicate: F) -> (A, B)
fn partition_map<A, B, F, L, R>(self, predicate: F) -> (A, B)
Iterator::partition
, each partition may
have a distinct type. Read moresource§fn partition_result<A, B, T, E>(self) -> (A, B)
fn partition_result<A, B, T, E>(self) -> (A, B)
Result
s into one list of all the Ok
elements
and another list of all the Err
elements. Read moresource§fn into_group_map<K, V>(self) -> HashMap<K, Vec<V>>
fn into_group_map<K, V>(self) -> HashMap<K, Vec<V>>
HashMap
of keys mapped to Vec
s of values. Keys and values
are taken from (Key, Value)
tuple pairs yielded by the input iterator. Read moresource§fn into_group_map_by<K, V, F>(self, f: F) -> HashMap<K, Vec<V>>
fn into_group_map_by<K, V, F>(self, f: F) -> HashMap<K, Vec<V>>
Iterator
on a HashMap
. Keys mapped to Vec
s of values. The key is specified
in the closure. Read moresource§fn into_grouping_map<K, V>(self) -> GroupingMap<Self>
fn into_grouping_map<K, V>(self) -> GroupingMap<Self>
GroupingMap
to be used later with one of the efficient
group-and-fold operations it allows to perform. Read moresource§fn into_grouping_map_by<K, V, F>(
self,
key_mapper: F
) -> GroupingMap<MapForGrouping<Self, F>>
fn into_grouping_map_by<K, V, F>( self, key_mapper: F ) -> GroupingMap<MapForGrouping<Self, F>>
GroupingMap
to be used later with one of the efficient
group-and-fold operations it allows to perform. Read moresource§fn min_set_by<F>(self, compare: F) -> Vec<Self::Item>
fn min_set_by<F>(self, compare: F) -> Vec<Self::Item>
source§fn min_set_by_key<K, F>(self, key: F) -> Vec<Self::Item>
fn min_set_by_key<K, F>(self, key: F) -> Vec<Self::Item>
source§fn max_set_by<F>(self, compare: F) -> Vec<Self::Item>
fn max_set_by<F>(self, compare: F) -> Vec<Self::Item>
source§fn max_set_by_key<K, F>(self, key: F) -> Vec<Self::Item>
fn max_set_by_key<K, F>(self, key: F) -> Vec<Self::Item>
source§fn minmax(self) -> MinMaxResult<Self::Item>
fn minmax(self) -> MinMaxResult<Self::Item>
source§fn minmax_by_key<K, F>(self, key: F) -> MinMaxResult<Self::Item>
fn minmax_by_key<K, F>(self, key: F) -> MinMaxResult<Self::Item>
source§fn minmax_by<F>(self, compare: F) -> MinMaxResult<Self::Item>
fn minmax_by<F>(self, compare: F) -> MinMaxResult<Self::Item>
source§fn position_max(self) -> Option<usize>
fn position_max(self) -> Option<usize>
source§fn position_max_by_key<K, F>(self, key: F) -> Option<usize>
fn position_max_by_key<K, F>(self, key: F) -> Option<usize>
source§fn position_max_by<F>(self, compare: F) -> Option<usize>
fn position_max_by<F>(self, compare: F) -> Option<usize>
source§fn position_min(self) -> Option<usize>
fn position_min(self) -> Option<usize>
source§fn position_min_by_key<K, F>(self, key: F) -> Option<usize>
fn position_min_by_key<K, F>(self, key: F) -> Option<usize>
source§fn position_min_by<F>(self, compare: F) -> Option<usize>
fn position_min_by<F>(self, compare: F) -> Option<usize>
source§fn position_minmax(self) -> MinMaxResult<usize>
fn position_minmax(self) -> MinMaxResult<usize>
source§fn position_minmax_by_key<K, F>(self, key: F) -> MinMaxResult<usize>
fn position_minmax_by_key<K, F>(self, key: F) -> MinMaxResult<usize>
source§fn position_minmax_by<F>(self, compare: F) -> MinMaxResult<usize>
fn position_minmax_by<F>(self, compare: F) -> MinMaxResult<usize>
source§fn exactly_one(self) -> Result<Self::Item, ExactlyOneError<Self>>where
Self: Sized,
fn exactly_one(self) -> Result<Self::Item, ExactlyOneError<Self>>where
Self: Sized,
source§fn at_most_one(self) -> Result<Option<Self::Item>, ExactlyOneError<Self>>where
Self: Sized,
fn at_most_one(self) -> Result<Option<Self::Item>, ExactlyOneError<Self>>where
Self: Sized,
source§fn multipeek(self) -> MultiPeek<Self>where
Self: Sized,
fn multipeek(self) -> MultiPeek<Self>where
Self: Sized,
.next()
values without advancing the base iterator. Read moresource§fn counts(self) -> HashMap<Self::Item, usize>
fn counts(self) -> HashMap<Self::Item, usize>
HashMap
which
contains each item that appears in the iterator and the number
of times it appears. Read moresource§fn counts_by<K, F>(self, f: F) -> HashMap<K, usize>
fn counts_by<K, F>(self, f: F) -> HashMap<K, usize>
HashMap
which
contains each item that appears in the iterator and the number
of times it appears,
determining identity using a keying function. Read moresource§fn multiunzip<FromI>(self) -> FromIwhere
Self: Sized + MultiUnzip<FromI>,
fn multiunzip<FromI>(self) -> FromIwhere
Self: Sized + MultiUnzip<FromI>,
source§impl<I> ItertoolsNum for I
impl<I> ItertoolsNum for I
source§impl<IT, A, FromA, B, FromB, C, FromC> MultiUnzip<(FromA, FromB, FromC)> for IT
impl<IT, A, FromA, B, FromB, C, FromC> MultiUnzip<(FromA, FromB, FromC)> for IT
source§fn multiunzip(self) -> (FromA, FromB, FromC)
fn multiunzip(self) -> (FromA, FromB, FromC)
source§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
source§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
self
from the equivalent element of its
superset. Read moresource§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
self
is actually part of its subset T
(and can be converted to it).source§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
self.to_subset
but without any property checks. Always succeeds.source§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
self
to the equivalent element of its superset.