Struct bio::data_structures::fmindex::FMIndex
source · pub struct FMIndex<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> { /* private fields */ }
Expand description
The Fast Index in Minute space (FM-Index, Ferragina and Manzini, 2000) for finding suffix array intervals matching a given pattern.
Implementations§
Trait Implementations§
source§impl<DBWT: Clone + Borrow<BWT>, DLess: Clone + Borrow<Less>, DOcc: Clone + Borrow<Occ>> Clone for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Clone + Borrow<BWT>, DLess: Clone + Borrow<Less>, DOcc: Clone + Borrow<Occ>> Clone for FMIndex<DBWT, DLess, DOcc>
source§impl<DBWT: Debug + Borrow<BWT>, DLess: Debug + Borrow<Less>, DOcc: Debug + Borrow<Occ>> Debug for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Debug + Borrow<BWT>, DLess: Debug + Borrow<Less>, DOcc: Debug + Borrow<Occ>> Debug for FMIndex<DBWT, DLess, DOcc>
source§impl<DBWT: Default + Borrow<BWT>, DLess: Default + Borrow<Less>, DOcc: Default + Borrow<Occ>> Default for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Default + Borrow<BWT>, DLess: Default + Borrow<Less>, DOcc: Default + Borrow<Occ>> Default for FMIndex<DBWT, DLess, DOcc>
source§impl<'de, DBWT, DLess, DOcc> Deserialize<'de> for FMIndex<DBWT, DLess, DOcc>where
DBWT: Deserialize<'de> + Borrow<BWT>,
DLess: Deserialize<'de> + Borrow<Less>,
DOcc: Deserialize<'de> + Borrow<Occ>,
impl<'de, DBWT, DLess, DOcc> Deserialize<'de> for FMIndex<DBWT, DLess, DOcc>where DBWT: Deserialize<'de> + Borrow<BWT>, DLess: Deserialize<'de> + Borrow<Less>, DOcc: Deserialize<'de> + Borrow<Occ>,
source§fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
__D: Deserializer<'de>,
fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where __D: Deserializer<'de>,
Deserialize this value from the given Serde deserializer. Read more
source§impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndexable for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndexable for FMIndex<DBWT, DLess, DOcc>
source§fn backward_search<'b, P: Iterator<Item = &'b u8> + DoubleEndedIterator>(
&self,
pattern: P
) -> BackwardSearchResult
fn backward_search<'b, P: Iterator<Item = &'b u8> + DoubleEndedIterator>( &self, pattern: P ) -> BackwardSearchResult
Perform backward search, yielding
BackwardSearchResult
enum that
contains the suffix array interval denoting exact occurrences of the given pattern
of length m in the text if it exists, or the suffix array interval denoting the
exact occurrences of a maximal matching suffix of the given pattern if it does
not exist. If none of the pattern can be matched, the BackwardSearchResult
is
Absent
.
Complexity: O(m). Read moresource§impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> From<FMIndex<DBWT, DLess, DOcc>> for FMDIndex<DBWT, DLess, DOcc>
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> From<FMIndex<DBWT, DLess, DOcc>> for FMDIndex<DBWT, DLess, DOcc>
source§fn from(fmindex: FMIndex<DBWT, DLess, DOcc>) -> FMDIndex<DBWT, DLess, DOcc>
fn from(fmindex: FMIndex<DBWT, DLess, DOcc>) -> FMDIndex<DBWT, DLess, DOcc>
Construct a new instance of the FMD index (see Heng Li (2012) Bioinformatics).
This expects a BWT that was created from a text over the DNA alphabet with N
(alphabets::dna::n_alphabet()
) consisting of the
concatenation with its reverse complement, separated by the sentinel symbol $
.
I.e., let T be the original text and R be its reverse complement.
Then, the expected text is T$R$. Further, multiple concatenated texts are allowed, e.g.
T1$R1$T2$R2$T3$R3$.
source§impl<DBWT: Hash + Borrow<BWT>, DLess: Hash + Borrow<Less>, DOcc: Hash + Borrow<Occ>> Hash for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Hash + Borrow<BWT>, DLess: Hash + Borrow<Less>, DOcc: Hash + Borrow<Occ>> Hash for FMIndex<DBWT, DLess, DOcc>
source§impl<DBWT: Ord + Borrow<BWT>, DLess: Ord + Borrow<Less>, DOcc: Ord + Borrow<Occ>> Ord for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Ord + Borrow<BWT>, DLess: Ord + Borrow<Less>, DOcc: Ord + Borrow<Occ>> Ord for FMIndex<DBWT, DLess, DOcc>
1.21.0 · source§fn max(self, other: Self) -> Selfwhere
Self: Sized,
fn max(self, other: Self) -> Selfwhere Self: Sized,
Compares and returns the maximum of two values. Read more
source§impl<DBWT: PartialEq + Borrow<BWT>, DLess: PartialEq + Borrow<Less>, DOcc: PartialEq + Borrow<Occ>> PartialEq<FMIndex<DBWT, DLess, DOcc>> for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: PartialEq + Borrow<BWT>, DLess: PartialEq + Borrow<Less>, DOcc: PartialEq + Borrow<Occ>> PartialEq<FMIndex<DBWT, DLess, DOcc>> for FMIndex<DBWT, DLess, DOcc>
source§impl<DBWT: PartialOrd + Borrow<BWT>, DLess: PartialOrd + Borrow<Less>, DOcc: PartialOrd + Borrow<Occ>> PartialOrd<FMIndex<DBWT, DLess, DOcc>> for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: PartialOrd + Borrow<BWT>, DLess: PartialOrd + Borrow<Less>, DOcc: PartialOrd + Borrow<Occ>> PartialOrd<FMIndex<DBWT, DLess, DOcc>> for FMIndex<DBWT, DLess, DOcc>
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 moresource§impl<DBWT, DLess, DOcc> Serialize for FMIndex<DBWT, DLess, DOcc>where
DBWT: Serialize + Borrow<BWT>,
DLess: Serialize + Borrow<Less>,
DOcc: Serialize + Borrow<Occ>,
impl<DBWT, DLess, DOcc> Serialize for FMIndex<DBWT, DLess, DOcc>where DBWT: Serialize + Borrow<BWT>, DLess: Serialize + Borrow<Less>, DOcc: Serialize + Borrow<Occ>,
impl<DBWT: Copy + Borrow<BWT>, DLess: Copy + Borrow<Less>, DOcc: Copy + Borrow<Occ>> Copy for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Eq + Borrow<BWT>, DLess: Eq + Borrow<Less>, DOcc: Eq + Borrow<Occ>> Eq for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> StructuralEq for FMIndex<DBWT, DLess, DOcc>
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> StructuralPartialEq for FMIndex<DBWT, DLess, DOcc>
Auto Trait Implementations§
impl<DBWT, DLess, DOcc> RefUnwindSafe for FMIndex<DBWT, DLess, DOcc>where DBWT: RefUnwindSafe, DLess: RefUnwindSafe, DOcc: RefUnwindSafe,
impl<DBWT, DLess, DOcc> Send for FMIndex<DBWT, DLess, DOcc>where DBWT: Send, DLess: Send, DOcc: Send,
impl<DBWT, DLess, DOcc> Sync for FMIndex<DBWT, DLess, DOcc>where DBWT: Sync, DLess: Sync, DOcc: Sync,
impl<DBWT, DLess, DOcc> Unpin for FMIndex<DBWT, DLess, DOcc>where DBWT: Unpin, DLess: Unpin, DOcc: Unpin,
impl<DBWT, DLess, DOcc> UnwindSafe for FMIndex<DBWT, DLess, DOcc>where DBWT: UnwindSafe, DLess: UnwindSafe, DOcc: UnwindSafe,
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
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<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.