[−][src]Struct bio::data_structures::fmindex::FMIndex
The Fast Index in Minute space (FM-Index, Ferragina and Manzini, 2000) for finding suffix array intervals matching a given pattern.
Methods
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndex<DBWT, DLess, DOcc>
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pub fn new(bwt: DBWT, less: DLess, occ: DOcc) -> Self
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Construct a new instance of the FM index.
Arguments
bwt
- the BWTless
- the less array of the BWTocc
- the occurence array of the BWT
Trait Implementations
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndexable for FMIndex<DBWT, DLess, DOcc>
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fn occ(&self, r: usize, a: u8) -> usize
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fn less(&self, a: u8) -> usize
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fn bwt(&self) -> &BWT
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Provide a reference to the underlying BWT.
fn backward_search<'b, P: Iterator<Item = &'b u8> + DoubleEndedIterator>(
&self,
pattern: P
) -> Interval
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&self,
pattern: P
) -> Interval
Perform backward search, yielding suffix array interval denoting exact occurrences of the given pattern of length m in the text. Complexity: O(m). Read more
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> From<FMIndex<DBWT, DLess, DOcc>> for FMDIndex<DBWT, DLess, DOcc>
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fn from(fmindex: FMIndex<DBWT, DLess, DOcc>) -> FMDIndex<DBWT, DLess, DOcc>
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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$R3$.
impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> Serialize for FMIndex<DBWT, DLess, DOcc> where
DBWT: Serialize,
DLess: Serialize,
DOcc: Serialize,
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DBWT: Serialize,
DLess: Serialize,
DOcc: Serialize,
fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
__S: Serializer,
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__S: Serializer,
impl<'de, DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> Deserialize<'de> for FMIndex<DBWT, DLess, DOcc> where
DBWT: Deserialize<'de>,
DLess: Deserialize<'de>,
DOcc: Deserialize<'de>,
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DBWT: Deserialize<'de>,
DLess: Deserialize<'de>,
DOcc: Deserialize<'de>,
fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
__D: Deserializer<'de>,
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__D: Deserializer<'de>,
Auto Trait Implementations
impl<DBWT, DLess, DOcc> Send for FMIndex<DBWT, DLess, DOcc> where
DBWT: Send,
DLess: Send,
DOcc: Send,
DBWT: Send,
DLess: Send,
DOcc: Send,
impl<DBWT, DLess, DOcc> Unpin for FMIndex<DBWT, DLess, DOcc> where
DBWT: Unpin,
DLess: Unpin,
DOcc: Unpin,
DBWT: Unpin,
DLess: Unpin,
DOcc: Unpin,
impl<DBWT, DLess, DOcc> Sync for FMIndex<DBWT, DLess, DOcc> where
DBWT: Sync,
DLess: Sync,
DOcc: Sync,
DBWT: Sync,
DLess: Sync,
DOcc: Sync,
impl<DBWT, DLess, DOcc> UnwindSafe for FMIndex<DBWT, DLess, DOcc> where
DBWT: UnwindSafe,
DLess: UnwindSafe,
DOcc: UnwindSafe,
DBWT: UnwindSafe,
DLess: UnwindSafe,
DOcc: UnwindSafe,
impl<DBWT, DLess, DOcc> RefUnwindSafe for FMIndex<DBWT, DLess, DOcc> where
DBWT: RefUnwindSafe,
DLess: RefUnwindSafe,
DOcc: RefUnwindSafe,
DBWT: RefUnwindSafe,
DLess: RefUnwindSafe,
DOcc: RefUnwindSafe,
Blanket Implementations
impl<T> From<T> for T
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impl<T, U> Into<U> for T where
U: From<T>,
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U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>,
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U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
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impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
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U: TryFrom<T>,
type Error = <U as TryFrom<T>>::Error
The type returned in the event of a conversion error.
fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>
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impl<T> BorrowMut<T> for T where
T: ?Sized,
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T: ?Sized,
fn borrow_mut(&mut self) -> &mut T
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impl<T> Borrow<T> for T where
T: ?Sized,
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T: ?Sized,
impl<T> Any for T where
T: 'static + ?Sized,
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T: 'static + ?Sized,
impl<T> DeserializeOwned for T where
T: Deserialize<'de>,
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T: Deserialize<'de>,