Struct bio::data_structures::fmindex::FMIndex

pub struct FMIndex<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> { /* private fields */ }

The Fast Index in Minute space (FM-Index, Ferragina and Manzini, 2000) for finding suffix array intervals matching a given pattern.

Implementations

impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndex<DBWT, DLess, DOcc>

pub fn new(bwt: DBWT, less: DLess, occ: DOcc) -> Self

Construct a new instance of the FM index.

Arguments

• sa - the suffix array (or sample)
• bwt - the BWT
• k - the sampling rate of the occ array: every k-th entry will be stored (higher k means less memory usage, but worse performance)
• alphabet - the alphabet of the underlying text, omitting the sentinel

Trait Implementations

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>,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
    __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndexable for FMIndex<DBWT, DLess, DOcc>

fn bwt(&self) -> &BWT

Provide a reference to the underlying BWT.

fn occ(&self, r: usize, a: u8) -> usize

Get occurrence count of symbol a in BWT[..r+1].

fn less(&self, a: u8) -> usize

Also known as

fn backward_search<'b, P: Iterator<Item = &'b u8> + DoubleEndedIterator>(
    &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).

impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> From<FMIndex<DBWT, DLess, DOcc>> for 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$.

impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> Serialize for FMIndex<DBWT, DLess, DOcc>where
    DBWT: Serialize,
    DLess: Serialize,
    DOcc: Serialize,

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>where
    __S: Serializer,

Serialize this value into the given Serde serializer.