Struct PrefixLookupTable

pub struct PrefixLookupTable {
    pub ranges: Vec<Range<usize>>,
    pub prefix_length: usize,
}

A table storing the SBWT intervals of all 4^p possible p-mers.

Fields

ranges: Vec<Range<usize>>

ranges[i] is the interval of the p-mer with colexicographic rank i in the sorted list of all possible p-mers. If the p-mer does not exist in the SBWT, the range is [0..0).

prefix_length: usize

Prefix length p.

Implementations

impl PrefixLookupTable

pub fn new_empty(n_sets_in_sbwt: usize) -> PrefixLookupTable

Create a new prefix lookup table containing only the interval of the empty string.

pub fn new<SS: SubsetSeq>( sbwt: &SbwtIndex<SS>, prefix_length: usize, ) -> PrefixLookupTable

Create a new prefix lookup table by searching all DNA strings of length prefix_length in the given sbwt.

pub fn lookup(&self, prefix: &[u8]) -> Range<usize>

Look up the colex interval of the prefix.

pub fn serialize<W: Write>(&self, out: &mut W) -> Result<usize>

Write the lookup table to the given writer. The lookup table can be then later loaded with PrefixLookupTable::load. Returns number of bytes written.

pub fn load<R: Read>(input: &mut R) -> Result<Self>

Loads a a prefix lookup table that was previosly serialized with PrefixLookupTable::serialize.

Trait Implementations

impl Clone for PrefixLookupTable

fn clone(&self) -> PrefixLookupTable

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for PrefixLookupTable

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl PartialEq for PrefixLookupTable

fn eq(&self, other: &PrefixLookupTable) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for PrefixLookupTable

impl StructuralPartialEq for PrefixLookupTable