Struct RangeSearch 

pub struct RangeSearch<'a, Q: ?Sized> { /* private fields */ }

A subsequence along with its starting index. This is used for restricting the search range when performing a search. See Restricting the search range for more details.

It is compatible with:

• Performing string search via the ByteSubstring trait
• Searching for k-mers using methods similar to those in FindKmers
• Searching for amino acids in a nucleotides sequence similar to methods in Translate. This requires the original type to implement Translate also

Note

All search methods called on a RangeSearch struct return indices with respect to the original sequence, not the subsequence.

Parameters

Q tracks the type of the original sequence type. This controls whether find_next_aa and find_next_aa_in_frame are available.

Implementations

impl<Q> RangeSearch<'_, Q>

where Q: Translate,

pub fn find_next_aa(self, aa: u8) -> Option<usize>

Slides base by base over the sequence until the next translated aa is found and returns that index (or None otherwise).

pub fn find_next_aa_in_frame(self, aa: u8) -> Option<usize>

Slides codon by codon over the sequence (reading frame starting from 0 in the full sequence) until the next translated aa is found and returns that index (or None otherwise).

This is different than calling Translate::find_next_aa_in_frame on a slice, since it uses the reading frame of the full sequence, irrelevant of the starting position of the search.

impl<'a, Q: ?Sized> RangeSearch<'a, Q>

pub fn position<P>(&self, predicate: P) -> Option<usize>

where P: FnMut(u8) -> bool,

Takes a closure and returns the index of the first byte found within the sequence that satisfies the closure. Wraps Iterator::position.

pub fn rposition<P>(&self, predicate: P) -> Option<usize>

where P: FnMut(u8) -> bool,

Takes a closure and returns the index of the last byte found within the sequence that satisfies the closure. Wraps Iterator::rposition.

pub fn find_kmers<const MAX_LEN: usize, T>( self, kmers: &T, ) -> Option<Range<usize>>

where T: FindKmersInSeq<MAX_LEN>,

Returns the indices of the leftmost occurrence of any of the k-mers in the passed collection.

If no occurrence is found, then None is returned. To find all matches rather than just the first, use find_all_kmers. A similar unrestricted version of this method exists in FindKmers.

pub fn find_kmers_rev<const MAX_LEN: usize, T>( self, kmers: &T, ) -> Option<Range<usize>>

where T: FindKmersInSeq<MAX_LEN>,

Returns the indices of the rightmost occurrence of any of the k-mers in the passed collection.

If no occurrence is found, then None is returned. To find all matches rather than just the last, use find_all_kmers. A similar unrestricted version of this method exists in FindKmers.

pub fn find_all_kmers<const MAX_LEN: usize, T>( self, kmers: &'a T, ) -> impl Iterator<Item = Range<usize>> + 'a

where Q: 'a, T: FindKmersInSeq<MAX_LEN>,

Returns an iterator over the indices of all matches between the k-mers in the sequence and those in the passed collection.

Consider using find_kmers if only a single match is needed. A similar unrestricted version of this method exists in FindKmers.

pub fn find_all_kmers_rev<const MAX_LEN: usize, T>( self, kmers: &'a T, ) -> impl Iterator<Item = Range<usize>> + 'a

where Q: 'a, T: FindKmersInSeq<MAX_LEN>,

Returns an iterator over the indices of all matches between the k-mers in the sequence and those in the passed collection, in reverse order.

Consider using find_kmers_rev if only a single match is needed. A similar unrestricted version of this method exists in FindKmers.

Trait Implementations

impl<Q: ?Sized> ByteSubstring for RangeSearch<'_, Q>

fn contains_substring(&self, needle: impl AsRef<[u8]>) -> bool

Returns true is the substring is found and false if not. Searches in the forward direction.

fn find_substring(&self, needle: impl AsRef<[u8]>) -> Option<Range<usize>>

Returns the substring’s index range if found or None if not. Searches in the forward direction.

fn find_fuzzy_substring<const DIFFERENCES_ALLOWED: usize>( &self, needle: impl AsRef<[u8]>, ) -> Option<Range<usize>>

Finds the needle in the haystack using inexact matching up to the DIFFERENCES_ALLOWED.

fn find_byte(&self, byte: u8) -> Option<usize>

Finds the first occurrence of the byte in the haystack.

fn find_repeating_byte(&self, needle: u8, size: usize) -> Option<Range<usize>>

Find contiguous, repeating byte characters in a byte slice. See find_k_repeating for more details.

fn find_repeating_at_start( &self, needle: u8, min_reps: usize, ) -> Option<Range<usize>>

Checks if the slice begins with some minimal number of consecutive byte repetitions and returns the largest contiguous range if so.

fn find_repeating_at_end( &self, needle: u8, min_reps: usize, ) -> Option<Range<usize>>

Checks if the slice ends with some minimal number of consecutive byte repetitions and returns the largest contiguous range if so.