Struct lt_fm_index::LtFmIndexBuilder

pub struct LtFmIndexBuilder { /* private fields */ }

The safe and concise builder for LtFmIndex

Implementations

impl LtFmIndexBuilder

pub fn build(self, text: Vec<u8>) -> Result<LtFmIndex, BuildError>

impl LtFmIndexBuilder

pub fn new() -> Self

New builder with default option

pub fn text_type_is_inferred(self) -> Self

Make the TextType to be inferred (This is default option)

• What is the difference from the specification of TextType manually?
  • If the ACGTY is used as Text, TextType is inferred as TextType::NucleotideWithNoise (ACGT and Y as wildcard)
  • However, when you specify the TextType as TextType::NucleotideOnly, you can force the both T and Y to be treated as wildcard.
    • Locating AATTAA, AAYYAA, AA@@AA, AA**AA, … all gives the same result.

pub fn text_type_is_nucleotide_only(self) -> Self

Mark the TextType as TextType::NucleotideOnly

pub fn text_type_is_nucleotide_with_noise(self) -> Self

Mark the TextType as TextType::NucleotideWithNoise

pub fn text_type_is_amino_acid_only(self) -> Self

Mark the TextType as TextType::AminoAcidOnly

pub fn text_type_is_amino_acid_with_noise(self) -> Self

Mark the TextType as TextType::AminoAcidWithNoise

pub fn bwt_block_size_is_default(self) -> Self

Use the default BWT block size

pub fn bwt_block_size_is_64(self) -> Self

Use the 64-sized BWT block

pub fn bwt_block_size_is_128(self) -> Self

Use the 128-sized BWT block

pub fn set_suffix_array_sampling_ratio_to_default(self) -> Self

Use the default suffix array sampling ratio

pub fn set_suffix_array_sampling_ratio(
    self,
    sampling_ratio: u64
) -> Result<Self, BuildError>

Set the suffix array sampling ratio

pub fn set_lookup_table_kmer_size_to_default(self) -> Self

Use the default kmer size for lookup table

pub fn set_lookup_table_kmer_size(
    self,
    kmer_size: usize
) -> Result<Self, BuildError>

Set the size of kmer in lookup table

Trait Implementations

impl Clone for LtFmIndexBuilder

fn clone(&self) -> LtFmIndexBuilder

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for LtFmIndexBuilder

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

Formats the value using the given formatter.

impl Default for LtFmIndexBuilder

fn default() -> Self

Returns the “default value” for a type.