Struct sourmash::sketch::minhash::KmerMinHash

pub struct KmerMinHash { /* private fields */ }

Implementations

impl KmerMinHash

pub fn builder() -> KmerMinHashBuilder<((), (), (), (), (), (), (), ())>

Create a builder for building KmerMinHash. On the builder, call .num(...), .ksize(...), .hash_function(...)(optional), .seed(...)(optional), .max_hash(...)(optional), .mins(...)(optional), .abunds(...)(optional), .md5sum(...)(optional) to set the values of the fields. Finally, call .build() to create the instance of KmerMinHash.

impl KmerMinHash

pub fn new( scaled: u64, ksize: u32, hash_function: HashFunctions, seed: u64, track_abundance: bool, num: u32, ) -> KmerMinHash

pub fn num(&self) -> u32

pub fn is_protein(&self) -> bool

pub fn max_hash(&self) -> u64

pub fn scaled(&self) -> u64

pub fn clear(&mut self)

pub fn is_empty(&self) -> bool

pub fn set_hash_function(&mut self, h: HashFunctions) -> Result<(), Error>

pub fn track_abundance(&self) -> bool

pub fn enable_abundance(&mut self) -> Result<(), Error>

pub fn disable_abundance(&mut self)

pub fn md5sum(&self) -> String

pub fn add_hash(&mut self, hash: u64)

pub fn add_hash_with_abundance(&mut self, hash: u64, abundance: u64)

pub fn set_hash_with_abundance(&mut self, hash: u64, abundance: u64)

pub fn add_word(&mut self, word: &[u8])

pub fn remove_hash(&mut self, hash: u64)

pub fn remove_from(&mut self, other: &KmerMinHash) -> Result<(), Error>

pub fn remove_many<T: IntoIterator<Item = u64>>( &mut self, hashes: T, ) -> Result<(), Error>

pub fn merge(&mut self, other: &KmerMinHash) -> Result<(), Error>

pub fn add_from(&mut self, other: &KmerMinHash) -> Result<(), Error>

pub fn add_many(&mut self, hashes: &[u64]) -> Result<(), Error>

pub fn add_many_with_abund( &mut self, hashes: &[(u64, u64)], ) -> Result<(), Error>

pub fn count_common( &self, other: &KmerMinHash, downsample: bool, ) -> Result<u64, Error>

pub fn intersection( &self, other: &KmerMinHash, ) -> Result<(Vec<u64>, u64), Error>

pub fn intersection_size( &self, other: &KmerMinHash, ) -> Result<(u64, u64), Error>

pub fn jaccard(&self, other: &KmerMinHash) -> Result<f64, Error>

pub fn angular_similarity(&self, other: &KmerMinHash) -> Result<f64, Error>

pub fn similarity( &self, other: &KmerMinHash, ignore_abundance: bool, downsample: bool, ) -> Result<f64, Error>

pub fn dayhoff(&self) -> bool

pub fn hp(&self) -> bool

pub fn mins(&self) -> Vec<u64>

pub fn iter_mins(&self) -> impl Iterator<Item = &u64>

pub fn abunds(&self) -> Option<Vec<u64>>

pub fn downsample_max_hash(&self, max_hash: u64) -> Result<KmerMinHash, Error>

pub fn sum_abunds(&self) -> u64

pub fn to_vec_abunds(&self) -> Vec<(u64, u64)>

pub fn as_hll(&self) -> HyperLogLog

pub fn n_unique_kmers(&self) -> u64

pub fn downsample_scaled(&self, scaled: u64) -> Result<KmerMinHash, Error>

pub fn inflate(&mut self, abunds_from: &KmerMinHash) -> Result<(), Error>

pub fn inflated_abundances( &self, abunds_from: &KmerMinHash, ) -> Result<(Vec<u64>, u64), Error>

Trait Implementations

impl Clone for KmerMinHash

fn clone(&self) -> Self

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for KmerMinHash

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

Formats the value using the given formatter.

impl Default for KmerMinHash

fn default() -> KmerMinHash

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for KmerMinHash

fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>

where D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl From<&KmerMinHashBTree> for KmerMinHash

fn from(other: &KmerMinHashBTree) -> KmerMinHash

Converts to this type from the input type.

impl From<KmerMinHash> for KmerMinHashBTree

fn from(other: KmerMinHash) -> KmerMinHashBTree

Converts to this type from the input type.

impl From<KmerMinHashBTree> for KmerMinHash

fn from(other: KmerMinHashBTree) -> KmerMinHash

Converts to this type from the input type.

impl PartialEq for KmerMinHash

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

This method tests for self and other values to be equal, and is used by ==.

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

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

impl Serialize for KmerMinHash

fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>

where S: Serializer,

Serialize this value into the given Serde serializer.

impl SigsTrait for KmerMinHash

fn size(&self) -> usize

fn to_vec(&self) -> Vec<u64>

fn ksize(&self) -> usize

fn seed(&self) -> u64

fn hash_function(&self) -> HashFunctions

fn add_hash(&mut self, hash: u64)

fn check_compatible(&self, other: &KmerMinHash) -> Result<(), Error>

fn add_sequence(&mut self, seq: &[u8], force: bool) -> Result<(), Error>

fn add_protein(&mut self, seq: &[u8]) -> Result<(), Error>

impl Update<HyperLogLog> for KmerMinHash

fn update(&self, other: &mut HyperLogLog) -> Result<(), Error>

impl Update<Nodegraph> for KmerMinHash

fn update(&self, other: &mut Nodegraph) -> Result<(), Error>