Struct Dictionary 

pub struct Dictionary { /* private fields */ }

The main dictionary structure

Note: Serialization support is limited due to underlying types. Use custom save/load methods instead.

Implementations

impl Dictionary

pub fn new( spss: SpectrumPreservingStringSet, control_map: MinimizersControlMap, index: SparseAndSkewIndex, k: usize, m: usize, canonical: bool, ) -> Self

Create a new dictionary from components

pub fn lookup<const K: usize>(&self, kmer: &Kmer<K>) -> u64

where Kmer<K>: KmerBits,

Look up a k-mer’s position in the dictionary.

pub fn query<const K: usize>(&self, kmer: &Kmer<K>) -> LookupResult

where Kmer<K>: KmerBits,

Query a k-mer and return a full LookupResult.

pub fn query_from_str<const K: usize>(&self, kmer_str: &str) -> LookupResult

where Kmer<K>: KmerBits,

Query a k-mer given as a DNA string.

pub fn debug_has_control_map_mphf(&self) -> bool

Debug: check if control map MPHF is present

pub fn debug_control_map_lookup(&self, minimizer: u64) -> bool

Debug: check if a minimizer exists in the control map

pub fn debug_extract_minimizer<const K: usize>( &self, kmer: &Kmer<K>, ) -> MinimizerInfo

where Kmer<K>: KmerBits,

Debug: extract minimizer info for a k-mer

pub fn debug_bucket_info<const K: usize>( &self, kmer: &Kmer<K>, ) -> Option<(u64, u64, u64)>

where Kmer<K>: KmerBits,

Debug: get bucket and locate info for a k-mer

pub fn lookup_with_orientation<const K: usize>( &self, kmer: &Kmer<K>, ) -> (u64, i8)

where Kmer<K>: KmerBits,

Look up a k-mer and return position + orientation

pub fn access<const K: usize>(&self, kmer: &Kmer<K>) -> bool

where Kmer<K>: KmerBits,

Check if a k-mer exists in the dictionary

pub fn create_streaming_query<const K: usize>( &self, ) -> StreamingQueryEngine<'_, K>

where Kmer<K>: KmerBits,

Create a streaming query engine for this dictionary

pub fn k(&self) -> usize

Get the k-mer size

pub fn m(&self) -> usize

Get the minimizer size

pub fn canonical(&self) -> bool

Check if canonical mode is enabled

pub fn spss(&self) -> &SpectrumPreservingStringSet

Get a reference to the underlying SPSS

pub fn control_map_ref(&self) -> &MinimizersControlMap

Get a reference to the control map

pub fn index_ref(&self) -> &SparseAndSkewIndex

Get a reference to the sparse and skew index

pub fn num_strings(&self) -> u64

Get the number of strings in the SPSS

pub fn string_length(&self, string_id: u64) -> usize

Get the length of a specific string in bases

pub fn locate_string(&self, absolute_pos: u64) -> Option<(u64, u64)>

Locate which string contains a given absolute position.

pub fn access_kmer<const K: usize>(&self, string_id: u64, pos: usize) -> Kmer<K>

where Kmer<K>: KmerBits,

Access a k-mer at a given position within a string

pub fn kmer_at_pos<const K: usize>(&self, absolute_base_pos: usize) -> Kmer<K>

where Kmer<K>: KmerBits,

Decode the k-mer at an absolute base position in the SPSS.

pub fn num_minimizers(&self) -> u64

Get the number of unique minimizers

pub fn num_bits(&self) -> u64

Get total memory usage in bits

pub fn print_space_breakdown(&self)

Print a detailed space breakdown of the index

pub fn save<P: AsRef<Path>>(&self, path: P) -> SerializationResult<()>

Serialize the dictionary to files

pub fn load<P: AsRef<Path>>(path: P) -> SerializationResult<Self>

Deserialize a dictionary from files