Struct ClosestSubstring 

pub struct ClosestSubstring { /* private fields */ }

The Closest Substring problem.

Given a finite alphabet Sigma = {0, ..., q - 1}, n input strings s_1, ..., s_n over Sigma (not necessarily of equal length), and a window length ell with ell <= |s_i| for every i, find a center c in Sigma^ell and per-string window start positions p_i in {0, ..., W_i - 1} (where W_i = |s_i| - ell + 1) minimizing

max_{1 <= i <= n} d_H(c, s_i[p_i .. p_i + ell)),

where d_H is the Hamming distance. Every choice in the discrete cube is syntactically feasible.

Implementations

impl ClosestSubstring

pub fn new( alphabet_size: usize, strings: Vec<Vec<usize>>, substring_length: usize, ) -> Result<Self, ConstructionError>

Create a new ClosestSubstring instance.

pub fn alphabet_size(&self) -> usize

Returns the alphabet size q.

pub fn strings(&self) -> &[Vec<usize>]

Returns the input strings.

pub fn num_strings(&self) -> usize

Returns the number of input strings n.

pub fn substring_length(&self) -> usize

Returns the common window length ell.

pub fn total_length(&self) -> usize

Returns the sum of input string lengths.

pub fn total_num_windows(&self) -> usize

Returns sum_i W_i, where W_i = |s_i| - substring_length + 1.

pub fn num_window_choice_product(&self) -> usize

Returns prod_i W_i, the number of distinct window-selection tuples.

Trait Implementations

impl BruteForceProblem for ClosestSubstring

fn dimensions(&self) -> Vec<usize>

Cardinality of each coordinate in the brute-force search space.

fn num_variables(&self) -> usize

Number of coordinates in the brute-force search space.

impl Clone for ClosestSubstring

fn clone(&self) -> ClosestSubstring

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ClosestSubstring

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

Formats the value using the given formatter.

impl DeclaredVariant for ClosestSubstring

impl<'de> Deserialize<'de> for ClosestSubstring

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

where D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Problem for ClosestSubstring

const NAME: &'static str = "ClosestSubstring"

Base name of this problem type (e.g., “MaximumIndependentSet”).

type Solution = Vec<usize>

Mathematical witness type for this problem.

type Value = Min<i64>

The evaluation value type.

fn parameter_names() -> &'static [&'static str]

Canonical parameter names for this problem model.

fn parameters(&self) -> ProblemParameters

Measure the complete canonical parameters of this concrete instance.

fn variant() -> Vec<(&'static str, &'static str)>

Returns variant attributes derived from type parameters.

fn evaluate(&self, config: &Self::Solution) -> Result<Min<i64>, EvaluationError>

Evaluate the problem on a solution.

fn problem_type() -> ProblemType

Look up this problem’s catalog entry.

impl ReduceTo<ILP<i64>> for ClosestSubstring

type Result = ReductionClosestSubstringToILP

The reduction result type.

fn reduce_to(&self) -> Result<Self::Result, ReductionError>

Reduce this problem to the target problem type.

fn target_construction(error: ConstructionError) -> ReductionError

where Self: Sized,

Attach this reduction edge to a target-construction failure.

fn exact_i64( value: usize, operation: impl Into<String>, ) -> Result<i64, ReductionError>

where Self: Sized,

Convert a structural count used by the target’s exact integer algebra.

impl Serialize for ClosestSubstring

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.