sigalign-core 0.2.1

A core crate for sigalign
Documentation 
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pub mod regulators;

/// `BufferedPatternLocator` represents types that can perform pattern searches within a buffered sequence.
///
/// This trait serves two main purposes:
///   - It provides pattern locations for algorithms.
///   - It can help the algorithm can be defined without knowing the exact type of the `Reference` struct.
pub trait BufferedPatternLocator {
    type Buffer: SequenceBuffer;

    fn locate(&self, pattern: &[u8], sorted_target_indices: &[u32]) -> Vec<PatternLocation>;
    fn fill_buffer(&self, target_index: u32, buffer: &mut Self::Buffer);
}

pub trait SequenceBuffer {
    fn buffered_sequence(&self) -> &[u8];
}

/// `PatternLocation` holds the index of a pattern within a target.
/// 
/// The positions within `PatternLocation` should be sorted in ascending order. In general,
/// these positions are automatically sorted when searching for an index within a target.
/// **Note that the algorithm does not perform reordering**.
/// 
/// Each position's value is restricted to the bounds of a `u32`, limiting the range of each position.
#[derive(Debug)]
pub struct PatternLocation {
    pub target_index: u32,
    pub sorted_positions: Vec<u32>,
}