zoe 0.0.30

use crate::data::array_types::{self, make_lowercase, position};
use std::ops::{Index, RangeInclusive};

/// A mapping from bytes to other bytes.
///
/// This struct has many potential use-cases:
///
/// 1. Representing a mapping from residues to other residues, such as for
///    switching alphabets.
/// 2. Mapping residues while also filtering them, by mapping invalid residues
///    to 0.
/// 3. Mapping residues to integers, as may be necessary for indexing or
///    encoding. If each integer has a single canonical byte that it represents,
///    consider using [`ByteIndexMap`] which also allows for converting back to
///    regular sequences again.
///
/// To build a custom map, start with a complete mapping such as
/// [`ByteMap::identity`] or [`ByteMap::all`], then apply cumulative overrides
/// with methods such as [`ByteMap::preserve`], [`ByteMap::map`], or
/// [`ByteMap::map_to_one`] (or the corresponding methods for ranges).
#[repr(transparent)]
#[derive(Debug, PartialEq, Eq, Clone, Hash)]
pub struct ByteMap([u8; 256]);

impl Default for ByteMap {
    #[inline]
    fn default() -> Self {
        Self([0; 256])
    }
}

impl ByteMap {
    /// Creates a new custom [`ByteMap`] from an existing mapping.
    #[inline]
    #[must_use]
    pub const fn new(mapping: [u8; 256]) -> Self {
        Self(mapping)
    }

    /// Creates a [`ByteMap`] that maps every byte to the same destination byte.
    #[inline]
    #[must_use]
    pub const fn all(dest: u8) -> Self {
        Self([dest; 256])
    }

    /// Creates a [`ByteMap`] that maps each byte to itself.
    #[must_use]
    pub const fn identity() -> Self {
        let mut mapping = [0; 256];
        let mut i = 0u8;
        loop {
            mapping[i as usize] = i;
            if i == u8::MAX {
                return Self(mapping);
            }
            i += 1;
        }
    }

    /// Returns the inner array of a [`ByteMap`].
    #[inline]
    #[must_use]
    pub const fn into_inner(self) -> [u8; 256] {
        self.0
    }

    /// Preserves the identity of the given bytes in the map.
    ///
    /// Any later calls can still override these mappings.
    #[must_use]
    pub const fn preserve<const S: usize>(self, bytes: &[u8; S]) -> Self {
        self.map(bytes, bytes)
    }

    /// Maps many source bytes to one destination byte.
    #[must_use]
    pub const fn map_to_one<const S: usize>(mut self, from: &[u8; S], to: u8) -> Self {
        Self::assert_unique(from);

        let mut i = 0;
        while i < S {
            self.set_byte(from[i], to);
            i += 1;
        }
        self
    }

    /// Maps source bytes to destination bytes pairwise.
    #[must_use]
    pub const fn map<const S: usize>(mut self, from: &[u8; S], to: &[u8; S]) -> Self {
        Self::assert_unique(from);

        let mut i = 0;
        while i < S {
            self.set_byte(from[i], to[i]);
            i += 1;
        }
        self
    }

    /// Preserves the identity of all bytes in the given range within the map.
    ///
    /// Any later calls can still override these mappings.
    #[must_use]
    pub const fn preserve_range(self, range: RangeInclusive<u8>) -> Self {
        // TODO: Fix this when clone in const context becomes available, or
        // ranges implement Copy
        self.map_range(*range.start()..=*range.end(), range)
    }

    /// Maps all bytes in the given range to one destination byte.
    #[must_use]
    #[allow(clippy::cast_possible_truncation)]
    pub const fn map_range_to_one(mut self, from: RangeInclusive<u8>, to: u8) -> Self {
        // Convert from inclusive range to exclusive range, bumping to usize in
        // case of overflow at end
        let from = *from.start() as usize..*from.end() as usize + 1;

        let mut src = from.start;
        while src < from.end {
            // Validity: this will not truncate since src is strictly less than
            // the original from.end()+1, which means it is at most from.end(),
            // which is a `u8`.
            self.set_byte(src as u8, to);
            src += 1;
        }
        self
    }

    /// Maps all bytes in the first range to the corresponding bytes in the
    /// second range.
    ///
    /// ## Panics
    ///
    /// The ranges must be the same length.
    #[must_use]
    #[allow(clippy::cast_possible_truncation)]
    pub const fn map_range(mut self, from: RangeInclusive<u8>, to: RangeInclusive<u8>) -> Self {
        // Saturation implies an empty range. If both ranges are empty, the
        // while loop does nothing.
        assert!(
            from.end().saturating_sub(*from.start()) == to.end().saturating_sub(*to.start()),
            "Attempted to map to a range of a different length!"
        );

        // Convert from inclusive range to exclusive range, bumping to usize in
        // case of overflow at end
        let from = *from.start() as usize..*from.end() as usize + 1;

        let mut src = from.start;
        while src < from.end {
            let dest = *to.start() as usize + src - from.start;

            // Validity: this will not truncate since src is strictly less than
            // the original from.end()+1, which means it is at most from.end(),
            // which is a `u8`. The cast for dest will not truncate since the
            // ranges are the same length.
            self.set_byte(src as u8, dest as u8);
            src += 1;
        }

        self
    }

    /// Maps the provided bytes to ascending indexes.
    ///
    /// This maps `bytes[0]` to `0`, `bytes[1]` to `1`, and so on.
    ///
    /// ## Panics
    ///
    /// `bytes` must contain at most 256 unique values.
    #[allow(clippy::cast_possible_truncation)]
    #[must_use]
    pub(crate) const fn indexing<const S: usize>(mut self, bytes: &[u8; S]) -> Self {
        assert!(S <= 256, "Cannot index more than 256 distinct bytes!");
        Self::assert_unique(bytes);

        let mut i = 0;
        while i < S {
            self.set_byte(bytes[i], i as u8);
            i += 1;
        }
        self
    }

    /// Sets the destination byte for a source byte.
    #[inline]
    pub(crate) const fn set_byte(&mut self, src: u8, dest: u8) {
        self.0[src as usize] = dest;
    }

    /// Ensures a byte slice does not contain duplicates.
    #[inline]
    const fn assert_unique<const S: usize>(bytes: &[u8; S]) {
        assert!(
            array_types::is_unique(bytes),
            "Attempted to map a byte multiple times in the same call!"
        );
    }

    /// Copies the value to which `b` maps.
    #[inline]
    #[must_use]
    const fn copy_mapped_val(&self, b: u8) -> u8 {
        self.0[b as usize]
    }
}

/// A mapping from bytes to indices.
///
/// For example, this could be a map from DNA bases to profile indices, such as
/// [`DNA_PROFILE_MAP`].
///
/// ## Parameters
///
/// `S`: The number of unique indices in the output of the mapping (such as 5
/// for DNA including *N*)
///
/// [`DNA_PROFILE_MAP`]: super::DNA_PROFILE_MAP
#[derive(Debug, PartialEq, Eq, Clone, Hash)]
pub struct ByteIndexMap<const S: usize> {
    index_map: ByteMap,
    byte_keys: [u8; S],
}

impl<const S: usize> ByteIndexMap<S> {
    /// Creates a new [`ByteIndexMap`] struct to represent a mapping between
    /// bytes and indices.
    ///
    /// For example, this could be a map from DNA bases to profile indices. Any
    /// byte that is not specified in `byte_keys` is mapped to the same thing as
    /// `catch_all`.
    ///
    /// ## Panics
    ///
    /// No duplicates can be present in `byte_keys`. `catch_all` must be present
    /// in `byte_keys`.
    #[allow(clippy::cast_possible_truncation)]
    #[must_use]
    pub const fn new(byte_keys: [u8; S], catch_all: u8) -> Self {
        let catch_all_index =
            position(&byte_keys, catch_all).expect("The catch_all must be present in the byte_keys.") as u8;

        Self {
            // `indexing` validates that `byte_keys` are unique.
            index_map: ByteMap::all(catch_all_index).indexing(&byte_keys),
            byte_keys,
        }
    }

    /// Creates a new [`ByteIndexMap`] struct to represent a mapping between
    /// bytes and indices, ignoring case.
    ///
    /// For example, this could be a map from DNA bases to profile indices. Both
    /// `byte_keys` and `catch_all` ignore case.
    ///
    /// ## Panics
    ///
    /// No duplicates can be present in `byte_keys`. `catch_all` must be present
    /// in `byte_keys`.
    #[allow(clippy::cast_possible_truncation)]
    #[must_use]
    pub const fn new_ignoring_case(mut byte_keys: [u8; S], catch_all: u8) -> Self {
        byte_keys = array_types::make_uppercase(&byte_keys);

        let catch_all_index = position(&byte_keys, catch_all.to_ascii_uppercase())
            .expect("The catch_all must be present in the byte_keys.") as u8;

        Self {
            // `indexing_ignore_case` validates that `byte_keys` are unique after
            // lowercasing them.
            index_map: ByteMap::all(catch_all_index)
                .indexing(&byte_keys)
                .indexing(&make_lowercase(&byte_keys)),
            byte_keys,
        }
    }

    /// Changes the [`ByteIndexMap`] so that `new_key` maps to the same thing as
    /// `previous_key`.
    #[inline]
    #[must_use]
    pub const fn add_synonym(mut self, new_key: u8, previous_key: u8) -> Self {
        self.index_map.set_byte(new_key, self.index_map.copy_mapped_val(previous_key));
        self
    }

    /// Sets the index for a byte, ignoring case.
    #[inline]
    pub(crate) const fn set_byte_ignoring_case(&mut self, byte: u8, index: u8) {
        self.index_map.set_byte(byte.to_ascii_lowercase(), index);
        self.index_map.set_byte(byte.to_ascii_uppercase(), index);
    }

    /// Adds source bytes as synonyms for the canonical byte, ignoring case.
    #[inline]
    #[must_use]
    pub const fn add_synonym_ignore_case(mut self, new_key: u8, previous_key: u8) -> Self {
        self.set_byte_ignoring_case(new_key, self.index_map.copy_mapped_val(previous_key));
        self
    }

    /// Gets the number of unique indices in the output of this mapping.
    #[inline]
    #[must_use]
    #[allow(clippy::len_without_is_empty)]
    pub const fn len(&self) -> usize {
        S
    }

    /// Gets the byte keys for this mapping.
    #[inline]
    #[must_use]
    pub const fn byte_keys(&self) -> &[u8; S] {
        &self.byte_keys
    }

    /// Converts a byte `b` into an index.
    #[inline]
    #[must_use]
    pub const fn to_index(&self, b: u8) -> usize {
        self.index_map.0[b as usize] as usize
    }

    /// Converts an index back into the corresponding byte.
    #[inline]
    #[must_use]
    pub const fn to_byte(&self, index: usize) -> u8 {
        self.byte_keys[index]
    }

    /// Returns whether a byte `b` is in `byte_keys`.
    #[inline]
    #[must_use]
    pub const fn in_byte_keys(&self, b: u8) -> bool {
        b == self.to_byte(self.to_index(b))
    }

    /// Returns the [`ByteIndexMap`] as a regular [`ByteMap`], which is
    /// compatible with [`Recode`].
    ///
    /// [`Recode`]: crate::data::Recode
    #[inline]
    #[must_use]
    pub const fn as_map(&self) -> &ByteMap {
        &self.index_map
    }
}

impl Index<u8> for ByteMap {
    type Output = u8;

    #[inline]
    fn index(&self, index: u8) -> &u8 {
        &self.0[index as usize]
    }
}

impl<const S: usize> Index<u8> for ByteIndexMap<S> {
    type Output = u8;

    #[inline]
    fn index(&self, index: u8) -> &u8 {
        &self.index_map[index]
    }
}