gfa 0.10.1

use bstr::ByteSlice;

use lazy_static::lazy_static;
use regex::bytes::Regex;

/// These type aliases are useful for configuring the parsers, as the
/// type of the optional field container must be given when creating a
/// GFAParser or GFA object.
pub type OptionalFields = Vec<OptField>;
pub type NoOptionalFields = ();

/// An optional field a la SAM. Identified by its tag, which is any
/// two characters matching [A-Za-z][A-Za-z0-9].
#[derive(Debug, Clone, PartialEq, PartialOrd)]
pub struct OptField {
    pub tag: [u8; 2],
    pub value: OptFieldVal,
}

/// enum for representing each of the SAM optional field types. The
/// `B` type, which denotes either an integer or float array, is split
/// in two variants, and they ignore the size modifiers in the spec,
/// instead always holding i64 or f32.
#[derive(Debug, Clone, PartialEq, PartialOrd)]
pub enum OptFieldVal {
    A(u8),
    Int(i64),
    Float(f32),
    Z(Vec<u8>),
    J(Vec<u8>),
    H(Vec<u32>),
    BInt(Vec<i64>),
    BFloat(Vec<f32>),
}

impl OptField {
    /// Panics if the provided tag doesn't match the regex
    /// [A-Za-z][A-Za-z0-9].
    pub fn tag(t: &[u8]) -> [u8; 2] {
        assert_eq!(t.len(), 2);
        assert!(t[0].is_ascii_alphabetic());
        assert!(t[1].is_ascii_alphanumeric());
        [t[0], t[1]]
    }

    /// Create a new OptField from a tag name and a value, panicking
    /// if the provided tag doesn't fulfill the requirements of
    /// OptField::tag().
    pub fn new(tag: &[u8], value: OptFieldVal) -> Self {
        let tag = OptField::tag(tag);
        OptField { tag, value }
    }

    /// Parses an optional field from a bytestring in the format
    /// <TAG>:<TYPE>:<VALUE>
    pub fn parse(input: &[u8]) -> Option<Self> {
        lazy_static! {
            static ref RE_TAG: Regex =
                Regex::new(r"(?-u)[A-Za-z][A-Za-z0-9]").unwrap();
            static ref RE_CHAR: Regex = Regex::new(r"(?-u)[!-~]").unwrap();
            static ref RE_INT: Regex = Regex::new(r"(?-u)[-+]?[0-9]+").unwrap();
            static ref RE_FLOAT: Regex =
                Regex::new(r"(?-u)[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?")
                    .unwrap();
            static ref RE_STRING: Regex = Regex::new(r"(?-u)[ !-~]+").unwrap();
            static ref RE_BYTES: Regex = Regex::new(r"(?-u)[0-9A-F]+").unwrap();
        }

        use OptFieldVal::*;

        let o_tag = input.get(0..=1)?;

        let o_type = input.get(3)?;

        let o_contents = input.get(5..)?;

        let o_val = match o_type {
            // char
            b'A' => RE_CHAR.find(o_contents).map(|s| s.as_bytes()[0]).map(A),
            // int
            b'i' => RE_INT
                .find(o_contents)
                .and_then(|s| s.as_bytes().to_str().ok())
                .and_then(|s| s.parse().ok())
                .map(Int),
            // float
            b'f' => RE_FLOAT
                .find(o_contents)
                .and_then(|s| s.as_bytes().to_str().ok())
                .and_then(|s| s.parse().ok())
                .map(Float),
            // string
            b'Z' => RE_STRING
                .find(o_contents)
                .map(|s| s.as_bytes().into())
                .map(Z),
            // JSON string
            b'J' => RE_STRING
                .find(o_contents)
                .map(|s| s.as_bytes().into())
                .map(J),
            // bytearray
            b'H' => RE_BYTES
                .find(o_contents)
                .and_then(|s| s.as_bytes().to_str().ok())
                .map(|s| s.chars().filter_map(|c| c.to_digit(16)))
                .map(|s| H(s.collect())),
            // float or int array
            b'B' => {
                let first = o_contents[0];
                let rest = o_contents[1..]
                    .split_str(b",")
                    .filter_map(|s| s.as_bytes().to_str().ok());
                if first == b'f' {
                    Some(BFloat(rest.filter_map(|s| s.parse().ok()).collect()))
                } else {
                    Some(BInt(rest.filter_map(|s| s.parse().ok()).collect()))
                }
            }
            _ => None,
        }?;

        Some(Self::new(o_tag, o_val))
    }
}

macro_rules! get_variant {
    ($from:ident, ref $var:path) => {
        if let $var(x) = &$from.value {
            Some(&x)
        } else {
            None
        }
    };
    ($from:ident, copy $var:path) => {
        if let $var(x) = $from.value {
            Some(x)
        } else {
            None
        }
    };
}

// Generate a function with name `$fn` for getting contents of variant
// `$var`, returning an Option containing `$out` or `&$out`. `$op` can
// be `ref` or `copy`: if it's `ref`, a reference to the value is
// returned, if it's `copy`, the value is dereferenced and an owned
// copy is returned.
macro_rules! get_opt_field_val {
    ($(#[$meta:meta])* $var:path, $op:tt $out:ty, $fn:ident) => {
        $(#[$meta])*
        pub fn $fn(&self) -> Option<$out> {
            get_variant!(self, $op $var)
        }
    };
}

impl OptField {
    get_opt_field_val!(
        /// If this field contains a single character, return it.
        OptFieldVal::A,      copy   u8,  get_char);

    get_opt_field_val!(
        /// If this field contains a single integer, return it.
        OptFieldVal::Int,    copy  i64,  get_int);

    get_opt_field_val!(
        /// If this field contains a single float, return it.
        OptFieldVal::Float,  copy  f32,  get_float);

    get_opt_field_val!(
        /// If this field contains a string, return a slice of it.
        OptFieldVal::Z,      ref &[ u8], get_string);

    get_opt_field_val!(
        /// If this field contains a JSON string, return a slice of it.
        OptFieldVal::J,      ref &[ u8], get_json);

    get_opt_field_val!(
        /// If this field contains a byte array, return a slice of it.
        OptFieldVal::H,      ref &[u32], get_byte_array);

    get_opt_field_val!(
        /// If this field contains an array of integers, return a slice of it.
        OptFieldVal::BInt,   ref &[i64], get_int_array);

    get_opt_field_val!(
        /// If this field contains an array of floats, return a slice of it.
        OptFieldVal::BFloat, ref &[f32], get_float_array);
}

/// The Display implementation produces spec-compliant strings in the
/// <TAG>:<TYPE>:<VALUE> format, and can be parsed back using
/// OptField::parse().
impl std::fmt::Display for OptField {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        use OptFieldVal::*;

        write!(f, "{}{}:", char::from(self.tag[0]), char::from(self.tag[1]))?;

        match &self.value {
            A(x) => write!(f, "A:{}", char::from(*x)),
            Int(x) => write!(f, "i:{}", x),
            Float(x) => write!(f, "f:{}", x),
            Z(x) => write!(f, "Z:{}", x.as_bstr()),
            J(x) => write!(f, "J:{}", x.as_bstr()),
            H(x) => {
                write!(f, "H:")?;
                for a in x {
                    write!(f, "{:x}", a)?
                }
                Ok(())
            }
            BInt(x) => {
                write!(f, "B:I{}", x[0])?;
                for a in x[1..].iter() {
                    write!(f, ",{}", a)?
                }
                Ok(())
            }
            BFloat(x) => {
                write!(f, "B:F{}", x[0])?;
                for a in x[1..].iter() {
                    write!(f, ",{}", a)?
                }
                Ok(())
            }
        }
    }
}

/// The OptFields trait describes how to parse, store, and query
/// optional fields. Each of the GFA line types and the GFA struct
/// itself are generic over the optional fields, so the choice of
/// OptFields implementor can impact memory usage, which optional
/// fields are parsed, and possibly more in the future
pub trait OptFields: Sized + Default + Clone {
    /// Return the optional field with the given tag, if it exists.
    fn get_field(&self, tag: &[u8]) -> Option<&OptField>;

    /// Return a slice over all optional fields. NB: This may be
    /// replaced by an iterator or something else in the future
    fn fields(&self) -> &[OptField];

    /// Given an iterator over bytestrings, each expected to hold one
    /// optional field (in the <TAG>:<TYPE>:<VALUE> format), parse
    /// them as optional fields to create a collection. Returns `Self`
    /// rather than `Option<Self>` for now, but this may be changed to
    /// become fallible in the future.
    fn parse<T>(input: T) -> Self
    where
        T: IntoIterator,
        T::Item: AsRef<[u8]>;
}

/// This implementation is useful for performance if we don't actually
/// need any optional fields. () takes up zero space, and all
/// methods are no-ops.
impl OptFields for () {
    fn get_field(&self, _: &[u8]) -> Option<&OptField> {
        None
    }

    fn fields(&self) -> &[OptField] {
        &[]
    }

    fn parse<T>(_input: T) -> Self
    where
        T: IntoIterator,
        T::Item: AsRef<[u8]>,
    {
    }
}

/// Stores all the optional fields in a vector. `get_field` simply
/// uses std::iter::Iterator::find(), but as there are only a
/// relatively small number of optional fields in practice, it should
/// be efficient enough.
impl OptFields for Vec<OptField> {
    fn get_field(&self, tag: &[u8]) -> Option<&OptField> {
        self.iter().find(|o| o.tag == tag)
    }

    fn fields(&self) -> &[OptField] {
        self.as_slice()
    }

    fn parse<T>(input: T) -> Self
    where
        T: IntoIterator,
        T::Item: AsRef<[u8]>,
    {
        input
            .into_iter()
            .filter_map(|f| OptField::parse(f.as_ref()))
            .collect()
    }
}