ahda 0.1.1

// ahda: Pseudoalignment compression and conversion between formats.
//
// Copyright 2025 Tommi Mäklin [tommi@maklin.fi].
//
// Copyrights in this project are retained by contributors. No copyright assignment
// is required to contribute to this project.
//
// Except as otherwise noted (below and/or in individual files), this
// project is licensed under the Apache License, Version 2.0
// <LICENSE-APACHE> or <http://www.apache.org/licenses/LICENSE-2.0> or
// the MIT license, <LICENSE-MIT> or <http://opensource.org/licenses/MIT>,
// at your option.
//
use std::io::Write;

use crate::PseudoAln;

type E = Box<dyn std::error::Error>;

/// Format a single pseudoalignment in Bifrost format
///
/// Writes bytes containing the formatted line containing the contents of
/// `aln` to `conn`.
///
/// Terminates with a [BifrostPrinterError](crate::errors::BifrostPrinterError)
/// if the `query_id` field of [PseudoAln] or the `ones` field
/// of [PseudoAln] is None.
///
pub fn format_bifrost_line<W: Write>(
    aln: &PseudoAln,
    n_targets: usize,
    conn: &mut W,
) -> Result<(), E> {
    let separator: char = '\t';
    let mut formatted: String = String::new();

    if let Some(name) = &aln.query_name {
        let q_name = String::from_utf8(name.clone())?;
        formatted += &q_name;
    } else {
        return Err(Box::new(crate::errors::PseudoAlnQueryNameIsEmpty{}))
    };

    if let Some(ones) = &aln.ones {
        let mut ones_bits: Vec<bool> = vec![false; n_targets];
        ones.iter().for_each(|is_set_idx| ones_bits[*is_set_idx as usize] = true);

        ones_bits.iter().for_each(|is_set| {
            formatted += &separator.to_string();
            formatted += &(*is_set as u32).to_string();

        });
        formatted += "\n";
    } else {
        return Err(Box::new(crate::errors::PseudoAlnOnesIsEmpty{}))
    }

    conn.write_all(formatted.as_bytes())?;
    Ok(())
}

/// Format a Bifrost header line
///
/// Writes bytes containing the string `query_name` and a tab separated list of
/// all target sequence names.
///
pub fn format_bifrost_header<W: Write>(
    targets: &[Vec<u8>],
    conn: &mut W,
) -> Result<(), E> {
    let separator: char = '\t';
    let mut formatted: String = String::new();

    if targets.is_empty() {
        return Err(Box::new(crate::errors::BifrostPrinterError{}))
    }

    formatted += "query_name";

    targets.iter().for_each(|target| {
        formatted += &separator.to_string();
        formatted += &target.iter().map(|x| *x as char).collect::<String>();
    });
    formatted += "\n";

    conn.write_all(formatted.as_bytes())?;
    Ok(())
}

// Tests
#[cfg(test)]
mod tests {

    #[test]
    fn format_bifrost_line_1st_aligned() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_id: None, ones: Some(vec![0]), query_name: Some("ERR4035126.1262940".as_bytes().to_vec()) };

        let expected: Vec<u8> = b"ERR4035126.1262940\t1\t0\n".to_vec();

        let mut got: Vec<u8> = Vec::new();
        format_bifrost_line(&data, 2, &mut got).unwrap();

        assert_eq!(got, expected)
    }

    #[test]
    fn format_bifrost_line_2nd_aligned() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_id: None, ones: Some(vec![1]), query_name: Some("ERR4035126.1262940".as_bytes().to_vec()) };

        let expected: Vec<u8> = b"ERR4035126.1262940\t0\t1\n".to_vec();

        let mut got: Vec<u8> = Vec::new();
        format_bifrost_line(&data, 2, &mut got).unwrap();

        assert_eq!(got, expected)
    }

    #[test]
    fn format_bifrost_line_both_aligned() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_id: None, ones: Some(vec![0,1]), query_name: Some("ERR4035126.1262940".as_bytes().to_vec()) };

        let expected: Vec<u8> = b"ERR4035126.1262940\t1\t1\n".to_vec();

        let mut got: Vec<u8> = Vec::new();
        format_bifrost_line(&data, 2, &mut got).unwrap();

        assert_eq!(got, expected)
    }

    #[test]
    fn format_bifrost_line_no_alignments() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_id: None, ones: Some(vec![]), query_name: Some("ERR4035126.1262940".as_bytes().to_vec()) };

        let expected: Vec<u8> = b"ERR4035126.1262940\t0\t0\n".to_vec();

        let mut got: Vec<u8> = Vec::new();
        format_bifrost_line(&data, 2, &mut got).unwrap();

        assert_eq!(got, expected)
    }

    #[test]
    fn format_bifrost_header() {
        use super::format_bifrost_header;

        let data = vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec()];

        let expected: Vec<u8> = b"query_name\tchr.fasta\tplasmid.fasta\n".to_vec();

        let mut got: Vec<u8> = Vec::new();
        format_bifrost_header(&data, &mut got).unwrap();

        assert_eq!(got, expected)
    }

        #[test]
    fn header_error_if_no_targets() {
        use super::format_bifrost_header;

        let data: Vec<Vec<u8>> = Vec::new();

        let got = format_bifrost_header(&data, &mut Vec::new());

        assert!(!got.is_ok());
    }

    #[test]
    fn line_error_if_no_query_name() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_name: None, ones: Some(vec![0, 3, 7, 11]), query_id: None};

        let got = format_bifrost_line(&data, 2, &mut Vec::new());

        assert!(!got.is_ok());
    }

    #[test]
    fn line_error_if_no_ones() {
        use crate::PseudoAln;
        use super::format_bifrost_line;

        let data = PseudoAln{ones_names: None, query_name: Some("ERR4035126.1262954".as_bytes().to_vec()), query_id: Some(128), ones: None};

        let got = format_bifrost_line(&data, 2, &mut Vec::new());

        assert!(!got.is_ok());
    }
}