termal-alignment 0.2.0

// SPDX-License-Identifier: MIT
// Copyright (c) 2025-2026 Thomas Junier

use std::fs::File;
use std::io::{BufRead, BufReader};
use std::path::Path;

use crate::error::AlignmentError;
use crate::seq::file::SeqFile;
use crate::seq::record::SeqRecord;

pub fn read_stockholm_file<P: AsRef<Path>>(path: P) -> Result<SeqFile, AlignmentError> {
    let file = File::open(path)?;
    let mut result: SeqFile = Vec::new();

    for line in BufReader::new(file).lines() {
        let l: String = line.unwrap();
        let first_char = l.chars().next().unwrap();
        match first_char {
            '/' => {
                break;
            } // Assuming '/' is the beginning of '//', which conceivably might not be
            // true
            '#' => {} // Annotation -> ignore.
            _ => {
                let mut fields = l.split_whitespace();

                match (fields.next(), fields.next(), fields.next()) {
                    (Some(seqname), Some(aln_seq), None) => {
                        let record = SeqRecord {
                            header: String::from(seqname),
                            sequence: String::from(aln_seq),
                        };
                        result.push(record);
                    }
                    _ => {
                        return Err(AlignmentError::InvalidFormat {
                            msg: String::from("Expected two fields"),
                        })
                    }
                }
            }
        }
    }

    Ok(result)
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_read_stockholm_file_len() {
        let path = "data/PF00571.sto";
        let fasta: SeqFile = read_stockholm_file(path).expect("Test file not found");
        assert_eq!(fasta.len(), 5);
    }

    #[test]
    fn test_read_stockholm_file_1st_record() {
        let path = "data/PF00571.sto";
        let fasta: SeqFile = read_stockholm_file(path).expect("Test file not found");
        assert_eq!(fasta[0].header, "O83071/192-246");
        assert_eq!(
            fasta[0].sequence,
            "MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS"
        );
    }

    #[test]
    fn test_read_stockholm_file_last_record() {
        let path = "data/PF00571.sto";
        let fasta: SeqFile = read_stockholm_file(path).expect("Test file not found");
        assert_eq!(fasta[4].header, "O31699/88-139");
        assert_eq!(
            fasta[4].sequence,
            "EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE"
        );
    }

    // TODO: more tests
}