gfa 0.10.1

use crate::{gfa::*, optfields::*};

use bstr::ByteSlice;
use std::fmt::Write;

/// This entire module will probably be removed, with the functions
/// replaced by Display implementations on GFA and the GFA line types,
/// but I haven't gotten around to it yet

fn write_optional_fields<U: OptFields, T: Write>(opts: &U, stream: &mut T) {
    for field in opts.fields() {
        write!(stream, "\t{}", field).unwrap_or_else(|err| {
            panic!(
                "Error writing optional field '{:?}' to stream, {:?}",
                field, err
            )
        })
    }
}

fn write_header<U: OptFields, T: Write>(header: &Header<U>, stream: &mut T) {
    write!(stream, "H").unwrap();
    if let Some(v) = &header.version {
        write!(stream, "\tVN:Z:{}", v.as_bstr()).unwrap();
    }
    write_optional_fields(&header.optional, stream);
}

// Write segment
fn write_segment<N: SegmentId, T: Write, U: OptFields>(
    seg: &Segment<N, U>,
    stream: &mut T,
) {
    write!(
        stream,
        "S\t{}\t{}",
        seg.name.display(),
        seg.sequence.as_bstr()
    )
    .expect("Error writing segment to stream");

    write_optional_fields(&seg.optional, stream);
}

// Write link
fn write_link<N: SegmentId, T: Write, U: OptFields>(
    link: &Link<N, U>,
    stream: &mut T,
) {
    write!(
        stream,
        "L\t{}\t{}\t{}\t{}\t{}",
        link.from_segment.display(),
        link.from_orient,
        link.to_segment.display(),
        link.to_orient,
        link.overlap.as_bstr(),
    )
    .expect("Error writing link to stream");

    write_optional_fields(&link.optional, stream);
}

// Write path
fn write_path<N, U: OptFields, T: Write>(path: &Path<N, U>, stream: &mut T) {
    write!(stream, "P\t{}\t", path.path_name.as_bstr())
        .expect("Error writing path to stream");

    write!(stream, "{}\t", path.segment_names.as_bstr()).unwrap();

    path.overlaps.iter().enumerate().for_each(|(i, o)| {
        if i != 0 {
            write!(stream, ",").unwrap();
        }
        match o {
            None => write!(stream, "*").unwrap(),
            // Some(o) => write!(stream, "{}", o.to_str().unwrap()).unwrap(),
            Some(o) => write!(stream, "{}", o).unwrap(),
        }
    });

    write_optional_fields(&path.optional, stream);
}

// Write GFA
pub fn write_gfa<N: SegmentId, T: Write, U: OptFields>(
    gfa: &GFA<N, U>,
    stream: &mut T,
) {
    write_header(&gfa.header, stream);
    writeln!(stream).unwrap();

    gfa.segments.iter().for_each(|s| {
        write_segment(s, stream);
        writeln!(stream).unwrap();
    });

    gfa.links.iter().for_each(|l| {
        write_link(l, stream);
        writeln!(stream).unwrap();
    });

    gfa.paths.iter().for_each(|p| {
        write_path(p, stream);
        writeln!(stream).unwrap();
    });
}

pub fn gfa_string(gfa: &GFA<Vec<u8>, OptionalFields>) -> String {
    let mut result = String::new();
    write_gfa(gfa, &mut result);
    result
}

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

    #[test]
    fn print_segment() {
        use OptFieldVal::*;
        let mut segment: Segment<Vec<u8>, OptionalFields> =
            Segment::new(b"seg1", b"GCCCTA");
        let opt_ij = OptField::new(b"IJ", A(b'x'));
        let opt_ab = OptField::new(b"AB", BInt(vec![1, 2, 3, 52124]));
        let opt_ur =
            OptField::new(b"UR", Z(Vec::<u8>::from("http://test.com/")));
        let opt_rc = OptField::new(b"RC", Int(123));
        segment.optional = vec![opt_rc, opt_ur, opt_ij, opt_ab];
        let expected = "S\tseg1\tGCCCTA\tRC:i:123\tUR:Z:http://test.com/\tIJ:A:x\tAB:B:I1,2,3,52124";
        let mut string = String::new();
        write_segment(&segment, &mut string);
        assert_eq!(string, expected);
    }

    #[test]
    fn print_link() {
        let link: Link<Vec<u8>, ()> = Link::new(
            b"13",
            Orientation::Forward,
            b"552",
            Orientation::Backward,
            b"0M",
        );
        let mut string = String::new();
        write_link(&link, &mut string);
        assert_eq!(string, "L\t13\t+\t552\t-\t0M");
    }

    #[test]
    fn print_path() {
        use crate::cigar::CIGAR;

        let cigars = vec![b"8M", b"1M", b"3M"]
            .iter()
            .map(|bs| CIGAR::from_bytestring(&bs[..]))
            .collect();

        let path: Path<Vec<u8>, _> =
            Path::new("path1".into(), "13+,51-,241+".into(), cigars, ());

        let mut string = String::new();
        write_path(&path, &mut string);
        assert_eq!(string, "P\tpath1\t13+,51-,241+\t8M,1M,3M");
    }

    #[test]
    fn print_gfa() {
        use std::io::Read;
        use std::path::PathBuf;

        let parser = crate::parser::GFAParser::new();
        let in_gfa: GFA<Vec<u8>, ()> =
            parser.parse_file(&"./test/gfas/lil.gfa").unwrap();

        let mut file =
            std::fs::File::open(&PathBuf::from("./test/gfas/lil.gfa")).unwrap();
        let mut file_string = String::new();
        file.read_to_string(&mut file_string).unwrap();

        let mut string = String::new();
        write_gfa(&in_gfa, &mut string);

        assert_eq!(string, file_string);
    }
}