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#![allow(dead_code)]
#![warn(clippy::all, clippy::pedantic, clippy::nursery)]
#![allow(
    clippy::must_use_candidate,
    clippy::cast_precision_loss,
    clippy::cast_possible_truncation,
    clippy::cast_sign_loss,
    clippy::wildcard_imports,
    clippy::module_name_repetitions,
    clippy::suboptimal_flops,
    clippy::too_many_lines
)]

#[cfg(test)]
mod fragmentation_tests;
#[macro_use]
mod formula;

pub mod align;
mod aminoacids;
mod element;
mod fragment;
mod glycan;
mod helper_functions;
mod isotopes;
mod model;
mod modification;
mod ontologies;
mod peptide;
mod placement_rules;
pub mod rawfile;
mod spectrum;
mod system;

pub use crate::element::*;
pub use crate::formula::*;
pub use crate::fragment::*;
pub use crate::glycan::*;
pub use crate::model::*;
pub use crate::peptide::*;
pub use crate::spectrum::*;
pub use crate::system::f64::*;
pub use aminoacids::AminoAcid;
pub use fragment::Fragment;
pub use model::Model;
pub use peptide::Peptide;
pub use uom::num_traits::Zero;

#[macro_use]
extern crate uom;

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

    #[test]
    fn simple_fragments() {
        let peptide = peptide::Peptide::pro_forma("WFWF").unwrap();
        let fragments = peptide
            .generate_theoretical_fragments(Charge::new::<e>(1.0), &Model::all())
            .unwrap();
        println!("{}", fragments.len());
        println!("{fragments:?}");
    }

    #[test]
    fn simple_matching() {
        let model = Model::all();
        let spectrum = rawfile::mgf::open("data/example.mgf").unwrap();
        let peptide = peptide::Peptide::pro_forma("WFWF").unwrap();
        let fragments = peptide
            .generate_theoretical_fragments(Charge::new::<e>(1.0), &model)
            .unwrap();
        let annotated = spectrum[0].annotate(peptide, &fragments, &model);
        println!("{annotated:?}");
    }
}