mzident 0.1.0

Handle all kinds of identified peptidoform files.
Documentation 
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use std::{
    borrow::Cow,
    marker::PhantomData,
    ops::Range,
    path::{Path, PathBuf},
};

use itertools::Itertools;
use serde::{Deserialize, Serialize};

use crate::{
    BoxedIdentifiedPeptideIter, FastaIdentifier, IdentifiedPeptidoform, IdentifiedPeptidoformData,
    IdentifiedPeptidoformSource, IdentifiedPeptidoformVersion, KnownFileFormat, MetaData,
    PeaksFamilyId, PeptidoformPresent, SpectrumId, SpectrumIds,
    common_parser::{Location, OptionalColumn, OptionalLocation},
};
use mzcore::{
    csv::{CsvLine, parse_csv},
    ontology::Ontologies,
    sequence::{
        AminoAcid, CompoundPeptidoformIon, FlankingSequence, Modification,
        PeptideModificationSearch, Peptidoform, SemiAmbiguous, SimpleModification,
        SloppyParsingParameters,
    },
    system::{Mass, MassOverCharge, Time, isize::Charge},
};

static NUMBER_ERROR: (&str, &str) = (
    "Invalid Peaks line",
    "This column is not a number but it is required to be a number in this peaks format",
);
static ID_ERROR: (&str, &str) = (
    "Invalid Peaks line",
    "This column is not a valid peaks ID but it is required to be in this peaks format\nExamples of valid IDs: '1234', 'F2:1234', 'F2:1234 12345'",
);

format_family!(
    Peaks,
    SemiAmbiguous, PeptidoformPresent, [&V13_DIA, &V12, &V11, &V11_FEATURES, &XPLUS, &AB, &X_PATCHED, &X, &DB_PEPTIDE, &DB_PSM, &DB_PROTEIN_PEPTIDE], b',', None;
    required {
        peptide: (FlankingSequence, Vec<Peptidoform<SemiAmbiguous>>, FlankingSequence), |location: Location, ontologies: &Ontologies| {
            let n_flanking: Option<AminoAcid>  =
                (location.as_str().chars().nth(1) == Some('.'))
                .then(|| location.as_str().chars().next().unwrap().try_into().map_err(|()|
                    BoxedError::new(BasicKind::Error,
                        "Invalid amino acid",
                        "This flanking residue is not a valid amino acid",
                        Context::line(Some(location.line.line_index() as u32), location.full_line(), location.location.start, 1).to_owned()))).transpose()?;

            let c_flanking: Option<AminoAcid> =
            (location.as_str().chars().nth_back(1) == Some('.'))
            .then(|| location.as_str().chars().next_back().unwrap().try_into().map_err(|()|
                    BoxedError::new(BasicKind::Error,
                        "Invalid amino acid",
                        "This flanking residue is not a valid amino acid",
                        Context::line(Some(location.line.line_index() as u32), location.full_line(), location.location.end-1, location.location.end).to_owned()))).transpose()?;

            if c_flanking.is_none() && n_flanking.is_none() {
                location.array(';').map(|l| Peptidoform::sloppy_pro_forma(
                    l.full_line(),
                    l.location.clone(),
                    ontologies,
                    &SloppyParsingParameters::default()
                ).map_err(BoxedError::to_owned)).unique()
                .collect::<Result<Vec<_>,_>>()
                .map(|sequences| (FlankingSequence::Unknown, sequences, FlankingSequence::Unknown))
            } else {
                Peptidoform::sloppy_pro_forma(
                    location.full_line(),
                    n_flanking.map_or(location.location.start, |_| location.location.start+2)..c_flanking.map_or(location.location.end, |_| location.location.end-2),
                    ontologies,
                    &SloppyParsingParameters::default()
                ).map_err(BoxedError::to_owned).map(|p| (
                    n_flanking.map_or(FlankingSequence::Terminal, FlankingSequence::AminoAcid),
                    vec![p],
                    c_flanking.map_or(FlankingSequence::Terminal, FlankingSequence::AminoAcid)
                ))
            }};
        mz: MassOverCharge, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(MassOverCharge::new::<mzcore::system::thomson>);
        rt: Time, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Time::new::<mzcore::system::time::min>);
        area: Option<f64>, |location: Location, _| location.or_empty().parse(NUMBER_ERROR);
    }
    optional {
        mass: Mass, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Mass::new::<mzcore::system::dalton>);
        ptm: Vec<SimpleModification>, |location: Location, ontologies: &Ontologies|
            location.or_empty().array(';').map(|v| {
                let v = v.trim();
                Modification::sloppy_modification(v.full_line(), v.location.clone(), None, ontologies).map_err(BoxedError::to_owned)
            }).unique().collect::<Result<Vec<_>,_>>();
        scan_number: Vec<PeaksFamilyId>, |location: Location, _| location.or_empty()
                        .map_or(Ok(Vec::new()), |l| l.array(';').map(|v| v.parse(ID_ERROR)).collect::<Result<Vec<_>,_>>());
        z: Charge, |location: Location, _| location.parse::<isize>(NUMBER_ERROR).map(Charge::new::<mzcore::system::e>);
        alc: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
        local_confidence: Vec<f64>, |location: Location, _| location
            .array(' ')
            .map(|l| l.parse::<f64>(NUMBER_ERROR))
            .collect::<Result<Vec<_>, _>>();
        fraction: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        raw_file: PathBuf, |location: Location, _| Ok(Some(Path::new(&location.get_string()).to_owned()));
        feature: PeaksFamilyId, |location: Location, _| location.or_empty().parse(ID_ERROR);
        de_novo_score: f64, |location: Location, _| location
                .parse::<f64>(NUMBER_ERROR);
        predicted_rt: Time, |location: Location, _| location.or_empty().parse::<f64>(NUMBER_ERROR).map(|o| o.map(Time::new::<mzcore::system::time::min>));
        accession: String, |location: Location, _|  Ok(Some(location.get_string()));
        tag: String, |location: Location, _| Ok(location.get_string());
        mode: String, |location: Location, _| Ok(location.get_string());
        logp: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
        area_tryp_ead: f64, |location: Location, _| location.or_empty().parse::<f64>(NUMBER_ERROR);
        ascore: String, |location: Location, _| Ok(location.get_string());
        found_by: String, |location: Location, _| Ok(location.get_string());
        feature_tryp_cid: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        feature_tryp_ead: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        id: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        from_chimera: bool, |location: Location, _| Ok(location.get_string().eq_ignore_ascii_case("yes"));
        unique: bool, |location: Location, _| Ok(location.get_string() == "Y");
        protein_group: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        protein_id: usize, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        protein_accession: FastaIdentifier<String>, |location: Location, _|  location.parse(NUMBER_ERROR).map(Some);
        start: u16, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        end: u16, |location: Location, _| location.parse(NUMBER_ERROR).map(Some);
        quality: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
        rt_begin: Time, |location: Location, _| location.or_empty().parse::<f64>(NUMBER_ERROR).map(|o| o.map(Time::new::<mzcore::system::time::s>));
        rt_end: Time, |location: Location, _| location.or_empty().parse::<f64>(NUMBER_ERROR).map(|o| o.map(Time::new::<mzcore::system::time::s>));
        precursor_id: isize, |location: Location, _| location.parse::<isize>(NUMBER_ERROR);
        k0_range: std::ops::RangeInclusive<f64>, |location: Location, _| location.split_once('-').map(|(start, end)| Ok(start.parse(NUMBER_ERROR)?..=end.parse(NUMBER_ERROR)?));
    }

    fn post_process(_source: &CsvLine, mut parsed: Self, _ontologies: &Ontologies) -> Result<Self, BoxedError<'static, BasicKind>> {
        // Add the meaningful modifications to replace mass modifications
        if let Some(ptm) = parsed.ptm.clone() {
            for pep in &mut parsed.peptide.1 {
                *pep = PeptideModificationSearch::in_modifications(ptm.clone())
                    .tolerance(mzcore::quantities::Tolerance::Absolute(mzcore::system::da(0.05)))
                    .search(pep.clone());
            }
        }
        Ok(parsed)
    }
);

/// Version 13 Dia de novo missing: Delta RT, MS2 correlation, #precursors, gene, database, ion intensity, positional confidence
pub const V13_DIA: PeaksFormat = PeaksFormat {
    version: PeaksVersion::V13Dia,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("caa (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area sample 1",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::NotAvailable,
    tag: OptionalColumn::Required("tag(>=0.0%)"),
    mode: OptionalColumn::NotAvailable,
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::NotAvailable,
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::Required("accession"),
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::Required("found by"),
    logp: OptionalColumn::Required("-10lgp"),
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};

/// An older version of a PEAKS export
pub const X: PeaksFormat = PeaksFormat {
    version: PeaksVersion::X,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag (>=0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::NotAvailable,
    feature: OptionalColumn::NotAvailable,
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version X of PEAKS export (made for build 31 January 2019)
pub const X_PATCHED: PeaksFormat = PeaksFormat {
    version: PeaksVersion::XPatched,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag (>=0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::Required("fraction"),
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("feature"),
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version X+ of PEAKS export (made for build 20 November 2019)
pub const XPLUS: PeaksFormat = PeaksFormat {
    version: PeaksVersion::XPlus,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag (>=0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::Required("fraction"),
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("feature"),
    de_novo_score: OptionalColumn::Required("denovo score"),
    predicted_rt: OptionalColumn::Required("predict rt"),
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version 11 of PEAKS export
pub const V11: PeaksFormat = PeaksFormat {
    version: PeaksVersion::V11,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag(>=0.0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("feature id"),
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::Optional("precursor id"),
    k0_range: OptionalColumn::Optional("1/k0 range"),
};
/// Version 11 of PEAKS export
pub const V11_FEATURES: PeaksFormat = PeaksFormat {
    version: PeaksVersion::V11Features,
    scan_number: OptionalColumn::NotAvailable,
    peptide: "denovo peptide",
    alc: OptionalColumn::Required("alc (%)"),
    quality: OptionalColumn::Required("quality"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::NotAvailable,
    rt: "rt",
    rt_begin: OptionalColumn::Required("rt begin"),
    rt_end: OptionalColumn::Required("rt end"),
    area: "area",
    ptm: OptionalColumn::NotAvailable,
    local_confidence: OptionalColumn::NotAvailable,
    tag: OptionalColumn::NotAvailable,
    mode: OptionalColumn::NotAvailable,
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("feature id"),
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version 12 of PEAKS export
pub const V12: PeaksFormat = PeaksFormat {
    version: PeaksVersion::V12,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag(>=0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("feature id"),
    de_novo_score: OptionalColumn::Required("deep novo score (%)"),
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version Ab of PEAKS export
pub const AB: PeaksFormat = PeaksFormat {
    version: PeaksVersion::Ab,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::Required("alc (%)"),
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::Required("local confidence (%)"),
    tag: OptionalColumn::Required("tag (>=0%)"),
    mode: OptionalColumn::Required("mode"),
    fraction: OptionalColumn::NotAvailable,
    raw_file: OptionalColumn::NotAvailable,
    feature: OptionalColumn::NotAvailable,
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::Required("accession"),
    ascore: OptionalColumn::NotAvailable,
    found_by: OptionalColumn::NotAvailable,
    logp: OptionalColumn::NotAvailable,
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version DB peptide of PEAKS export
pub const DB_PEPTIDE: PeaksFormat = PeaksFormat {
    version: PeaksVersion::DBPeptide,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::NotAvailable,
    mz: "m/z",
    z: OptionalColumn::NotAvailable,
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area tryp-cid",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::NotAvailable,
    tag: OptionalColumn::NotAvailable,
    mode: OptionalColumn::NotAvailable,
    fraction: OptionalColumn::Required("fraction"),
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::Required("#feature"),
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::Required("accession"),
    ascore: OptionalColumn::Required("ascore"),
    found_by: OptionalColumn::Required("found by"),
    logp: OptionalColumn::Required("-10lgp"),
    feature_tryp_cid: OptionalColumn::Required("#feature tryp-cid"),
    feature_tryp_ead: OptionalColumn::Required("#feature tryp ead"),
    area_tryp_ead: OptionalColumn::Required("area tryp ead"),
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version DB psm of PEAKS export
pub const DB_PSM: PeaksFormat = PeaksFormat {
    version: PeaksVersion::DBPSM,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::NotAvailable,
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::NotAvailable,
    tag: OptionalColumn::NotAvailable,
    mode: OptionalColumn::NotAvailable,
    fraction: OptionalColumn::Required("fraction"),
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::NotAvailable,
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::Required("accession"),
    ascore: OptionalColumn::Required("ascore"),
    found_by: OptionalColumn::Required("found by"),
    logp: OptionalColumn::Required("-10lgp"),
    feature_tryp_cid: OptionalColumn::NotAvailable,
    feature_tryp_ead: OptionalColumn::NotAvailable,
    area_tryp_ead: OptionalColumn::NotAvailable,
    id: OptionalColumn::Required("id"),
    from_chimera: OptionalColumn::Required("from chimera"),
    unique: OptionalColumn::NotAvailable,
    protein_group: OptionalColumn::NotAvailable,
    protein_id: OptionalColumn::NotAvailable,
    protein_accession: OptionalColumn::NotAvailable,
    start: OptionalColumn::NotAvailable,
    end: OptionalColumn::NotAvailable,
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};
/// Version DB protein peptide of PEAKS export
/// protein group, protein id, protein accession, unique, start, end,
pub const DB_PROTEIN_PEPTIDE: PeaksFormat = PeaksFormat {
    version: PeaksVersion::DBProteinPeptide,
    scan_number: OptionalColumn::Required("scan"),
    peptide: "peptide",
    alc: OptionalColumn::NotAvailable,
    mz: "m/z",
    z: OptionalColumn::Required("z"),
    mass: OptionalColumn::Required("mass"),
    rt: "rt",
    area: "area tryp-cid",
    ptm: OptionalColumn::Required("ptm"),
    local_confidence: OptionalColumn::NotAvailable,
    tag: OptionalColumn::NotAvailable,
    mode: OptionalColumn::NotAvailable,
    fraction: OptionalColumn::Required("fraction"),
    raw_file: OptionalColumn::Required("source file"),
    feature: OptionalColumn::NotAvailable,
    de_novo_score: OptionalColumn::NotAvailable,
    predicted_rt: OptionalColumn::NotAvailable,
    accession: OptionalColumn::NotAvailable,
    ascore: OptionalColumn::Required("ascore"),
    found_by: OptionalColumn::Required("found by"),
    logp: OptionalColumn::Required("-10lgp"),
    feature_tryp_cid: OptionalColumn::Required("#feature tryp-cid"),
    feature_tryp_ead: OptionalColumn::Required("#feature tryp ead"),
    area_tryp_ead: OptionalColumn::Required("area tryp ead"),
    id: OptionalColumn::NotAvailable,
    from_chimera: OptionalColumn::NotAvailable,
    unique: OptionalColumn::Required("unique"),
    protein_group: OptionalColumn::Required("protein group"),
    protein_id: OptionalColumn::Required("protein id"),
    protein_accession: OptionalColumn::Required("protein accession"),
    start: OptionalColumn::Required("start"),
    end: OptionalColumn::Required("end"),
    quality: OptionalColumn::NotAvailable,
    rt_begin: OptionalColumn::NotAvailable,
    rt_end: OptionalColumn::NotAvailable,
    precursor_id: OptionalColumn::NotAvailable,
    k0_range: OptionalColumn::NotAvailable,
};

/// All possible peaks versions
#[derive(
    Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Default, Serialize, Deserialize,
)]
#[expect(clippy::upper_case_acronyms)]
pub enum PeaksVersion {
    /// An older version of a PEAKS export
    X,
    /// Version X of PEAKS export (made for build 31 January 2019)
    XPatched,
    /// Version X+ of PEAKS export (made for build 20 November 2019)
    XPlus,
    /// Version DB peptide of PEAKS export
    DBPeptide,
    /// Version DB PSM of PEAKS export
    DBPSM,
    /// Version DB Protein Peptide of PEAKS export
    DBProteinPeptide,
    /// Version Ab of PEAKS export
    Ab,
    /// Version 11 denovo file
    V11,
    /// Version 11 features file
    V11Features,
    /// Version 12
    #[default]
    V12,
    /// Version 13 Dia
    V13Dia,
}

impl std::fmt::Display for PeaksVersion {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> Result<(), std::fmt::Error> {
        write!(f, "{}", self.name())
    }
}

impl IdentifiedPeptidoformVersion<PeaksFormat> for PeaksVersion {
    fn format(self) -> PeaksFormat {
        match self {
            Self::X => X,
            Self::XPatched => X_PATCHED,
            Self::XPlus => XPLUS,
            Self::DBPeptide => DB_PEPTIDE,
            Self::DBPSM => DB_PSM,
            Self::DBProteinPeptide => DB_PROTEIN_PEPTIDE,
            Self::Ab => AB,
            Self::V11 => V11,
            Self::V11Features => V11_FEATURES,
            Self::V12 => V12,
            Self::V13Dia => V13_DIA,
        }
    }
    fn name(self) -> &'static str {
        match self {
            Self::X => "X",
            Self::XPatched => "X patched",
            Self::XPlus => "X+",
            Self::DBPeptide => "DB peptide",
            Self::DBPSM => "DB PSM",
            Self::DBProteinPeptide => "DB protein peptide",
            Self::Ab => "Ab",
            Self::V11 => "11",
            Self::V11Features => "11 features",
            Self::V12 => "12",
            Self::V13Dia => "V13 Dia",
        }
    }
}

impl MetaData for PeaksData {
    fn compound_peptidoform_ion(&self) -> Option<Cow<'_, CompoundPeptidoformIon>> {
        Some(Cow::Owned(self.peptide.1.clone().into()))
    }

    fn format(&self) -> KnownFileFormat {
        KnownFileFormat::Peaks(self.version)
    }

    fn id(&self) -> String {
        self.id.map_or_else(
            || {
                self.scan_number.as_ref().map_or_else(
                    || {
                        self.feature
                            .as_ref()
                            .map_or_else(|| "-".to_string(), ToString::to_string)
                    },
                    |s| s.iter().join(";"),
                )
            },
            |i| i.to_string(),
        )
    }

    fn confidence(&self) -> Option<f64> {
        self.de_novo_score
            .or(self.alc)
            .map(|v| v / 100.0)
            .or_else(|| {
                self.logp
                    .map(|v| 2.0 * (1.0 / (1.0 + 1.025_f64.powf(-v)) - 0.5))
            })
    }

    fn local_confidence(&self) -> Option<Cow<'_, [f64]>> {
        self.local_confidence
            .as_ref()
            .map(|lc| lc.iter().map(|v| *v / 100.0).collect())
    }

    fn original_confidence(&self) -> Option<f64> {
        self.de_novo_score.or(self.alc).or(self.logp)
    }

    fn original_local_confidence(&self) -> Option<&[f64]> {
        self.local_confidence.as_deref()
    }

    fn charge(&self) -> Option<Charge> {
        self.z
    }

    fn mode(&self) -> Option<Cow<'_, str>> {
        self.mode.as_deref().map(Cow::Borrowed)
    }

    fn retention_time(&self) -> Option<Time> {
        Some(self.rt)
    }

    fn scans(&self) -> SpectrumIds {
        self.scan_number
            .as_ref()
            .map_or(SpectrumIds::None, |scan_number| {
                self.raw_file.clone().map_or_else(
                    || {
                        SpectrumIds::FileNotKnown(
                            scan_number
                                .iter()
                                .flat_map(|s| s.scans.clone())
                                .map(SpectrumId::Number)
                                .collect(),
                        )
                    },
                    |raw_file| {
                        SpectrumIds::FileKnown(vec![(
                            raw_file,
                            scan_number
                                .iter()
                                .flat_map(|s| s.scans.clone())
                                .map(SpectrumId::Number)
                                .collect(),
                        )])
                    },
                )
            })
    }

    fn experimental_mz(&self) -> Option<MassOverCharge> {
        Some(self.mz)
    }

    fn experimental_mass(&self) -> Option<Mass> {
        self.mass
            .map_or_else(|| self.z.map(|z| self.mz * z.to_float()), Some)
    }

    fn protein_names(&self) -> Option<Cow<'_, [FastaIdentifier<String>]>> {
        self.protein_accession
            .as_ref()
            .map(|v| Cow::Borrowed(std::slice::from_ref(v)))
    }

    fn protein_id(&self) -> Option<usize> {
        self.protein_id
    }

    fn protein_location(&self) -> Option<Range<u16>> {
        self.start.and_then(|s| self.end.map(|e| s..e))
    }

    fn flanking_sequences(&self) -> (&FlankingSequence, &FlankingSequence) {
        (&self.peptide.0, &self.peptide.2)
    }

    fn database(&self) -> Option<(&str, Option<&str>)> {
        None
    }
}