mzdata 0.63.4

use std::{
    collections::HashMap,
    convert::TryInto,
    fs,
    io::{self, prelude::*, SeekFrom},
    marker::PhantomData,
    str,
};

use log::warn;
use thiserror::Error;

use mzpeaks::{CentroidLike, CentroidPeak, DeconvolutedCentroidLike, DeconvolutedPeak};

use super::super::{
    offset_index::OffsetIndex,
    traits::{
        ChromatogramSource, MZFileReader, RandomAccessSpectrumIterator, SeekRead,
        SpectrumAccessError, SpectrumSource,
    },
    utils::DetailLevel,
};

use crate::{
    meta::{
        DataProcessing, FileDescription, InstrumentConfiguration, MSDataFileMetadata,
        MassSpectrometryRun, Sample, Software,
    }, params::Value, prelude::SpectrumLike
};

use crate::params::{ControlledVocabulary, Param, ParamDescribed};

use crate::spectrum::{
    bindata::{BuildArrayMapFrom, BuildFromArrayMap},
    spectrum_types::{CentroidSpectrumType, MultiLayerSpectrum},
    Chromatogram, Precursor, PrecursorSelection, SelectedIon, SignalContinuity,
    SpectrumDescription,
};
use crate::utils::neutral_mass;

#[derive(PartialEq, Debug)]
pub enum MGFParserState {
    Start,
    FileHeader,
    ScanHeaders,
    Peaks,
    Between,
    Done,
    Error,
}

#[derive(Debug, Error)]
pub enum MGFError {
    #[error("No error occurred")]
    NoError,
    #[error("Encountered a malformed peak line")]
    MalformedPeakLine,
    #[error("Encountered a malformed header line: {0}")]
    MalformedHeaderLine(String),
    #[error("Too many columns for peak line encountered")]
    NotEnoughColumnsForPeakLine,
    #[error("Encountered an IO error: {0}")]
    IOError(
        #[from]
        #[source]
        io::Error,
    ),
}

#[derive(Debug)]
pub(crate) struct SpectrumBuilder<
    C: CentroidLike + From<CentroidPeak> = CentroidPeak,
    D: DeconvolutedCentroidLike + From<DeconvolutedPeak> = DeconvolutedPeak,
> {
    pub description: SpectrumDescription,
    pub mz_array: Vec<f64>,
    pub intensity_array: Vec<f32>,
    pub charge_array: Vec<i32>,
    pub has_charge: u32,
    pub precursor_charge: Option<i32>,
    pub detail_level: DetailLevel,
    empty_metadata: bool,
    centroided_type: PhantomData<C>,
    deconvoluted_type: PhantomData<D>,
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > SpectrumBuilder<C, D>
{
    pub fn is_empty(&self) -> bool {
        self.empty_metadata && self.mz_array.is_empty()
    }
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > Default for SpectrumBuilder<C, D>
{
    fn default() -> Self {
        let description = SpectrumDescription {
            signal_continuity: SignalContinuity::Centroid,
            ms_level: 2,
            ..Default::default()
        };
        Self {
            description,
            empty_metadata: true,
            mz_array: Default::default(),
            intensity_array: Default::default(),
            charge_array: Default::default(),
            has_charge: Default::default(),
            precursor_charge: Default::default(),
            detail_level: Default::default(),
            centroided_type: Default::default(),
            deconvoluted_type: Default::default(),
        }
    }
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > SpectrumBuilder<C, D>
{
    pub fn into_spectrum(self, spectrum: &mut MultiLayerSpectrum<C, D>) {
        if self.has_charge > 0 {
            spectrum.deconvoluted_peaks = Some(
                self.mz_array
                    .into_iter()
                    .zip(self.intensity_array)
                    .zip(self.charge_array)
                    .map(|((mz, inten), z)| {
                        DeconvolutedPeak {
                            neutral_mass: neutral_mass(mz, if z != 0 { z } else { 1 }),
                            intensity: inten,
                            charge: if z != 0 { z } else { 1 },
                            ..Default::default()
                        }
                        .into()
                    })
                    .collect(),
            )
        } else {
            spectrum.peaks = Some(
                self.mz_array
                    .into_iter()
                    .zip(self.intensity_array)
                    .map(|(mz, inten)| {
                        CentroidPeak {
                            mz,
                            intensity: inten,
                            ..Default::default()
                        }
                        .into()
                    })
                    .collect(),
            )
        }
        spectrum.description = self.description;
    }
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > From<SpectrumBuilder<C, D>> for MultiLayerSpectrum<C, D>
{
    fn from(builder: SpectrumBuilder<C, D>) -> MultiLayerSpectrum<C, D> {
        let mut spec = MultiLayerSpectrum::default();
        builder.into_spectrum(&mut spec);
        spec
    }
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > From<SpectrumBuilder<C, D>> for CentroidSpectrumType<C>
where
    C: BuildFromArrayMap + BuildArrayMapFrom,
    D: BuildFromArrayMap + BuildArrayMapFrom,
{
    fn from(builder: SpectrumBuilder<C, D>) -> CentroidSpectrumType<C> {
        let spec: MultiLayerSpectrum<C, D> = builder.into();
        spec.try_into().unwrap()
    }
}

/// A parsed spectrum title which is conventionally parsed for metadata
#[derive(Debug, Default, Clone, PartialEq)]
pub struct MGFTitle {
    pub identifier: Option<String>,
    pub fields: HashMap<String, Value>,
}

impl MGFTitle {
    pub fn new(identifier: Option<String>, fields: HashMap<String, Value>) -> Self {
        Self { identifier, fields }
    }
}

/// MGF spectrum title parsing behavior following for extracting attributes
/// from structured text strings
pub trait MGFTitleParsing: Send + Sync {
    /// Parse the title string into an [`MGFTitle`].
    ///
    /// Because not all MGF file writers follow a pattern, or not
    /// all spectra in a single MGF file follow the same pattern, this
    /// method is fallible.
    fn parse_title(&self, title: &str, collect_fields: bool) -> Option<MGFTitle>;
}

/// The default title parser that simply treats the title as the identifier
#[derive(Debug, Default, Clone, PartialEq)]
pub struct DefaultTitleParser();

impl MGFTitleParsing for DefaultTitleParser {
    #[allow(unused_variables)]
    fn parse_title(&self, title: &str, collect_fields: bool) -> Option<MGFTitle> {
        Some(MGFTitle::new(Some(title.to_string()), Default::default()))
    }
}


/// A title parser that recognizes the default Trans-Proteomics Pipeline (TPP) title
/// format: `<RunId>.<ScanNumber1>.<ScanNumber2>.<ChargeState> File:"<^SourcePath>", NativeID:"<^Id>"`
///
/// Each of the labeled groups will be stored in [`MGFTitle::fields`] except `Id`, which will be
/// the [`MGFTitle::identifier`]. `SourceFile` and `Id` may be absent.
#[derive(Debug, Default, Clone, PartialEq)]
pub struct TPPTitleParser();

impl MGFTitleParsing for TPPTitleParser {
    fn parse_title(&self, title: &str, collect_fields: bool) -> Option<MGFTitle> {
        let mut result = MGFTitle::default();
        if let Some((run_id, after_run_id)) = title.trim().split_once(".") {
            if collect_fields {
                result
                    .fields
                    .insert("RunId".into(), run_id.parse().unwrap());
            }
            if let Some((scan1, after_scan1)) = after_run_id.split_once(".") {
                if collect_fields {
                    result
                        .fields
                        .insert("ScanNumber1".into(), scan1.parse().unwrap());
                }
                if let Some((scan2, after_scan2)) = after_scan1.split_once(".") {
                    if collect_fields {
                        result
                            .fields
                            .insert("ScanNumber2".into(), scan2.parse().unwrap());
                    }
                    if let Some((charge, after_charge)) = after_scan2.split_once(" ") {
                        if collect_fields {
                            result
                                .fields
                                .insert("Charge".into(), charge.parse().unwrap());
                        }
                        if let Some(tail) = after_charge.strip_prefix("File:\"") {
                            if let Some((head, rest)) = tail.split_once('"') {
                                if collect_fields {
                                    result
                                        .fields
                                        .insert("File".into(), Value::String(head.into()));
                                }
                                if let Some(tail) = rest.strip_prefix(", NativeID:\"") {
                                    if let Some((head, _rest)) = tail.split_once('"') {
                                        if collect_fields {
                                            result.fields.insert(
                                                "NativeID".into(),
                                                Value::String(head.into()),
                                            );
                                        }
                                        result.identifier = Some(head.into());
                                    }
                                }
                            }
                        }
                    } else {
                        warn!("Title {title} does not conform to TPPTitleParser pattern: Charge not found")
                    }
                } else {
                    warn!("Title {title} does not conform to TPPTitleParser pattern: ScanNumber2 not found")
                }
            } else {
                warn!("Title {title} does not conform to TPPTitleParser pattern: ScanNumber1 not found")
            }
        } else {
            warn!("Title {title} does not conform to TPPTitleParser pattern: RunId not found")
        }
        Some(result)
    }
}


/// A strategy for deciding how to index an MGF file.
pub trait MGFIndexing: Send + Sync {
    /// Check if this scan header is to be indexed
    fn is_index_key(&self, key: &str) -> bool;

    /// Convert the `value` of scan header `key` into the index key for the
    /// spectrum.
    ///
    /// The default implementation simply returns the value-as-is.
    #[allow(unused_variables)]
    fn handle_key(&self, key: &str, value: &str) -> String {
        value.trim().into()
    }
}

/// The default indexing strategy for MGFs that use the full text
/// of the `TITLE` scan header
#[derive(Debug, Default, Clone, Copy)]
pub struct DefaultTitleIndexing();

impl MGFIndexing for DefaultTitleIndexing {
    fn is_index_key(&self, key: &str) -> bool {
        key == "TITLE"
    }
}

/// Indexing strategy for an MGF using the `SCANS` scan header.
#[derive(Debug, Default, Clone, Copy)]
pub struct ScansIndexing();

impl MGFIndexing for ScansIndexing {
    fn is_index_key(&self, key: &str) -> bool {
        key == "SCANS"
    }
}


/// Indexing strategy for an MGF using the `TITLE` scan header, parsed
/// according to the Trans-Proteomics Pipeline notation's `NativeID`
/// component.
///
/// See [`TPPTitleParser`] for more information.
#[derive(Debug, Default)]
pub struct TPPTitleParsingNativeIDIndexing {
    parser: TPPTitleParser,
}

impl MGFIndexing for TPPTitleParsingNativeIDIndexing {
    fn is_index_key(&self, key: &str) -> bool {
        key == "TITLE"
    }

    #[allow(unused_variables)]
    fn handle_key(&self, key: &str, value: &str) -> String {
        if let Some(val) = self.parser.parse_title(value, true) {
            match val.identifier {
                Some(ident) => ident,
                None => value.into(),
            }
        } else {
            value.into()
        }
    }
}


/// Indexing strategy for an MGF using the `TITLE` scan header, parsed
/// according to the Trans-Proteomics Pipeline notation's `ScanNumber1`
/// component.
///
/// See [`TPPTitleParser`] for more information.
#[derive(Debug, Default)]
pub struct TPPTitleParsingScanNumberIndexing {
    parser: TPPTitleParser,
}

impl MGFIndexing for TPPTitleParsingScanNumberIndexing {
    fn is_index_key(&self, key: &str) -> bool {
        key == "TITLE"
    }

    #[allow(unused_variables)]
    fn handle_key(&self, key: &str, value: &str) -> String {
        if let Some(val) = self.parser.parse_title(value, true) {
            match val.fields.get("ScanNumber1") {
                Some(ident) => ident.to_string(),
                None => value.into(),
            }
        } else {
            value.into()
        }
    }
}


/// An MGF (Mascot Generic Format) file parser that supports iteration and random access.
/// The parser produces [`Spectrum`](crate::spectrum::Spectrum) instances. These may be
/// converted directly into [`CentroidSpectrum`](crate::spectrum::CentroidSpectrum)
/// instances which better represent the nature of this preprocessed data type.
pub struct MGFReaderType<
    R: io::Read,
    C: CentroidLike = CentroidPeak,
    D: DeconvolutedCentroidLike + From<DeconvolutedPeak> = DeconvolutedPeak,
> {
    pub handle: io::BufReader<R>,
    pub state: MGFParserState,
    pub offset: usize,
    pub error: Option<MGFError>,
    index: OffsetIndex,
    file_description: FileDescription,
    instrument_configurations: HashMap<u32, InstrumentConfiguration>,
    softwares: Vec<Software>,
    samples: Vec<Sample>,
    data_processings: Vec<DataProcessing>,
    run: MassSpectrometryRun,
    read_counter: usize,
    pub detail_level: DetailLevel,
    centroid_type: PhantomData<C>,
    deconvoluted_type: PhantomData<D>,
    indexing: Box<dyn MGFIndexing>,
}

pub(crate) trait MGFLineParsing<
    C: CentroidLike + From<CentroidPeak>,
    D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
>
{
    fn state(&self) -> &MGFParserState;
    fn state_mut(&mut self) -> &mut MGFParserState;
    fn error_mut(&mut self) -> &mut Option<MGFError>;

    fn set_error(&mut self, error: MGFError) {
        *self.state_mut() = MGFParserState::Error;
        *self.error_mut() = Some(error);
    }

    fn parse_peak_from_line(
        &mut self,
        line: &str,
        builder: &mut SpectrumBuilder<C, D>,
    ) -> Option<bool> {
        let mut chars = line.chars();
        let first = chars.next()?;
        if first.is_numeric() {
            let mut it = line.split_ascii_whitespace();
            let mz_token = it.next()?;
            let mut intensity_token = "";
            let mut charge_token_opt = None;

            let nparts = if let Some(i) = it.next() {
                intensity_token = i;
                charge_token_opt = it.next();
                if charge_token_opt.is_some() {
                    3
                } else {
                    2
                }
            } else {
                1
            };

            if nparts < 2 {
                self.set_error(MGFError::NotEnoughColumnsForPeakLine);
                return None;
            }
            if !matches!(builder.detail_level, DetailLevel::MetadataOnly) {
                let Ok(mz) = mz_token.parse::<f64>() else {
                    self.set_error(MGFError::MalformedPeakLine);
                    return None;
                };

                let Ok(intensity) = intensity_token.parse::<f32>() else {
                    self.set_error(MGFError::MalformedPeakLine);
                    return None;
                };

                builder.mz_array.push(mz);
                builder.intensity_array.push(intensity);

                if nparts == 3 {
                    let Ok(charge) = charge_token_opt.unwrap().parse::<i32>() else {
                        self.set_error(MGFError::MalformedPeakLine);
                        return None;
                    };
                    builder.charge_array.push(charge);
                    builder.has_charge += 1;
                } else {
                    builder.charge_array.push(0);
                }
            }
            Some(true)
        } else {
            None
        }
    }

    fn handle_scan_header(&mut self, line: &str, builder: &mut SpectrumBuilder<C, D>) -> bool {
        let peak_line = self.parse_peak_from_line(line, builder).unwrap_or(false);
        if peak_line {
            *self.state_mut() = MGFParserState::Peaks;
            true
        } else if line == "END IONS" {
            *self.state_mut() = MGFParserState::Between;
            true
        } else if line.contains('=') {
            let (key, value) = line.split_once('=').unwrap();
            let value = value.trim();
            builder.empty_metadata = false;
            match key {
                "TITLE" => builder.description.id = value.to_string(),
                "RTINSECONDS" => {
                    let scan_ev = builder
                        .description
                        .acquisition
                        .first_scan_mut()
                        .expect("Automatically adds scan event");
                    scan_ev.start_time = value.parse::<f64>().unwrap() / 60.0
                }
                "PEPMASS" => {
                    let mut parts = value.split_ascii_whitespace();
                    let mz = match parts.next() {
                        Some(s) => s,
                        None => {
                            *self.state_mut() = MGFParserState::Error;
                            *self.error_mut() = Some(MGFError::MalformedHeaderLine(
                                "No m/z value in PEPMASS header".into(),
                            ));
                            return false;
                        }
                    };
                    let mz: f64 = match mz.parse() {
                        Ok(mz) => mz,
                        Err(e) => {
                            *self.state_mut() = MGFParserState::Error;
                            *self.error_mut() = Some(MGFError::MalformedHeaderLine(format!(
                                "Malformed m/z value in PEPMASS header {value}: {e}"
                            )));
                            return false;
                        }
                    };

                    let intensity: f32 = parts
                        .next()
                        .map(|v| v.parse())
                        .unwrap_or_else(|| Ok(0.0))
                        .map_err(|e| warn!("Failed to parse PEPMASS intensity {value}: {e}"))
                        .unwrap_or_default();
                    let charge: Option<i32> = match parts.next() {
                        Some(c) => self.parse_charge(c),
                        None => builder.precursor_charge,
                    };
                    builder.description.precursor.push(Precursor {
                        ions: vec![SelectedIon {
                            mz,
                            intensity,
                            charge,
                            ..Default::default()
                        }],
                        ..Default::default()
                    });
                }
                "CHARGE" => {
                    builder.precursor_charge = self.parse_charge(value);
                    if builder.description.precursor.is_empty() {
                        builder.description.precursor.push(Default::default());
                    }
                    if let Some(ion) = builder
                        .description
                        .precursor.last_mut().and_then(|v| v.iter_mut().last())

                    {
                        if ion.charge.is_none() {
                            ion.charge = builder.precursor_charge
                        }
                    }
                }
                &_ => {
                    builder
                        .description
                        .add_param(Param::new_key_value(key.to_lowercase(), value));
                }
            };

            true
        } else {
            self.set_error(MGFError::MalformedHeaderLine(
                "No '=' in header line".into(),
            ));
            false
        }
    }

    fn parse_charge(&mut self, value: &str) -> Option<i32> {
        let (sign, value, tail_sign) = if let Some(stripped) = value.strip_suffix('+') {
            (1, stripped, true)
        } else if let Some(stripped) = value.strip_suffix('-') {
            (-1, stripped, true)
        } else {
            (1, value, false)
        };

        if tail_sign && (value.starts_with('-') || value.starts_with('+')) {
            self.set_error(MGFError::MalformedHeaderLine(format!(
                "Could not parse charge value {value}"
            )));
            return None;
        }

        match value.parse::<i32>() {
            Ok(z) => Some(sign * z),
            Err(e) => {
                self.set_error(MGFError::MalformedHeaderLine(format!(
                    "Could not parse charge value {value} : {e}"
                )));
                None
            }
        }
    }

    fn handle_peak(&mut self, line: &str, builder: &mut SpectrumBuilder<C, D>) -> bool {
        let peak_line = self.parse_peak_from_line(line, builder).unwrap_or(false);
        if peak_line {
            true
        } else if line == "END IONS" {
            *self.state_mut() = MGFParserState::Between;
            false
        } else {
            self.set_error(MGFError::MalformedPeakLine);
            false
        }
    }

    fn handle_start(&mut self, line: &str) -> bool {
        if line.contains('=') {
            match self.state() {
                MGFParserState::Start => {
                    *self.state_mut() = MGFParserState::FileHeader;
                    true
                }
                MGFParserState::FileHeader => true,
                _ => false,
            }
        } else if line == "BEGIN IONS" {
            *self.state_mut() = MGFParserState::ScanHeaders;
            true
        } else {
            false
        }
    }

    fn handle_between(&mut self, line: &str) -> bool {
        if line == "BEGIN IONS" {
            *self.state_mut() = MGFParserState::ScanHeaders;
        }
        true
    }

    #[allow(clippy::borrowed_box, unused)]
    fn indexer(&self) -> &Box<dyn MGFIndexing>;

    /// Set the indexing strategy implementing [`MGFIndexing`].
    ///
    /// This method should invalidate any existing [`OffsetIndex`].
    fn set_indexer(&mut self, indexer: Box<dyn MGFIndexing>);
}

impl<
        R: io::Read,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > MGFLineParsing<C, D> for MGFReaderType<R, C, D>
{
    fn state(&self) -> &MGFParserState {
        &self.state
    }

    fn state_mut(&mut self) -> &mut MGFParserState {
        &mut self.state
    }

    fn error_mut(&mut self) -> &mut Option<MGFError> {
        &mut self.error
    }

    #[inline(always)]
    fn indexer(&self) -> &Box<dyn MGFIndexing> {
        &self.indexing
    }

    fn set_indexer(&mut self, indexer: Box<dyn MGFIndexing>) {
        self.indexing = indexer;
        self.index = OffsetIndex::new("spectrum".into());
    }
}

impl<
        R: io::Read,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > MGFReaderType<R, C, D>
{
    fn read_line(&mut self, buffer: &mut String) -> io::Result<usize> {
        self.handle.read_line(buffer)
    }

    /// Read the next spectrum from the file, if there is one.
    pub fn read_next(&mut self) -> Option<MultiLayerSpectrum<C, D>> {
        let mut builder = SpectrumBuilder {
            detail_level: self.detail_level,
            ..Default::default()
        };
        self._parse_into(&mut builder)
            .ok()
            .and_then(|(_, started_spectrum)| {
                let mut spec: Option<MultiLayerSpectrum<C, D>> =
                    (started_spectrum && !builder.is_empty()).then(|| builder.into());
                if let Some(spec) = spec.as_mut() {
                    spec.description_mut().index = self.read_counter;
                    self.read_counter += 1;
                }
                spec
            })
    }

    /// Read the next spectrum's contents directly into the passed [`SpectrumBuilder`].
    fn _parse_into(
        &mut self,
        builder: &mut SpectrumBuilder<C, D>,
    ) -> Result<(usize, bool), MGFError> {
        let mut buffer = String::new();
        let mut work = true;
        let mut offset: usize = 0;
        let mut had_begin_ions = false;

        while work {
            buffer.clear();
            let b = match self.read_line(&mut buffer) {
                Ok(b) => b,
                Err(err) => {
                    self.state = MGFParserState::Error;
                    return Err(MGFError::IOError(err));
                }
            };

            // Count how many bytes we've read from the source
            offset += b;
            if b == 0 {
                self.state = MGFParserState::Done;
                break;
            }

            let line = buffer.trim();

            // Skip empty lines
            if line.is_empty() {
                continue;
            }

            work = match self.state {
                MGFParserState::Start | MGFParserState::FileHeader => self.handle_start(line),
                MGFParserState::ScanHeaders => {
                    had_begin_ions = true;
                    self.handle_scan_header(line, builder)
                }
                MGFParserState::Peaks => self.handle_peak(line, builder),
                MGFParserState::Between => self.handle_between(line),
                MGFParserState::Done => false,
                MGFParserState::Error => {
                    return Err(self.error.take().unwrap_or(MGFError::NoError));
                }
            };

            if self.state == MGFParserState::Error {
                return Err(self.error.take().unwrap_or(MGFError::NoError));
            }
        }
        Ok((offset, had_begin_ions))
    }

    pub fn read_into(
        &mut self,
        spectrum: &mut MultiLayerSpectrum<C, D>,
    ) -> Result<usize, MGFError> {
        let mut accumulator = SpectrumBuilder {
            detail_level: self.detail_level,
            ..Default::default()
        };
        match self._parse_into(&mut accumulator) {
            Ok((sz, started_spectrum)) => {
                if !started_spectrum {
                    Err(MGFError::IOError(io::Error::new(
                        io::ErrorKind::UnexpectedEof,
                        "EOF found before spectrum started",
                    )))
                } else {
                    accumulator.into_spectrum(spectrum);
                    spectrum.description_mut().index = self.read_counter;
                    self.read_counter += 1;
                    Ok(sz)
                }
            }
            Err(err) => Err(err),
        }
    }

    fn default_file_description() -> FileDescription {
        let mut fd = FileDescription::default();
        let mut term = Param::new();
        term.name = "MSn spectrum".to_owned();
        term.accession = Some(1000580);
        term.controlled_vocabulary = Some(ControlledVocabulary::MS);
        fd.add_param(term);
        fd
    }


    /// Get the current indexing strategy implementing [`MGFIndexing`]
    #[allow(clippy::borrowed_box)]
    pub fn indexer(&self) -> &Box<dyn MGFIndexing> {
        &self.indexing
    }

    /// Set the indexing strategy implementing [`MGFIndexing`].
    ///
    /// This invalidates any existing [`OffsetIndex`].
    pub fn set_indexer(&mut self, indexer: Box<dyn MGFIndexing>) {
        <Self as MGFLineParsing<C, D>>::set_indexer(self, indexer);
    }

    /// Create a new, unindexed MGF parser
    pub fn new(file: R) -> MGFReaderType<R, C, D> {
        let handle = io::BufReader::with_capacity(500, file);
        MGFReaderType {
            handle,
            state: MGFParserState::Start,
            offset: 0,
            error: None,
            index: OffsetIndex::new("spectrum".to_owned()),
            centroid_type: PhantomData,
            deconvoluted_type: PhantomData,
            instrument_configurations: HashMap::new(),
            data_processings: Vec::new(),
            softwares: Vec::new(),
            samples: Vec::new(),
            file_description: Self::default_file_description(),
            detail_level: DetailLevel::Full,
            run: MassSpectrometryRun::default(),
            read_counter: 0,
            indexing: Box::new(DefaultTitleIndexing()),
        }
    }
}

impl<
        R: io::Read,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > Iterator for MGFReaderType<R, C, D>
{
    type Item = MultiLayerSpectrum<C, D>;

    /// Read the next spectrum from the file.
    fn next(&mut self) -> Option<Self::Item> {
        self.read_next()
    }
}

impl<
        R: SeekRead,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > MGFReaderType<R, C, D>
{
    /// Construct a new MGFReaderType and build an offset index
    /// using [`Self::build_index`]
    pub fn new_indexed(file: R) -> MGFReaderType<R, C, D> {
        let mut reader = Self::new(file);
        reader.build_index();
        reader
    }


    /// Construct a new [`MGFReaderType`] and build an offset index
    /// using [`Self::build_index`] using the specified indexer.
    pub fn new_indexed_with(file: R, indexer: Box<dyn MGFIndexing>) -> MGFReaderType<R, C, D> {
        let mut reader = Self::new(file);
        reader.set_indexer(indexer);
        reader.build_index();
        reader
    }

    pub fn seek(&mut self, pos: SeekFrom) -> io::Result<u64> {
        self.handle.seek(pos)
    }

    /// Builds an offset index to each `BEGIN IONS` line
    /// by doing a fast pre-scan of the text file.
    pub fn build_index(&mut self) -> u64 {
        let mut offset: u64 = 0;
        let mut last_start: u64 = 0;

        let mut found_start = false;

        let start = self
            .handle
            .stream_position()
            .expect("Failed to save restore location");
        self.seek(SeekFrom::Start(0))
            .expect("Failed to reset stream to beginning");

        let mut buffer: Vec<u8> = Vec::new();
        let mut index = OffsetIndex::new("spectrum".into());
        loop {
            buffer.clear();
            let b = match self.handle.read_until(b'\n', &mut buffer) {
                Ok(b) => b,
                Err(err) => {
                    panic!("Error while reading file: {}", err);
                }
            };
            if b == 0 {
                break;
            }
            if buffer.starts_with(b"BEGIN IONS") {
                found_start = true;
                last_start = offset;
            } else if found_start {
                let string_buffer = String::from_utf8_lossy(&buffer);
                let indexer = self.indexer();
                if let Some((key, value)) = string_buffer.split_once('=') {
                    if indexer.is_index_key(key) {
                        index.insert(indexer.handle_key(key, value), last_start);
                        found_start = false;
                        last_start = 0;
                    }
                }
            }
            offset += b as u64;
        }
        self.seek(SeekFrom::Start(start))
            .expect("Failed to restore location");
        index.init = true;
        self.set_index(index);
        if self.index.is_empty() {
            warn!("An index was built but no entries were found")
        }
        offset
    }
}

impl<
        R: SeekRead,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > SpectrumSource<C, D, MultiLayerSpectrum<C, D>> for MGFReaderType<R, C, D>
{
    fn detail_level(&self) -> &DetailLevel {
        &self.detail_level
    }

    fn set_detail_level(&mut self, detail_level: DetailLevel) {
        self.detail_level = detail_level;
    }

    /// Retrieve a spectrum by it's native ID
    fn get_spectrum_by_id(&mut self, id: &str) -> Option<MultiLayerSpectrum<C, D>> {
        let offset = self.index.get(id)?;
        let index = self.index.index_of(id)?;
        let start = self
            .handle
            .stream_position()
            .expect("Failed to save checkpoint");
        self.seek(SeekFrom::Start(offset))
            .expect("Failed to move seek to offset");
        let result = self.read_next();
        self.seek(SeekFrom::Start(start))
            .expect("Failed to restore offset");
        result.map(|mut scan| {
            scan.description.index = index;
            scan
        })
    }

    /// Retrieve a spectrum by it's integer index
    fn get_spectrum_by_index(&mut self, index: usize) -> Option<MultiLayerSpectrum<C, D>> {
        let (_id, byte_offset) = self.index.get_index(index)?;
        let start = self
            .handle
            .stream_position()
            .expect("Failed to save checkpoint");
        self.seek(SeekFrom::Start(byte_offset)).ok()?;
        let result = self.read_next();
        self.seek(SeekFrom::Start(start))
            .expect("Failed to restore offset");
        result.map(|mut scan| {
            scan.description.index = index;
            scan
        })
    }

    /// Return the data stream to the beginning
    fn reset(&mut self) {
        self.seek(SeekFrom::Start(0))
            .expect("Failed to reset file stream");
        self.read_counter = 0;
    }

    fn get_index(&self) -> &OffsetIndex {
        if !self.index.init {
            warn!("Attempting to use an uninitialized offset index on MGFReaderType")
        }
        &self.index
    }

    fn set_index(&mut self, index: OffsetIndex) {
        self.index = index;
    }
}

impl<
        R: SeekRead,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > RandomAccessSpectrumIterator<C, D, MultiLayerSpectrum<C, D>> for MGFReaderType<R, C, D>
{
    fn start_from_id(&mut self, id: &str) -> Result<&mut Self, SpectrumAccessError> {
        match self._offset_of_id(id) {
            Some(offset) => match self.seek(SeekFrom::Start(offset)) {
                Ok(_) => {
                    self.read_counter = self.index.index_of(id).unwrap();
                    Ok(self)
                }
                Err(err) => Err(SpectrumAccessError::IOError(Some(err))),
            },
            None => Err(SpectrumAccessError::SpectrumIdNotFound(id.to_string())),
        }
    }

    fn start_from_index(&mut self, index: usize) -> Result<&mut Self, SpectrumAccessError> {
        match self._offset_of_index(index) {
            Some(offset) => match self.seek(SeekFrom::Start(offset)) {
                Ok(_) => {
                    self.read_counter = index;
                    Ok(self)
                }
                Err(err) => Err(SpectrumAccessError::IOError(Some(err))),
            },
            None => Err(SpectrumAccessError::SpectrumIndexNotFound(index)),
        }
    }

    fn start_from_time(&mut self, time: f64) -> Result<&mut Self, SpectrumAccessError> {
        let scan = self.get_spectrum_by_time(time);
        let index = match scan {
            Some(scan) => scan.index(),
            None => return Err(SpectrumAccessError::SpectrumNotFound),
        };
        match self._offset_of_index(index) {
            Some(offset) => match self.seek(SeekFrom::Start(offset)) {
                Ok(_) => {
                    self.read_counter = index;
                    Ok(self)
                }
                Err(err) => Err(SpectrumAccessError::IOError(Some(err))),
            },
            None => Err(SpectrumAccessError::SpectrumNotFound),
        }
    }
}

impl<
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > MZFileReader<C, D, MultiLayerSpectrum<C, D>> for MGFReaderType<fs::File, C, D>
{
    fn open_file(source: fs::File) -> io::Result<Self> {
        Ok(Self::new(source))
    }

    fn construct_index_from_stream(&mut self) -> u64 {
        self.build_index()
    }
}

/// The MGF format does not contain any consistent metadata, but additional
/// information can be included after creation.
impl<
        R: io::Read,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > MSDataFileMetadata for MGFReaderType<R, C, D>
{
    crate::impl_metadata_trait!();

    fn spectrum_count_hint(&self) -> Option<u64> {
        if self.index.init {
            Some(self.index.len() as u64)
        } else {
            None
        }
    }

    fn run_description(&self) -> Option<&MassSpectrometryRun> {
        Some(&self.run)
    }

    fn run_description_mut(&mut self) -> Option<&mut MassSpectrometryRun> {
        Some(&mut self.run)
    }
}

impl<
        R: Read,
        C: CentroidLike + From<CentroidPeak>,
        D: DeconvolutedCentroidLike + From<DeconvolutedPeak>,
    > ChromatogramSource for MGFReaderType<R, C, D>
{
    fn get_chromatogram_by_id(&mut self, _: &str) -> Option<Chromatogram> {
        None
    }

    fn get_chromatogram_by_index(&mut self, _: usize) -> Option<Chromatogram> {
        None
    }

    fn count_chromatograms(&self) -> usize {
        0
    }
}

pub type MGFReader<R> = MGFReaderType<R, CentroidPeak, DeconvolutedPeak>;