mzdata 0.63.4

A library to read mass spectrometry data formats and a data model for mass spectra
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//! The data structures and components that represent a mass spectrum and how
//! to access their data.
//!
//! A mass spectrum is made up of multiple components, the spectrum's signal data
//! itself, plus all the metadata that describes how that data was acquired by
//! the instrument.
//!
//! # Components
//! - [`bindata`] includes structures for dealing with raw binary data arrays that may or may not
//!   be byte-encoded but not strongly typed, though it does not include signal processing as that
//!   is outside the scope of this crate.
//!
//! # Spectra
//!
//! Represent the collection of attributes and data that compose a single mass spectrum.
//!
//! Because a mass spectrum may be obtained from sources with varying levels of detail,
//! several alternative structures are provided with a common set of trait-based methods
//! to unify access:
//!
//! 1. [`RawSpectrum`] for representing a spectrum that has not been decoded into distinct
//!    peaks yet, but whose data may be continuous or discrete.
//! 2. [`CentroidSpectrum`] for representing spectra from sources which are guaranteed to
//!    be pre-centroided, like those from MGF files or other simple text representations.
//! 3. [`MultiLayerSpectrum`] for representing a multi-layer representation of a spectrum where both
//!    raw data and a distinct peak list are available.
//! 4. [`DeconvolutedSpectrum`] for representing spectra from sources which are guaranteed to be
//!    pre-centroided, deisotoped and charge state deconvoluted.
//!
//! These structures all implement the [`SpectrumLike`] trait
//!
//! The [`SpectrumLike`] trait is included in the crate prelude, and gives the caller
//! read-only access to components that describe a spectrum's metadata.
//!
//! ```rust
//! use mzpeaks::Tolerance;
//! use mzdata::MzMLReader;
//! use mzdata::prelude::*;
//! use mzdata::spectrum::SignalContinuity;
//!
//! let reader = MzMLReader::open_path("./test/data/small.mzML").unwrap();
//! for spectrum in reader {
//!     println!("Scan {} => BP {}", spectrum.id(), spectrum.peaks().base_peak().mz);
//!
//!     if spectrum.signal_continuity() < SignalContinuity::Profile {
//!         let peak_picked = spectrum.into_centroid().unwrap();
//!         println!("Matches for 579.155: {:?}",
//!                  peak_picked.peaks.all_peaks_for(
//!                      579.155, Tolerance::Da(0.02)));
//!     }
//! }
//! ```
//!
//! More examples can be found in the [spectrum tutorial](crate::tutorial::spectrum).

pub mod bindata;
pub(crate) mod chromatogram;
pub(crate) mod frame;
pub(crate) mod group;
pub(crate) mod peaks;
pub(crate) mod scan_properties;
pub(crate) mod spectrum_types;
pub mod utils;

pub use crate::spectrum::bindata::{ArrayType, BinaryArrayMap, BinaryDataArrayType, DataArray};
pub use crate::spectrum::chromatogram::{Chromatogram, ChromatogramLike};
pub use crate::spectrum::scan_properties::*;
pub use crate::spectrum::spectrum_types::{
    CentroidPeakAdapting, CentroidSpectrum, CentroidSpectrumType, DeconvolutedPeakAdapting,
    DeconvolutedSpectrum, DeconvolutedSpectrumType, MultiLayerSpectrum, RawSpectrum, Spectrum,
    SpectrumConversionError, SpectrumLike, SpectrumProcessingError,
};

pub use crate::spectrum::peaks::{
    PeakDataIter, PeakDataIterDispatch, PeakDataLevel, RawIter, RefPeakDataIter, RefPeakDataLevel,
    SpectrumSummary,
};

pub use utils::HasIonMobility;

pub use frame::{
    FeatureDataLevel, IonMobilityFrameDescription, IonMobilityFrameLike,
    MultiLayerIonMobilityFrame, RefFeatureDataLevel
};

pub use group::{
    IonMobilityFrameGroup, IonMobilityFrameGroupIntoIter, IonMobilityFrameGroupIter,
    IonMobilityFrameGroupingIterator, SpectrumGroup, SpectrumGroupIntoIter, SpectrumGroupIter,
    SpectrumGroupingIterator, SpectrumGrouping, IonMobilityFrameGrouping,
};

#[cfg(feature = "mzsignal")]
pub use group::{
    average_spectra, DeferredSpectrumAveragingIterator, SpectrumAveragingIterator,
    SpectrumGroupAveraging,
};