Struct rustyms::spectrum::RawSpectrum

pub struct RawSpectrum {

    pub title: String,
    pub num_scans: u64,
    pub rt: Time,
    pub charge: Charge,
    pub mass: Mass,
    pub intensity: Option<f64>,
    pub sequence: Option<String>,
    pub raw_file: Option<String>,
    pub raw_scan_number: Option<usize>,
    pub raw_index: Option<usize>,
    pub sample: Option<usize>,
    pub period: Option<usize>,
    pub cycle: Option<usize>,
    pub experiment: Option<usize>,
    pub controller_type: Option<usize>,
    pub controller_number: Option<usize>,
    /* private fields */
}

A raw spectrum (meaning not annotated yet)

Fields

title: String

The title (as used in MGF)

num_scans: u64

The number of scans

rt: Time

The retention time

charge: Charge

The found precursor charge

mass: Mass

The found precursor mass

intensity: Option<f64>

The found precursor intensity

sequence: Option<String>

MGF: if present the SEQUENCE line

raw_file: Option<String>

MGF TITLE: if present the raw file where this mgf was made from

raw_scan_number: Option<usize>

MGF TITLE: if present the raw file scan number

raw_index: Option<usize>

MGF TITLE: index number

sample: Option<usize>

MGF TITLE: sample number

period: Option<usize>

MGF TITLE: period number

cycle: Option<usize>

MGF TITLE: cycle number

experiment: Option<usize>

MGF TITLE: experiment number

controller_type: Option<usize>

MGF TITLE: controllerType number

controller_number: Option<usize>

MGF TITLE: controllerNumber number

Implementations

impl RawSpectrum

pub fn relative_noise_filter(&mut self, filter_threshold: f64)

Filter the spectrum to retain all with an intensity above filter_threshold times the maximal intensity.

Panics

It panics if any peaks has an intensity that is NaN.

pub fn absolute_noise_filter(&mut self, filter_threshold: f64)

Filter the spectrum to retain all with an intensity above filter_threshold.

pub fn top_x_filter(&mut self, window_size: f64, top: usize)

Filter a spectrum by dividing it in windows and within each window only retain the top number of peaks.

pub fn annotate( &self, peptide: ComplexPeptide, theoretical_fragments: &[Fragment], model: &Model, mode: MassMode ) -> AnnotatedSpectrum

Annotate this spectrum with the given peptide and given fragments see crate::ComplexPeptide::generate_theoretical_fragments.

Panics

If any fragment does not have a defined m/z

Trait Implementations

impl Clone for RawSpectrum

fn clone(&self) -> RawSpectrum

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for RawSpectrum

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for RawSpectrum

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for RawSpectrum

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Extend<RawPeak> for RawSpectrum

fn extend<T: IntoIterator<Item = RawPeak>>(&mut self, iter: T)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl Index<usize> for RawSpectrum

type Output = RawPeak

The returned type after indexing.

fn index(&self, index: usize) -> &Self::Output

Performs the indexing (container[index]) operation.

impl IntoIterator for RawSpectrum

type Item = RawPeak

The type of the elements being iterated over.

type IntoIter = IntoIter<RawPeak>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl PartialEq for RawSpectrum

fn eq(&self, other: &RawSpectrum) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for RawSpectrum

fn partial_cmp(&self, other: &RawSpectrum) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl PeakSpectrum for RawSpectrum

fn binary_search(&self, low: MassOverCharge, high: MassOverCharge) -> &[RawPeak]

Return the slice of peaks that is within the given tolerance bounds.

type PeakType = RawPeak

The type of peaks this spectrum contains

type Iter<'a> = Iter<'a, <RawSpectrum as PeakSpectrum>::PeakType>

The type of spectrum iterator this spectrum generates

fn spectrum(&self) -> Self::Iter<'_>

Get the full spectrum

fn add_peak(&mut self, item: Self::PeakType)

Add a single peak

impl Serialize for RawSpectrum

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl StructuralPartialEq for RawSpectrum