Enum NativeSpectrumIdentifierFormatTerm 

pub enum NativeSpectrumIdentifierFormatTerm {
    NativeSpectrumIdentifierFormat,
    ThermoNativeIDFormat,
    WatersNativeIDFormat,
    WIFFNativeIDFormat,
    BrukerAgilentYEPNativeIDFormat,
    BrukerBAFNativeIDFormat,
    BrukerFIDNativeIDFormat,
    MultiplePeakListNativeIDFormat,
    SinglePeakListNativeIDFormat,
    ScanNumberOnlyNativeIDFormat,
    SpectrumIdentifierNativeIDFormat,
    BrukerU2NativeIDFormat,
    NoNativeIDFormat,
    ShimadzuBiotechNativeIDFormat,
    MobilionMBINativeIDFormat,
    SCIEXTOFTOFNativeIDFormat,
    AgilentMassHunterNativeIDFormat,
    SpectrumFromDatabaseIntegerNativeIDFormat,
    MascotQueryNumber,
    SpectrumFromProteinScapeDatabaseNativeIDFormat,
    SpectrumFromDatabaseStringNativeIDFormat,
    SCIEXTOFTOFT2DNativeIDFormat,
    ScaffoldNativeIDFormat,
    BrukerContainerNativeIDFormat,
    UIMFNativeIDFormat,
    BrukerTDFNativeIDFormat,
    ShimadzuBiotechQTOFNativeIDFormat,
    BrukerTSFNativeIDFormat,
}

A text-based schema that defines how native spectrum identifiers are formatted. These patterns are often found in mzML-compatible formats.

Variants

NativeSpectrumIdentifierFormat

native spectrum identifier format - (.+)

ThermoNativeIDFormat

Thermo nativeID format - controllerType=(?<controllerType>\d+) controllerNumber=(?<controllerNumber>\d+) scan=(?<scan>\d+)

WatersNativeIDFormat

Waters nativeID format - function=(?<function>\d+) process=(?<process>\d+) scan=(?<scan>\d+)

WIFFNativeIDFormat

WIFF nativeID format - sample=(?<sample>\d+) period=(?<period>\d+) cycle=(?<cycle>\d+) experiment=(?<experiment>\d+)

BrukerAgilentYEPNativeIDFormat

Bruker/Agilent YEP nativeID format - scan=(?<scan>\d+)

BrukerBAFNativeIDFormat

Bruker BAF nativeID format - scan=(?<scan>\d+)

BrukerFIDNativeIDFormat

Bruker FID nativeID format - file=(?<file>\S+)

MultiplePeakListNativeIDFormat

multiple peak list nativeID format - index=(?<index>\d+)

SinglePeakListNativeIDFormat

single peak list nativeID format - file=(?<file>\S+)

ScanNumberOnlyNativeIDFormat

scan number only nativeID format - scan=(?<scan>\d+)

SpectrumIdentifierNativeIDFormat

spectrum identifier nativeID format - spectrum=(?<spectrum>\d+)

BrukerU2NativeIDFormat

Bruker U2 nativeID format - declaration=(?<declaration>\d+) collection=(?<collection>\d+) scan=(?<scan>\d+)

NoNativeIDFormat

no nativeID format - (.+)

ShimadzuBiotechNativeIDFormat

Shimadzu Biotech nativeID format - source=(?<source>\S+) start=(?<start>\d+) end=(?<end>\d+)

MobilionMBINativeIDFormat

Mobilion MBI nativeID format - frame=(?<frame>\d+) scan=(?<scan>\d+)

SCIEXTOFTOFNativeIDFormat

SCIEX TOF/TOF nativeID format - jobRun=(?<jobRun>\d+) spotLabel=(?<spotLabel>\S+) spectrum=(?<spectrum>\d+)

AgilentMassHunterNativeIDFormat

Agilent MassHunter nativeID format - scanId=(?<scanId>\d+)

SpectrumFromDatabaseIntegerNativeIDFormat

spectrum from database integer nativeID format - databasekey=(?<databasekey>-?\d+)

MascotQueryNumber

Mascot query number - query=(?<query>\d+)

SpectrumFromProteinScapeDatabaseNativeIDFormat

spectrum from ProteinScape database nativeID format - databasekey=(?<databasekey>-?\d+)

SpectrumFromDatabaseStringNativeIDFormat

spectrum from database string nativeID format - databasekey=(?<databasekey>\S+)

SCIEXTOFTOFT2DNativeIDFormat

SCIEX TOF/TOF T2D nativeID format - file=(?<file>\S+)

ScaffoldNativeIDFormat

Scaffold nativeID format - (.+)

BrukerContainerNativeIDFormat

Bruker Container nativeID format - (.+)

UIMFNativeIDFormat

UIMF nativeID format - frame=(?<frame>\d+) scan=(?<scan>\d+) frameType=(?<frameType>\d+)

BrukerTDFNativeIDFormat

Bruker TDF nativeID format - frame=(?<frame>\d+) scan=(?<scan>\d+)

ShimadzuBiotechQTOFNativeIDFormat

Shimadzu Biotech QTOF nativeID format - scan=(?<scan>\d+)

BrukerTSFNativeIDFormat

Bruker TSF nativeID format - frame=(?<frame>\d+)

Implementations

impl NativeSpectrumIdentifierFormatTerm

These methods are part of the controlled vocabulary mapping

pub const fn accession(&self) -> u32

Retrieve the accession number for this term, independent of its controlled vocabulary

pub const fn controlled_vocabulary(&self) -> ControlledVocabulary

Retrieve the controlled vocabulary this term belongs to

pub const fn name(&self) -> &'static str

Retrieve the plain text human readable name for this term

pub fn from_name(name: &str) -> Option<NativeSpectrumIdentifierFormatTerm>

Attempt to map a string by name to retrieve one of the terms from this set.

If no match is found, None is returned.

pub const fn from_accession( accession: u32, ) -> Option<NativeSpectrumIdentifierFormatTerm>

Attempt to map the numeric accession number to retrieve one of the terms from this set.

If no match is found, None is returned.

pub const fn to_param(self) -> ParamCow<'static>

Convert this term into a ParamCow without a value.

pub const fn from_curie( curie: &CURIE, ) -> Option<NativeSpectrumIdentifierFormatTerm>

Convert a CURIE by accession.

If no match is found, None is returned.

pub const fn from_param( p: &ParamCow<'static>, ) -> Option<NativeSpectrumIdentifierFormatTerm>

Attempt to convert a ParamCow to a term from this set.

If no match is found, None is returned.

Note

This method can be called in const contexts, requiring the type be ParamCow with a 'static lifetime parameter, but the regular From trait is implemented for all ParamLike types.

pub fn flags(&self) -> &str

Retrieve a term set specific set of flags

pub fn parents(&self) -> Vec<NativeSpectrumIdentifierFormatTerm>

Retrieve the list of zero or more terms in the set which are parents of this term.

impl NativeSpectrumIdentifierFormatTerm

pub fn parser(&self) -> Regex

Create a new regex::Regex for this identifier format.

pub fn parse<'h>(&self, ident: &'h str) -> Option<Captures<'h>>

This parses the provided string, returning the captured groups of the ID pattern if they are present in a regex::Captures structure that can be indexed by group number.

Note

This method creates a new regular expression on each invocation, making it expensive to invoke. If you must call this repeatedly, instead use NativeSpectrumIdentifierFormatTerm::build to create a the regular expression once and re-use it directly.

pub fn build(&self) -> NativeSpectrumIDFormat

Create a NativeSpectrumIDFormat that owns the Regex produced by NativeSpectrumIdentifierFormatTerm::parser

pub fn format<'h>( &self, values: impl IntoIterator<Item = ValueRef<'h>>, ) -> String

Given the field values of a nativeID format, create string in that format

Note

This method creates a new expression formatter every time. Use NativeSpectrumIdentifierFormatTerm::build to create a re-useable parser/formatter.

pub fn parse_named<'h>(&self, ident: &'h str) -> Vec<(Option<String>, &'h str)>

This parses the provided string, returning the capture groups as (name, value) pairs they are present.

Note

This method creates a new regular expression on each invocation, making it expensive to invoke. If you must call this repeatedly, instead use NativeSpectrumIdentifierFormatTerm::build to create a the regular expression once and re-use it directly.

Trait Implementations

impl Clone for NativeSpectrumIdentifierFormatTerm

fn clone(&self) -> NativeSpectrumIdentifierFormatTerm

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for NativeSpectrumIdentifierFormatTerm

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

Formats the value using the given formatter.

impl From<&NativeSpectrumIdentifierFormatTerm> for Param

fn from(value: &NativeSpectrumIdentifierFormatTerm) -> Param

Converts to this type from the input type.

impl From<&NativeSpectrumIdentifierFormatTerm> for ParamCow<'static>

fn from(value: &NativeSpectrumIdentifierFormatTerm) -> ParamCow<'static>

Converts to this type from the input type.

impl From<NativeSpectrumIdentifierFormatTerm> for NativeSpectrumIDFormat

fn from(value: NativeSpectrumIdentifierFormatTerm) -> NativeSpectrumIDFormat

Converts to this type from the input type.

impl From<NativeSpectrumIdentifierFormatTerm> for Param

fn from(value: NativeSpectrumIdentifierFormatTerm) -> Param

Converts to this type from the input type.

impl From<NativeSpectrumIdentifierFormatTerm> for ParamCow<'static>

fn from(value: NativeSpectrumIdentifierFormatTerm) -> ParamCow<'static>

Converts to this type from the input type.

impl<P> From<P> for NativeSpectrumIdentifierFormatTerm

where P: ParamLike,

fn from(value: P) -> NativeSpectrumIdentifierFormatTerm

Converts to this type from the input type.

impl PartialEq for NativeSpectrumIdentifierFormatTerm

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl Copy for NativeSpectrumIdentifierFormatTerm

impl Eq for NativeSpectrumIdentifierFormatTerm

impl StructuralPartialEq for NativeSpectrumIdentifierFormatTerm