SpectrumNativeIDParser Class Reference

Parser for extracting scan numbers from spectrum native IDs. More...

#include <OpenMS/METADATA/SpectrumNativeIDParser.h>

Static Public Member Functions
static Int	extractScanNumber (const String &native_id, const boost::regex &scan_regexp, bool no_error=false)
	Extract the scan number from the native ID of a spectrum using a regular expression.
static Int	extractScanNumber (const String &native_id, const String &native_id_type_accession)
	Extract the scan number from the native ID using a CV accession.
static std::string	getRegExFromNativeID (const String &native_id)
	Determine the regular expression to extract scan/index numbers from native IDs.
static bool	isNativeID (const String &id)
	Check if a spectrum identifier is a native ID from a vendor file.

Detailed Description

Parser for extracting scan numbers from spectrum native IDs.

This class provides static functions for parsing native ID strings from various mass spectrometry file formats. Native IDs are vendor-specific identifiers that encode information such as scan numbers, file indices, and experiment numbers.

Supported Native ID Formats

The parser supports the following native ID formats based on CV (Controlled Vocabulary) accessions from the PSI-MS ontology:

CV Accession	Vendor/Format	Native ID Pattern	Example
MS:1000768	Thermo	scan=NUMBER	scan=42
MS:1000769	Waters	function=X process=Y scan=NUMBER	function=2 process=1 scan=100
MS:1000770	WIFF (AB Sciex)	sample=X period=Y cycle=Z experiment=W	sample=1 period=1 cycle=42 experiment=1
MS:1000771	Bruker/Agilent	scan=NUMBER	scan=42
MS:1000772	Bruker BAF	scan=NUMBER	scan=42
MS:1000773	Bruker FID	file=NUMBER	file=42
MS:1000774	Index-based	index=NUMBER	index=42 (returns 43)
MS:1000775	Single peak list	file=NUMBER	file=42
MS:1000776	Thermo/Bruker TDF	scan=NUMBER	scan=42
MS:1000777	Generic spectrum	spectrum=NUMBER	spectrum=42
MS:1001508	Agilent MassHunter	scanId=NUMBER	scanId=42
MS:1001530	Numeric-only	NUMBER	42

Usage Examples

// Extract scan number using CV accession
Int scan = SpectrumNativeIDParser::extractScanNumber("scan=42", "MS:1000768");  // returns 42
 
// Get regex pattern from native ID format
String regex = SpectrumNativeIDParser::getRegExFromNativeID("scan=123");  // returns "scan=(?<GROUP>\d+)"
 
// Check if string is a native ID
bool is_native = SpectrumNativeIDParser::isNativeID("scan=123");  // returns true

See also

SpectrumLookup

Member Function Documentation

extractScanNumber() [1/2]

static Int extractScanNumber ( const String &  native_id, const boost::regex &  scan_regexp, bool  no_error = false  )

static

Extract the scan number from the native ID of a spectrum using a regular expression.

Parameters

[in]	native_id	Spectrum native ID string
[in]	scan_regexp	Regular expression to use (must contain the named group "?<SCAN>")
[in]	no_error	Suppress the exception on failure and return -1 instead

Exceptions

Exception::ParseError

if the scan number could not be extracted (unless no_error is set)

Returns

Scan number of the spectrum (or -1 on failure to extract)

Note

The regular expression must contain a capture group, and the last matching subgroup is used as the scan number.

extractScanNumber() [2/2]

static Int extractScanNumber ( const String &  native_id, const String &  native_id_type_accession  )

static

Extract the scan number from the native ID using a CV accession.

Parameters

[in]	native_id	Spectrum native ID string
[in]	native_id_type_accession	CV accession specifying the native ID format (e.g., "MS:1000768" for Thermo, "MS:1000770" for WIFF)

Returns

Scan number of the spectrum (or -1 on failure to extract)

Note

For WIFF files (MS:1000770), the return value is computed as cycle * 1000 + experiment.

For index-based native IDs (MS:1000774), the return value is index + 1 for pepXML compatibility.

getRegExFromNativeID()

static std::string getRegExFromNativeID ( const String &  native_id )

static

Determine the regular expression to extract scan/index numbers from native IDs.

Parameters

[in]

native_id

A native ID string to analyze

Returns

Regular expression string with named group (?<GROUP>\d+) that matches the scan or index number in the native ID

This function examines the prefix of the native ID to determine the appropriate regular expression pattern:

• scan=, controllerType=, function= → scan=(?<GROUP>\d+)
• index= → index=(?<GROUP>\d+)
• scanId=, scanID= → scanId=(?<GROUP>\d+) or scanID=(?<GROUP>\d+)
• spectrum= → spectrum=(?<GROUP>\d+)
• file= → file=(?<GROUP>\d+)
• Plain number → (?<GROUP>\d+)

isNativeID()

static bool isNativeID ( const String &  id )

static

Check if a spectrum identifier is a native ID from a vendor file.

Parameters

[in]

id

Spectrum identifier string to check

Returns

True if the string matches a known native ID prefix pattern

Recognized prefixes: scan=, scanId=, scanID=, controllerType=, function=, sample=, index=, spectrum=, file=