Class for holding a list of ms_fragment objects. More...

#include <ms_fragmentvector.hpp>

Public Types
enum	MATCH_PEAKS { MATCH_MOST_INTENSE_PEAK = 0x0000 , MATCH_CLOSEST_PEAK = 0x0001 }
	Flags for matching experimental peaks to calculated peaks. More...

enum	TOLERANCE_UNIT { TOLERANCE_DALTON , TOLERANCE_MMU , TOLERANCE_PERCENT , TOLERANCE_PPM }
	Flags for tolerance units used for matching peaks. More...

Public Member Functions
	ms_fragmentvector ()
	Default constructor.

	ms_fragmentvector (const ms_fragmentvector &src)
	Copying constructor.

virtual	~ms_fragmentvector ()
	Destructor.

bool	addExperimentalData (const ms_mascotresfilebase *resfile, const int query, const int flags=MATCH_MOST_INTENSE_PEAK, const int peaksUsedFromIons1=-1, const int peaksUsedFromIons2=-1, const int peaksUsedFromIons3=-1)
	Find matches to peaks lists from a Mascot results file.

bool	addExperimentalData (const peaklist_t &peakList, const double tolerance, const std::string &toleranceUnits, const bool updateMatchList=true)
	Find matches to peak list.

bool	addExperimentalData (const std::string &peakList, const int numPeaks, const double tolerance, const std::string &toleranceUnits, const bool updateMatchList=true)
	Find matches to peak list.

void	appendFragment (const ms_fragment *item)
	Adds a new fragment to the end of the vector.

void	clearFragments ()
	Deletes all fragments from the vector.

void	copyFrom (const ms_fragmentvector *right)
	Copies all content from another instance.

const ms_fragment *	getFragmentByNumber (const unsigned int numFrag) const
	Return a fragment object by its number.

int	getNumberOfFragments () const
	Returns a number of fragments currently held in the vector.

frag_vector *	getVector ()
	Return a pointer to the STL vector of ms_fragment objects.

const frag_vector *	getVector () const
	Return a const pointer to the STL vector of ms_fragment objects.

ms_fragmentvector &	operator= (const ms_fragmentvector &right)
	C++ style assignment operator.

Static Public Member Functions
static void	getMassesWithinTolerance (const double mass, const double toleranceValue, const TOLERANCE_UNIT toleranceUnit, double &minMass, double &maxMass)
	Get minimum and maximum masses within tolerance for a specified mass.

Detailed Description

Class for holding a list of ms_fragment objects.

This class is necessary when using Mascot Parser from programming language other than C++. It is used when calling ms_aahelper::calcFragments().

C++ users will generally just want to use a std::vector<ms_fragment> as it is easier.

Examples: tools_aahelper.cpp.

Member Enumeration Documentation

◆ MATCH_PEAKS

enum MATCH_PEAKS

Flags for matching experimental peaks to calculated peaks.

Used as flags for addExperimentalData() when passing a ms_mascotresfilebase object.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
MATCH_MOST_INTENSE_PEAK	Match the most intense peak in the region.
MATCH_CLOSEST_PEAK	Match the peak with the closest m/z value (not currently supported).

◆ TOLERANCE_UNIT

enum TOLERANCE_UNIT

Flags for tolerance units used for matching peaks.

Used as flags for getMassesWithinTolerance()

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
TOLERANCE_DALTON	Simple Daltons.
TOLERANCE_MMU	milli mass units (1000th of a Dalton)
TOLERANCE_PERCENT	Percentage of the fragment or peptide mass.
TOLERANCE_PPM	Parts per million of the fragment or peptide mass.

Constructor & Destructor Documentation

◆ ms_fragmentvector() [1/2]

ms_fragmentvector ( )

Default constructor.

Create a default empty list of fragments.

◆ ms_fragmentvector() [2/2]

ms_fragmentvector ( const ms_fragmentvector & src )

Copying constructor.

Note: This constructor can only be used from C++. Use copyFrom() from other programming languages.

Parameters

src	is the original list to base the new list on.

◆ ~ms_fragmentvector()

~ms_fragmentvector ( )

virtual

Destructor.

No need to call this directly. Frees the list of fragments.

Member Function Documentation

◆ addExperimentalData() [1/2]

bool addExperimentalData	(	const ms_mascotresfilebase *	resfile,
		const int	query,
		const int	flags = `MATCH_MOST_INTENSE_PEAK`,
		const int	peaksUsedFromIons1 = `-1`,
		const int	peaksUsedFromIons2 = `-1`,
		const int	peaksUsedFromIons3 = `-1`
	)

Find matches to peaks lists from a Mascot results file.

This function matches experimental data to the calculated fragment matches. To find which peaks are matched, use ms_fragment::getMatchedIonMass() and ms_fragment::getMatchedIonIntensity(). The peak list is extracted from the results file using the query number specified.

Parameters

resfile	is the Mascot results file from which the fragments were initially calculated. The results file is used to find the peak list and the tolerances to be used for matching.
query	is the query number in the range 1..ms_mascotresfilebase::getNumQueries().
flags	is a MATCH_PEAKS value. Currently only MATCH_MOST_INTENSE_PEAK is supported.
peaksUsedFromIons1	is the number of peaks from the peak list in the passed the results file to be used for matching. Use -1 to indicate all peaks. See also ms_peptide::getPeaksUsedFromIons1() and ms_inputquery::getStringIons1().
peaksUsedFromIons2	is the number of peaks from the peak list in the passed the results file to be used for matching. Use -1 to indicate all peaks. See also ms_peptide::getPeaksUsedFromIons2() and ms_inputquery::getStringIons2().
peaksUsedFromIons3	is the number of peaks from the peak list in the passed the results file to be used for matching. Use -1 to indicate all peaks. See also ms_peptide::getPeaksUsedFromIons3() and ms_inputquery::getStringIons3().

Returns: indicates if the function was successful. It will only fail if the results file is invalid or if the query number is invalid.

◆ addExperimentalData() [2/2]

bool addExperimentalData	(	const std::string &	peakList,
		const int	numPeaks,
		const double	tolerance,
		const std::string &	toleranceUnits,
		const bool	updateMatchList = `true`
	)

Find matches to peak list.

This function matches the peakList to the calculated fragment matches. To find which peaks are matched, use ms_fragment::getMatchedIonMass() and ms_fragment::getMatchedIonIntensity().

Parameters

peakList	will be of the form `136.070000:42.95,175.110000:133.1, 299.060000:710.1,415.030000:144.6 .` and may be retrieved using ms_inputquery::getStringIons1().
numPeaks	is the number of peaks to be used from the list. If this is -1, then all peaks are used. To only match peaks used for matching by the search engine, pass ms_peptide::getPeaksUsedFromIons1().
tolerance	is the tolerance to be used for matching the ions. This can be found from ms_searchparams::getITOL().
toleranceUnits	must be "Da", "mmu" or "ppm". This can be found from ms_searchparams::getITOLU().
updateMatchList	should be set to true if you want to recalculate the list of matches. If this function is to be called multiple times, then set it to false except for the last call.

Returns: indicates if the function was successful. It will only fail if toleranceUnits are invalid.

◆ appendFragment()

void appendFragment ( const ms_fragment * item )

Adds a new fragment to the end of the vector.

A copy of the ms_fragment is made and added to the list, so there is no requirement to keep the original in memory.

Parameters

item	is a new item to add to the list.

Examples: tools_aahelper.cpp.

◆ clearFragments()

void clearFragments ( )

Deletes all fragments from the vector.

After calling this, getNumberOfFragments() will return 0.

◆ copyFrom()

void copyFrom ( const ms_fragmentvector * right )

Copies all content from another instance.

Copy everything from right onto this fragment object.

Parameters

right const pointer to a valid ms_fragmentvector object

Examples: tools_aahelper.cpp.

◆ getFragmentByNumber()

const ms_fragment * getFragmentByNumber ( const unsigned int numFrag ) const

Return a fragment object by its number.

Parameters

numFrag is the fragment to return. This must be in the range 0 to getNumberOfFragments() -1.

Returns: A pointer to the ms_fragment object. See Maintaining object references: two rules of thumb.

Examples: tools_aahelper.cpp.

◆ getMassesWithinTolerance()

void getMassesWithinTolerance	(	const double	mass,
		const double	toleranceValue,
		const TOLERANCE_UNIT	toleranceUnit,
		double &	minMass,
		double &	maxMass
	)

static

Get minimum and maximum masses within tolerance for a specified mass.

This function can be used with any masses - fragments or peptides, and works with relative masses or m/z values. Mascot server applies tolerances to observed m/z values.

See Static functions in Perl, Java, Python and C#

Parameters

[in]	mass	is the mass of the fragment or peptide or protein
[in]	toleranceValue	the tolerance in the units specified by toleranceUnit
[in]	toleranceUnit	any of the four ms_fragmentvector::TOLERANCE_UNIT values
[out]	minMass	Used to return the minimum mass in the range
[out]	maxMass	Used to return the maximum mass in the range

◆ getNumberOfFragments()

int getNumberOfFragments ( ) const

Returns a number of fragments currently held in the vector.

See also: getFragmentByNumber().

Returns: number of fragments

Examples: tools_aahelper.cpp.

◆ getVector() [1/2]

ms_fragmentvector::frag_vector * getVector ( )

Return a pointer to the STL vector of ms_fragment objects.

Note: This function would only ever be of use in C++.

This class is just a wrapper for std::vector<ms_fragment> so it possible to get a pointer to the STL vector if required.

Returns: A pointer to the STL vector.

◆ getVector() [2/2]

const ms_fragmentvector::frag_vector * getVector ( ) const

Return a const pointer to the STL vector of ms_fragment objects.

See also: getVector()

Returns: A pointer to the STL vector.

◆ operator=()

ms_fragmentvector & operator= ( const ms_fragmentvector & right )

C++ style assignment operator.

Parameters

right is the original list to copy to the new list.

Returns: reference to the current object

The documentation for this class was generated from the following files:

ms_fragmentvector.hpp
ms_fragmentvector.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ MATCH_PEAKS

◆ TOLERANCE_UNIT

Constructor & Destructor Documentation

◆ ms_fragmentvector() [1/2]

◆ ms_fragmentvector() [2/2]

◆ ~ms_fragmentvector()

Member Function Documentation

◆ addExperimentalData() [1/2]

◆ addExperimentalData() [2/2]

◆ appendFragment()

◆ clearFragments()

◆ copyFrom()

◆ getFragmentByNumber()

◆ getMassesWithinTolerance()

◆ getNumberOfFragments()

◆ getVector() [1/2]

◆ getVector() [2/2]

◆ operator=()