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...
Public Member Functions
	ms_fragmentvector ()
	Default constructor.
	ms_fragmentvector (const ms_fragmentvector &src)
	Copying constructor.
virtual	~ms_fragmentvector ()
	Destructor.
bool	addExperimentalData (const ms_mascotresfile *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 std::string &peakList, const int numPeaks, const double tolerance, const std::string &toleranceUnits, const bool updateMatchList=true)
	Find matches to peak list.
bool	addExperimentalData (const peaklist_t &peakList, 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.
const frag_vector *	getVector () const
	Return a const pointer to the STL vector of ms_fragment objects.
frag_vector *	getVector ()
	Return a 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 &fragmentMass, const double &fragmentToleranceValue, const TOLERANCE_UNIT &fragmentToleranceUnit, double &minMass, double &maxMass)

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

enum MATCH_PEAKS

Flags for matching experimental peaks to calculated peaks.

Used as flags for addExperimentalData() when passing a ms_mascotresfile 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).

Constructor & Destructor Documentation

ms_fragmentvector ( )

Default constructor.

Create a default empty list of fragments.

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 ( ) [virtual]

Destructor.

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

Member Function Documentation

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.

bool addExperimentalData	(	const ms_mascotresfile *	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_mascotresfile::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.

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.

void clearFragments ( )

Deletes all fragments from the vector.

After calling this, getNumberOfFragments() will return 0.

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.

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.

void getMassesWithinTolerance	(	const double &	fragmentMass,
		const double &	fragmentToleranceValue,
		const TOLERANCE_UNIT &	fragmentToleranceUnit,
		double &	minMass,
		double &	maxMass
	)		`[static]`

Parameters:

[in]	fragmentMass	is the mass of the fragment
[in]	fragmentToleranceValue	the tolerance in the units specified by fragmentToleranceUnit
[in]	fragmentToleranceUnit	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

int getNumberOfFragments ( ) const

Returns a number of fragments currently held in the vector.

See also:: getFragmentByNumber().

Returns:: number of fragments

Examples:: tools_aahelper.cpp.

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.

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.

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

ms_fragmentvector Class Reference [Classes for calculating masses of peptides and fragments.]

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

ms_fragmentvector Class Reference
[Classes for calculating masses of peptides and fragments.]