This class encapsulates the input queries (peak lists) in the Mascot results file. More...

#include <ms_inputquery.hpp>

Public Member Functions
	ms_inputquery (const ms_mascotresfilebase &resfile, const int q)
	Use this contructor to create an object to get the input data.

bool	getAverageCharge (int averageCharge, double averageChargeDbl=0) const
	For Waters MS^E data, return the average charge.

std::string	getCharge () const
	Returns a string that represents the supplied charge for the query.

std::string	getComp (int comp_no) const
	Returns a string that represents one of the sequence queries.

int	getIndex () const
	Returns the zero based index of the peak list in an MGF, PKL or DTA file.

std::string	getINSTRUMENT (const bool unescaped=true) const
	Returns an `INSTRUMENT` string if this has been specified at the query level.

double	getIntMax () const
	Returns the maximum intensity of any ion.

double	getIntMin () const
	Returns the minimum intensity of any ion.

double	getIonMobility () const
	Returns the ion mobility specified using the ION_MOBILITY= line.

std::string	getIT_MODS (const bool unescaped=true) const
	Returns the names of variable modifications if such have been specified at the query level.

std::string	getLocalVarModName (const int num) const
	Returns the query-level modification name by 1-based index.

std::string	getLocus () const
	Returns the locus specified in the MGF file using the LOCUS= line.

double	getMassMax () const
	Returns the maximum mass of any ion.

double	getMassMin () const
	Returns the minimum mass of any ion.

double	getMaxInternalMass () const
	Returns the maximum mass to be considered for internal fragments if an `INSTRUMENT` has been specified at the query level.

double	getMinInternalMass () const
	Returns the minimum mass to be considered for internal fragemnts if an `INSTRUMENT` has been specified at the query level.

int	getNumberOfLocalVarMods () const
	Returns the number of query-level variable modifications.

int	getNumberOfPeaks (const int ions) const
	Returns the number of ions peaks in an ms-ms spectrum.

int	getNumUsed () const
	Returns the number of ions used for matching - value no longer available.

int	getNumVals () const
	Returns the number of ions.

int	getPeakCharge (const int ions, const int peakNo) const
	Returns the charge of a particular ions peak.

double	getPeakIntensity (const int ions, const int peakNo) const
	Returns the intensity of a particular ions peak.

std::vector< std::pair< double, double > >	getPeakList (const int ions) const
	Returns a list of ions peaks for a query.

double	getPeakMass (const int ions, const int peakNo) const
	Returns the mass of a particular ions peak.

double	getPepTol () const
	Returns the peptide tolerance for this query.

std::string	getPepTolString () const
	Returns the peptol string .

std::string	getPepTolUnits () const
	Returns the peptide tolerance units for this query.

int	getQueryNumber () const
	Returns the Mascot query number.

std::string	getRawfile () const
	Returns the rawfile specified in the MGF file using the RAWFILE= line.

std::string	getRawScans (const int rawFileIdx=-1) const
	Returns the rawscan number(s) that were used to generate this peak list.

void	getRawScans (std::vector< int > &index, std::vector< std::string > &rawscans) const
	Returns all rawscan numbers that were used to generate this peak list.

std::string	getRetentionTimes (const int rawFileIdx=-1) const
	Returns the retention time(s) in seconds of the scans that were used to generate this peak list.

void	getRetentionTimes (std::vector< int > &index, std::vector< std::string > &times) const
	Returns all retention times in seconds of the scans that were used to generate this peak list.

std::string	getRULES () const
	Returns the instrument rules if this has been specified at the query level.

std::string	getScanNumbers (const int rawFileIdx=-1) const
	Returns the scan number(s) that were used to generate this peak list.

void	getScanNumbers (std::vector< int > &index, std::vector< std::string > &scans) const
	Returns all scan numbers that were used to generate this peak list.

std::string	getSeq (int seq_no) const
	Returns a string that represents one of the sequence queries.

std::string	getStringIons1 (bool includeCharges=false) const
	Returns the peak list for the ions as a string.

std::string	getStringIons2 (bool includeCharges=false) const
	Returns the peak list for the ions as a string.

std::string	getStringIons3 (bool includeCharges=false) const
	Returns the peak list for the ions as a string.

std::string	getStringTitle (bool unescaped) const
	Returns the title for the ms-ms data (if any).

std::string	getTag (int tag_no) const
	Returns a string that represents one of the sequence tag queries.

double	getTotalIonsIntensity () const
	Returns the sum of all the ions intensities.

bool	hasINTERNALS () const
	Returns true if this spectrum has specific internal masses.

Detailed Description

This class encapsulates the input queries (peak lists) in the Mascot results file.

Thread safe: This class is safe to use from multiple threads. See also Using Parser in multithreaded applications.

Examples: resfile_input.cpp.

Constructor & Destructor Documentation

◆ ms_inputquery()

ms_inputquery	(	const ms_mascotresfilebase &	resfile,
		const int	q
	)

Use this contructor to create an object to get the input data.

Constructor for ms_inputquery.

See Maintaining object references: two rules of thumb.

Parameters

resfile	Must be a valid ms_mascotresfilebase object.
q	is the query number and must be in the range 1 to ms_mascotresfilebase::getNumQueries().

Member Function Documentation

◆ getAverageCharge()

bool getAverageCharge	(	int *	averageCharge,
		double *	averageChargeDbl = `0`
	)		const

For Waters MS^E data, return the average charge.

Peak lists form Waters MS^E DIA scan data will most likely have a charge state of 1+ by default. Peptide matches will have been matched based on this charge state. If the datasource is MS^E then it should have valid average charge values. If the average charge value is valid (ie non-zero) then substitute this one instead. MDRO puts the average charge into the query title, so we can check for that and parse it if available.

The only time this is really needed is when searching the survey (MS1) scans for the m/z for the peptide. The values recorded in the search results file for the m/z and mr values are 'decharged' to 1+. To find the true m/z, recalulate it using the mr value and the average charge.

The average charge will normally be a floating point value. Suppose the data is made from one 2+ ion and three 3+ ions. The average might then be 2.75. This value will be returned in averageChargeDbl but it is generally more useful to use the rounded integer value which would be 3 in this case.

See Multiple return values in Perl, Java, Python and C#.

Parameters

[out]	averageCharge	will be set to this if found. If not, the value will be set to 0. This is the rounded integer value
[out]	averageChargeDbl	is the floating point value. Passing a null value is acceptable.

Returns: True if an average charge value was found, false if not

◆ getCharge()

std::string getCharge ( ) const

Returns a string that represents the supplied charge for the query.

This value will only be present if a charge was specified at the query level in the input (MGF, PKL, mzData, DTA) file. It will normally be one of the following strings:

'8-'
'7-'
'6-'
'5-'
'4-'
'3-'
'2- and 3-'
'2-'
'1-, 2- and 3-'
'1-'
'Mr'
'1+'
'1+, 2+ and 3+'
'2+'
'2+ and 3+'
'3+'
'4+'
'5+'
'6+'
'7+'
'8+'

The charge can also be any comma separated list of charge states.

See also: https://www.matrixscience.com/help/search_field_help.html#TWO for further information.

The default charge states are available from ms_searchparams::getCHARGE. Use ms_peptide::getCharge to return the actual charge state that was used for a peptide match.

Returns: The charge(s) as a string.

◆ getComp()

std::string getComp ( int comp_no ) const

Returns a string that represents one of the sequence queries.

Up to 20 sets of composition data can be entered for each peptide mass.

See also: https://www.matrixscience.com/help/search_field_help.html#QUE for further information.

Parameters

comp_no is an index for the comp() command. The input data is available as COMP1, COMP2 COMP3 etc. To get all composition data, call this function with numbers from 1 to 20.

Returns: the comp() command as a string

◆ getIndex()

int getIndex ( ) const

Returns the zero based index of the peak list in an MGF, PKL or DTA file.

In Mascot 2.3 and later, the index of each spectrum is saved as an index= value in each query section or query__data table. This can be useful, because the query numbers are not the same as the index into the text file, and if there are non-unique titles, then it is hard to get back from the query to the original spectrum in the MGF, PKL or DTA file

The index is stored in mzIdentML files using the CV term:

[Term]
id: MS:1000774
name: multiple peak list nativeID format
def: "index=xsd:nonNegativeInteger" [PSI:MS]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a: MS:1000767 ! native spectrum identifier format

Returns: A zero based index, or -1 if the value is not available.

◆ getINSTRUMENT()

std::string getINSTRUMENT ( const bool unescaped = true ) const

Returns an INSTRUMENT string if this has been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when INSTRUMENT is specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     INSTRUMENT=ETD_TRAP
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the INSTRUMENT= line in the relevant query section or query__data table of the results file. If there is no instrument specified at the query level, then the INSTRUMENT specified in the search form is used. This can be retrieved using ms_searchparams::getINSTRUMENT().

See also ms_inputquery::getRULES(). It is preferable to use the rules rather than this name to determine which ions series were searched since the user can change the definition of the instrument name.

See also: https://www.matrixscience.com/help/search_field_help.html#INSTRUMENT for further information.

Parameters

unescaped has to be TRUE for human-readable instrument name and FALSE for generating input for a mascot search.

Returns: The INSTRUMENT string, or an empty string if no instrument was specified at the query level.

◆ getIntMax()

double getIntMax ( ) const

Returns the maximum intensity of any ion.

Returns: The maximum intensity. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the maximum intensity of any ion.

◆ getIntMin()

double getIntMin ( ) const

Returns the minimum intensity of any ion.

Returns: The minimum intensity. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the minimum intensity of any ion.

◆ getIonMobility()

double getIonMobility ( ) const

Returns the ion mobility specified using the ION_MOBILITY= line.

The value is only available if client software specified it in the MGF file. Ion mobility could be 1/k_0 or some other value. The unit and dimension depends on what the client software provided.

Returns: The ion mobility.

◆ getIT_MODS()

std::string getIT_MODS ( const bool unescaped = true ) const

Returns the names of variable modifications if such have been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when variable modifications are specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     IT_MODS=Phospho (STY)
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the IT_MODS= line in the relevant query section or query__data table of the results file. If there are no modifications specified at the query level, then the IT_MODS specified in the search parameters are used. These can be retrieved using ms_searchparams::getIT_MODS().

See also: https://www.matrixscience.com/help/search_field_help.html#MODS

Parameters

unescaped has to be TRUE for human readable modification names and FALSE for generating input for a mascot search.

Returns: The IT_MODS string, or an empty string if no local modifications were specified.

◆ getLocalVarModName()

std::string getLocalVarModName ( const int num ) const

Returns the query-level modification name by 1-based index.

This method returns unescaped modification names as returned by getIT_MODS(), but accessible with a 1-based numerical index. You can produce the same vector of modification titles by splitting the return value of getIT_MODS(true) on comma ",".

Parameters

num	Index of the query-level modification between 1 and getNumberOfLocalVarMods().

Returns: The modification name, or the empty string if num is outside the index range.

◆ getLocus()

std::string getLocus ( ) const

Returns the locus specified in the MGF file using the LOCUS= line.

LOCUS is an optional attribute for an MS-MS peak list in an MGF file.

LOCUS was introduced in Mascot 2.4

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Returns: The locus= value in the query section or query__data table.

◆ getMassMax()

double getMassMax ( ) const

Returns the maximum mass of any ion.

Returns: The maximum mass. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the maximum mass of any ion.

◆ getMassMin()

double getMassMin ( ) const

Returns the minimum mass of any ion.

Returns: The minimum mass. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the minimum mass of any ion.

◆ getMaxInternalMass()

double getMaxInternalMass ( ) const

Returns the maximum mass to be considered for internal fragments if an INSTRUMENT has been specified at the query level.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

The value specified for the instrument is saved in the parameters section or search__parameters table of the results file. If there is no INTERNALS= line, the default value of 700.0 is returned. A different instrument can be specified for each MS-MS spectrum, in which case the values are returned using this function and ms_inputquery::getMinInternalMass

See also: getMinInternalMass(), getRULES() and getINSTRUMENT()

Returns: The maximum internal mass considered for this spectrum in this search If no instrument was specified at the query level, then this function will return -1.

◆ getMinInternalMass()

double getMinInternalMass ( ) const

Returns the minimum mass to be considered for internal fragemnts if an INSTRUMENT has been specified at the query level.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

The value specified for the instrument is saved in the parameters section or search__parameters table of the results file. A different instrument can be specified for each MS-MS spectrum, in which case the values are returned using this function and ms_inputquery::getMaxInternalMass.

See also: ms_searchparams::getMinInternalMass(), ms_searchparams::getMaxInternalMass()

Returns: The minimum internal mass considered for this spectrum in this search. If no instrument was specified at the query level, then this function will return -1.

◆ getNumberOfLocalVarMods()

int getNumberOfLocalVarMods ( ) const

Returns the number of query-level variable modifications.

Returns: The number of unescaped modification names from getIT_MODS().

◆ getNumberOfPeaks()

int getNumberOfPeaks ( const int ions ) const

Returns the number of ions peaks in an ms-ms spectrum.

See also: getPeakList(), getPeakMass() and getPeakIntensity()

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series – see https://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as Ions1, Ions2 and Ions3 in the results file. For data uploaded from a file, only ions1 values will be found.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

ions	will be a value of 1..3.

Returns: The number of peaks in the peak list.

◆ getNumUsed()

int getNumUsed ( ) const

Returns the number of ions used for matching - value no longer available.

Parser 2.8 and earlier incorrectly stated that this method returns -1. This method always returns 0.

To find the number of ions peaks used for scoring, see ms_peptide::getPeaksUsedFromIons1, ms_peptide::getPeaksUsedFromIons2 and ms_peptide::getPeaksUsedFromIons3.

Returns: 0

◆ getNumVals()

int getNumVals ( ) const

Returns the number of ions.

This is retrieved from the num_vals= line of the query section or query__data table.

Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the number of all ions.

Returns: The number of ions.

◆ getPeakCharge()

int getPeakCharge	(	const int	ions,
		const int	peakNo
	)		const

Returns the charge of a particular ions peak.

See also: getPeakList(), getNumberOfPeaks() and getPeakMass()

Fragment charge is an optional "third column" in MGF format peak lists. Support was added in Mascot Server 2.7. If fragment charge is unspecified, this method returns 0.

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series – see https://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as Ions1, Ions2 and Ions3 in the results file. For data uploaded from a file, only Ions1 values will be found.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

ions	will be a value of 1..3.
peakNo	should be in the range 1.. getNumberOfPeaks().

Returns: If there is no peak information, then the return value will be 0.

◆ getPeakIntensity()

double getPeakIntensity	(	const int	ions,
		const int	peakNo
	)		const

Returns the intensity of a particular ions peak.

See also: getPeakList(), getNumberOfPeaks() and getPeakMass()

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series – see https://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as Ions1, Ions2 and Ions3 in the results file. For data uploaded from a file, only Ions1 values will be found.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

ions	will be a value of 1..3.
peakNo	should be in the range 1.. getNumberOfPeaks().

Returns: If there is no peak information, then the return value will be 0.

◆ getPeakList()

std::vector< std::pair< double, double > > getPeakList ( const int ions ) const

Returns a list of ions peaks for a query.

This function only works from C++.

For other languages, Use getNumberOfPeaks(), getPeakMass() and getPeakIntensity() instead.

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series – see https://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as Ions1, Ions2 and Ions3 in the results file. For data uploaded from a file, only Ions1 values will be found.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

ions	ions value, can be 1, 2 or 3

Returns: The peak list.

◆ getPeakMass()

double getPeakMass	(	const int	ions,
		const int	peakNo
	)		const

Returns the mass of a particular ions peak.

See also: getPeakList(), getNumberOfPeaks() and getPeakIntensity()

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of b-series, y-series or either series – see https://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as Ions1, Ions2 and Ions3 in the results file. For data uploaded from a file, only Ions1 values will be found.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

ions	will be a value of 1..3.
peakNo	should be in the range 1.. getNumberOfPeaks().

Returns: If there is no peak information, then the return value will be 0.

◆ getPepTol()

double getPepTol ( ) const

Returns the peptide tolerance for this query.

peptol(tolerance,unit) may be used to specify a mass tolerance for an individual query, over-riding the search form default. For example, peptol(10,%) or peptol(2,Da).

Returns: Will return 0 if there is no peptide tolerance override for this query.

◆ getPepTolString()

std::string getPepTolString ( ) const

Returns the peptol string .

Returns, for example, peptol(2.01,Da). The number is always returned in 'fixed' notation. Trailing zeros apart from the one (if any) after the decimal are removed.

This function is intended to be used to create a sequence query string rather than for use to display in a report.

See also: getPepTolUnits(), getPepTol()

Returns: Will return an empty string if there is no peptide tolerance override for this query.

◆ getPepTolUnits()

std::string getPepTolUnits ( ) const

Returns the peptide tolerance units for this query.

In the search form, the command peptol(tolerance,unit) may be used override the default mass tolerance for an individual query. For example, peptol(10,%) or peptol(2,Da).

The units will be one of:

%: fraction expressed as a percentage
mmu: absolute milli-mass units, i.e. units of .001 Da
Da: absolute units of Da
ppm: fraction expressed as parts per million
Da: absolute units of Da

Returns: Will return an empty string if there is no peptide tolerance override for this query.

◆ getQueryNumber()

int getQueryNumber ( ) const

Returns the Mascot query number.

Returns: A 1-based Mascot query number, which was passed as the constructor argument.

◆ getRawfile()

std::string getRawfile ( ) const

Returns the rawfile specified in the MGF file using the RAWFILE= line.

RAWFILE is an optional attribute for an MS-MS peak list in an MGF file.

RAWFILE was introduced in Mascot 2.4.

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Returns: The rawfile= value in the query section or query__data table.

◆ getRawScans() [1/2]

std::string getRawScans ( const int rawFileIdx = -1 ) const

Returns the rawscan number(s) that were used to generate this peak list.

RAWSCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rawscans" with no brackets or zero or more "rawscans[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getRawScans(std::vector<int>&, std::vector<std::string>&).

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

rawFileIdx is the raw file index for MGF files that were created from multiple raw files.

Returns: The scan number(s) in the form a[[-b][,c[-d]]]

◆ getRawScans() [2/2]

void getRawScans	(	std::vector< int > &	index,
		std::vector< std::string > &	rawscans
	)		const

Returns all rawscan numbers that were used to generate this peak list.

RAWSCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rawscans" with no brackets or zero or more "rawscans[i]" lines.

This method returns all rawscans lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query has

rawscans=sn13

then both index and times will have one element. index[0] will be -1 (unbracketed) and rawscans[0] will be sn13. If the query instead has

rawscans[3]=sn13
rawscans[5]=sn24

then index[0] == 3, index[1] == 5 and rawscans[0] == "sn13", rawscans[1] == "sn24".

If you already know which lines are present in the query, you can use ms_inputquery::getRawScans(const int) to access the individual lines.

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

[out]	index	Vector of index numbers for corresponding "rawscans" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]	rawscans	Vector of values from the "rawscans" lines in the same order as the index vector.

◆ getRetentionTimes() [1/2]

std::string getRetentionTimes ( const int rawFileIdx = -1 ) const

Returns the retention time(s) in seconds of the scans that were used to generate this peak list.

RTINSECONDS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rtinseconds" with no brackets or zero or more "rtinseconds[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getRetentionTimes(std::vector<int>&, std::vector<std::string>&).

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

rawFileIdx is the raw file index for MGF files that were created from multiple raw files.

Returns: The retention time(s) in the form v[[-w][,x[-y]]].

◆ getRetentionTimes() [2/2]

void getRetentionTimes	(	std::vector< int > &	index,
		std::vector< std::string > &	times
	)		const

Returns all retention times in seconds of the scans that were used to generate this peak list.

RTINSECONDS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rtinseconds" with no brackets or zero or more "rtinseconds[i]" lines.

This method returns all rtinseconds lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query has

rtinseconds=1234.0

then both index and times will have one element. index[0] will be -1 (unbracketed) and times[0] will be 1234.0. If the query instead has

rtinseconds[3]=1234.0
rtinseconds[5]=1244.0

then index[0] == 3, index[1] == 5 and times[0] == 1234.0, times[1] == 1244.0.

If you already know which lines are present in the query, you can use ms_inputquery::getRetentionTimes(const int) to access the individual lines.

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

[out]	index	Vector of index numbers for corresponding "rtinseconds" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]	times	Vector of values from the "rtinseconds" lines in the same order as the index vector.

◆ getRULES()

std::string getRULES ( ) const

Returns the instrument rules if this has been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when INSTRUMENT is specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     INSTRUMENT=ETD_TRAP
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the RULES= line in the relevant query section or query__data table of the results file. If there is no instrument specified at the query level, then RULES specified in the search form, and the rules for this query are the global rules which can be retrieved using ms_searchparams::getRULES().

It is preferable to use the rules rather than the instrument name to determine which ions series were searched since the user can change the definition of the instrument name.

See also: getINSTRUMENT()

Returns: The RULES string, or an empty string if no instrument was specified. See ms_searchparams::getRULES() for a full definition of the rules.

◆ getScanNumbers() [1/2]

std::string getScanNumbers ( const int rawFileIdx = -1 ) const

Returns the scan number(s) that were used to generate this peak list.

SCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "scans" with no brackets or zero or more "scans[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getScanNumbers(std::vector<int>&, std::vector<std::string>&).

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

rawFileIdx is the raw file index for MGF files that were created from multiple raw files.

Returns: The scan number(s) in the form a[[-b][,c[-d]]].

◆ getScanNumbers() [2/2]

void getScanNumbers	(	std::vector< int > &	index,
		std::vector< std::string > &	scans
	)		const

Returns all scan numbers that were used to generate this peak list.

SCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "scans" with no brackets or zero or more "scans[i]" lines.

This method returns all scans lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query has

scans=1

then both index and scans will have one element. index[0] will be -1 (unbracketed) and scans[0] will be 1. If the query instead has

scans[3]=13
scans[5]=26

then index[0] == 3, index[1] == 5 and scans[0] == 13, scans[1] == 26.

If you already know which lines are present in the query, you can use ms_inputquery::getScanNumbers(const int) to access the individual lines.

See also: https://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters

[out]	index	Vector of index numbers for corresponding "scans" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]	scans	Vector of values from the "scans" lines in the same order as the index vector.

◆ getSeq()

std::string getSeq ( int seq_no ) const

Returns a string that represents one of the sequence queries.

Up to 20 sets of sequence information can be entered for each peptide mass.

See also: https://www.matrixscience.com/help/search_field_help.html#QUE for further information.

Parameters

seq_no is an index for the seq() command. The input data is available as SEQ1, SEQ2 SEQ3 etc. To get all sequence data, call this function with numbers from 1 to 20.

Returns: the seq() command as a string.

◆ getStringIons1()

std::string getStringIons1 ( bool includeCharges = false ) const

Returns the peak list for the ions as a string.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

includeCharges will add any supplied charges to the returned string, so the format will be: m/z[:intensity[:charge]], m/z[:intensity[:charge]]... if no intensities were applied initially, then the string returned will be the same as if this parameter was false

Returns: The Ions1= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .

◆ getStringIons2()

std::string getStringIons2 ( bool includeCharges = false ) const

Returns the peak list for the ions as a string.

The ions2= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

includeCharges will add any supplied charges to the returned string, so the format will be: m/z[:intensity[:charge]], m/z[:intensity[:charge]]... if no intensities were applied initially, then the string returned will be the same as if this parameter was false

Returns: The ions2= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .

◆ getStringIons3()

std::string getStringIons3 ( bool includeCharges = false ) const

Returns the peak list for the ions as a string.

The ions3= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters

includeCharges will add any supplied charges to the returned string, so the format will be: m/z[:intensity[:charge]], m/z[:intensity[:charge]]... if no intensities were applied initially, then the string returned will be the same as if this parameter was false

Returns: The ions3= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .

◆ getStringTitle()

std::string getStringTitle ( bool unescaped ) const

Returns the title for the ms-ms data (if any).

The string will have a maximum length of 30k characters. It might for example be:

1: Scan 2443 (rt=1651.36) [P:\\service\\on_campus\\Nunari\\Laura\\ft20061020.RAW]

Parameters

unescaped - If this is false, then any non alpha-numeric characters in the string will be converted to %xx where the xx are the hex representation of the character.

Returns: The title string.

◆ getTag()

std::string getTag ( int tag_no ) const

Returns a string that represents one of the sequence tag queries.

Up to 20 tag/etag commands can be entered for each peptide mass.

See also: https://www.matrixscience.com/help/search_field_help.html#QUE for further information.

Parameters

tag_no is an index for the tag() command. The input data is available as TAG1, TAG2 TAG3 etc. To get all tags, call this function with numbers from 1 to 20.

Returns: the tag() command as a string in the format e,977.4,[Q|K][Q|K][Q|K]EE,1619.7 where the first character will be 'e' for etag and 't' for tag.

◆ getTotalIonsIntensity()

double getTotalIonsIntensity ( ) const

Returns the sum of all the ions intensities.

See also ms_mascotresfilebase::getObservedIntensity. If the precursor intensity wasn't supplied in the input file, this function can be called instead. Processing this function for a large number of spectra may take some time since it will need to load the Ions1= values from disk and sum all the intensities.

See also ms_peptide::getIonsIntensity which just calls this function.

The Ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Returns: Will return 0 if there is no MS-MS data.

◆ hasINTERNALS()

bool hasINTERNALS ( ) const

Returns true if this spectrum has specific internal masses.

Different values of maximum and minimum internal masses to those in the parameters section or search__parameters table can be specified for each spectrum.

See also: getMinInternalMass() and getMaxIntenalMass()

Returns: true if the minimum and maximum masses are specified for this spectrum

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

ms_inputquery.hpp
ms_inputquery.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_inputquery()

Member Function Documentation

◆ getAverageCharge()

◆ getCharge()

◆ getComp()

◆ getIndex()

◆ getINSTRUMENT()

◆ getIntMax()

◆ getIntMin()

◆ getIonMobility()

◆ getIT_MODS()

◆ getLocalVarModName()

◆ getLocus()

◆ getMassMax()

◆ getMassMin()

◆ getMaxInternalMass()

◆ getMinInternalMass()

◆ getNumberOfLocalVarMods()

◆ getNumberOfPeaks()

◆ getNumUsed()

◆ getNumVals()

◆ getPeakCharge()

◆ getPeakIntensity()

◆ getPeakList()

◆ getPeakMass()

◆ getPepTol()

◆ getPepTolString()

◆ getPepTolUnits()

◆ getQueryNumber()

◆ getRawfile()

◆ getRawScans() [1/2]

◆ getRawScans() [2/2]

◆ getRetentionTimes() [1/2]

◆ getRetentionTimes() [2/2]

◆ getRULES()

◆ getScanNumbers() [1/2]

◆ getScanNumbers() [2/2]

◆ getSeq()

◆ getStringIons1()

◆ getStringIons2()

◆ getStringIons3()

◆ getStringTitle()

◆ getTag()

◆ getTotalIonsIntensity()

◆ hasINTERNALS()