cParameters.h File Reference

Definitions of program parameters. More...

#include <iostream>
#include <fstream>
#include <set>
#include "core/utilities.h"
#include "core/cGlobalPreferences.h"
#include "core/cPeakListSeries.h"
#include "core/cBricksDatabase.h"
#include "core/cSequenceDatabase.h"

Go to the source code of this file.

Classes
class	cParameters
	The class storing parameters of the application. More...
struct	hintStructure
	An auxiliary structure for search hints. More...

Enumerations
enum	ePeakListFileFormat {   txt = 0 , mgf , mzML , mzXML ,   baf , raw , dat , imzML ,   mis , ser }
	Peak list file formats supported by the application.
enum	eScoreType {   number_of_matched_peaks = 0 , sum_of_relative_intensities = 1 , number_of_b_ions = 2 , number_of_y_ions = 3 ,   number_of_b_and_y_ions = 4 , weighted_ratio_of_matched_peaks = 5 , cosine_similarity = 6 }
	The types of scores between an experimental and a theoretical spectrum.

Functions
bool	checkSeniorRules (vector< int > &combarray, vector< int > &valences, int maxcomponents)
	Check Senior's filtering rules. More...
bool	checkAdvancedFilteringRules (bool noratiocheck, double sumofmasses, vector< int > &countsofelements, vector< string > &namesofelements)
	Check advanced filtering rules. More...
	Q_DECLARE_METATYPE (cParameters)
	Register cParameters by Qt.
bool	compareHints (const hintStructure &a, const hintStructure &b)
	An auxiliary comparator for search hints.
void	searchHintForDeNovo (double mzratio, vector< hintStructure > &experimentalpeaks, double fragmentmasserrortolerance, set< int > &hintset)
	Get IDs of spectra in which the theoretical m/z ratio can be found. More...

Detailed Description

Definitions of program parameters.

Function Documentation

checkAdvancedFilteringRules()

bool checkAdvancedFilteringRules	(	bool	noratiocheck,
		double	sumofmasses,
		vector< int > &	countsofelements,
		vector< string > &	namesofelements
	)

Check advanced filtering rules.

noratiocheck if true, N/O ratio check is enabled

sumofmasses sum of masses

countsofelements counts of elements

namesofelelements names of elements

Return values

bool	true, if advanced filtering rules are NOT ok

checkSeniorRules()

bool checkSeniorRules	(	vector< int > &	combarray,
		vector< int > &	valences,
		int	maxcomponents
	)

Check Senior's filtering rules.

Parameters

combarray	current combination of elements
valences	vector of valences
maxcomponents	maximum number of components in a graph

Return values

bool	true, if Senior's rules are ok

searchHintForDeNovo()

void searchHintForDeNovo	(	double	mzratio,
		vector< hintStructure > &	experimentalpeaks,
		double	fragmentmasserrortolerance,
		set< int > &	hintset
	)

Get IDs of spectra in which the theoretical m/z ratio can be found.

Parameters

mzratio	theoretical m/z ratio
experimentalpeaks	a sorted vector of hint structures
fragmentmasserrortolerance	m/z error tolerance
hintset	output set of spectra IDs