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CycloBranch
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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... | |
Definitions of program parameters.
| 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
| bool | true, if advanced filtering rules are NOT ok |
| bool checkSeniorRules | ( | vector< int > & | combarray, |
| vector< int > & | valences, | ||
| int | maxcomponents | ||
| ) |
Check Senior's filtering rules.
| combarray | current combination of elements |
| valences | vector of valences |
| maxcomponents | maximum number of components in a graph |
| bool | true, if Senior's rules are ok |
| 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.
| mzratio | theoretical m/z ratio |
| experimentalpeaks | a sorted vector of hint structures |
| fragmentmasserrortolerance | m/z error tolerance |
| hintset | output set of spectra IDs |