cParameters.h

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#ifndef _CPARAMETERS_H
#define _CPARAMETERS_H
 
#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"
 
 
class cMainThread;
 
 
using namespace std;
using namespace boost;
 
 
enum ePeakListFileFormat {
    txt = 0,
    mgf,
    mzML,
    mzXML,
    baf,
    raw,
    dat, 
    imzML,
    mis,
    ser
};
 
 
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
};
 
 
bool checkSeniorRules(vector<int>& combarray, vector<int>& valences, int maxcomponents);
 
 
bool checkAdvancedFilteringRules(bool noratiocheck, double sumofmasses, vector<int>& countsofelements, vector<string>& namesofelements);
 
 
class cParameters {
 
    cMainThread* os;
 
    void fixIntensities(cPeaksList& centroidspectrum, cPeaksList& profilespectrum);
 
    void pushLossItem(vector<neutralLoss>& lossitems, string lossstr);
 
    //double getMassAndCounts(vector<int>& combarray, vector<int>& countsofelements, vector<double>& massesofelements);
 
 
public:
 
 
    cFragmentIons iondefinitions;
    
 
    ePeptideType peptidetype;
 
 
    vector<string> peaklistfilenames;
 
 
    string originalpeaklistfilenames;
 
 
    bool useprofiledata;
 
 
    bool convertprofiledata;
 
 
    string profiledatafilename;
 
 
    int linebafprocessing;
 
 
    vector<ePeakListFileFormat> peaklistfileformats;
 
 
    vector<cPeakListSeries> peaklistseriesvector;
 
 
    int scannumber;
 
 
    double precursormass;
 
 
    string precursoradduct;
 
 
    vector<string> metaladducts;
 
 
    double precursormasserrortolerance;
 
 
    int precursorcharge;
 
 
    double fragmentmasserrortolerance;
 
 
    double minimumrelativeintensitythreshold;
 
 
    unsigned minimumabsoluteintensitythreshold;
 
 
    double minimummz;
 
 
    double maximummz;
 
 
    double minimumrt;
 
 
    double maximumrt;
 
 
    double fwhm;
 
 
    bool enableratio54Fe56Fe;
 
 
    double minratio54Fe56Fe;
 
 
    double maxratio54Fe56Fe;
 
 
    bool enableratio60Ni58Ni;
 
 
    double minratio60Ni58Ni;
 
 
    double maxratio60Ni58Ni;
 
 
    bool enableratio62Ni58Ni;
 
 
    double minratio62Ni58Ni;
 
 
    double maxratio62Ni58Ni;
 
 
    bool enableratio65Cu63Cu;
 
 
    double minratio65Cu63Cu;
 
 
    double maxratio65Cu63Cu;
 
 
    bool enableratio66Zn64Zn;
 
 
    double minratio66Zn64Zn;
 
 
    double maxratio66Zn64Zn;
 
 
    bool enableratio67Zn64Zn;
 
 
    double minratio67Zn64Zn;
 
 
    double maxratio67Zn64Zn;
 
 
    bool enableratio68Zn64Zn;
 
 
    double minratio68Zn64Zn;
 
 
    double maxratio68Zn64Zn;
 
 
    string bricksdatabasefilename;
 
 
    cBricksDatabase bricksdatabase;
 
 
    int maximumbricksincombinationbegin;
 
 
    int maximumbricksincombinationmiddle;
 
 
    int maximumbricksincombinationend;
 
 
    int maximumbricksincombination;
 
 
    double maximumcumulativemass;
 
 
    string modificationsfilename;
 
 
    int maximumnumberofthreads;
 
 
    eModeType mode;
 
 
    eScoreType scoretype;
 
    
    int maximumcombinedlosses;
 
 
    int maximumcombinedelements;
 
 
    //bool clearhitswithoutparent;
 
 
    bool reportunmatchedtheoreticalpeaks;
 
 
    bool generateisotopepattern;
 
 
    int minimumpatternsize;
 
 
    int minimumfeaturesize;
 
 
    int minimumiontypes;
 
 
    bool basicformulacheck;
 
 
    bool advancedformulacheck;
 
 
    bool noratiocheck;
 
 
    bool calculatefdrs;
 
 
    double minimumannotationintensityrelative;
 
 
    unsigned minimumannotationintensityabsolute;
 
 
    double mzdifftolerance;
 
 
    double intensitytolerance;
 
 
    bool cyclicnterminus;
 
 
    bool cycliccterminus;
 
 
    bool internalfragments;
 
 
    bool enablescrambling;
 
 
    bool similaritysearch;
 
 
    bool regularblocksorder;
 
 
    int hitsreported;
 
 
    string sequencetag;
 
 
    string originalsequencetag;
 
 
    string searchedsequence;
 
 
    string originalsearchedsequence;
 
 
    string searchedsequenceNtermmodif;
 
    
    string searchedsequenceCtermmodif;
 
    
    string searchedsequenceTmodif;
 
 
    string searchedsequenceformula;
 
 
    int maximumnumberofcandidates;
 
 
    int blindedges;
 
 
    string sequencedatabasefilename;
 
 
    cSequenceDatabase sequencedatabase;
 
 
    vector<cFragmentIonType> searchedmodifications;
 
 
    vector<eFragmentIonType> fragmentionsfordenovograph;
 
 
    vector<cIonType> ionsfortheoreticalspectraMS1;
 
 
    vector<eFragmentIonType> ionsfortheoreticalspectraMS2;
 
 
    vector<neutralLoss> neutrallossesdefinitions;
 
 
    vector<neutralLoss> originalneutrallossesdefinitions;
 
 
    vector<int> neutrallossesfortheoreticalspectra;
 
 
    int numberofgeneratedneutrallosses;
 
 
    vector<int> originalneutrallossesfortheoreticalspectra;
 
 
    vector<neutralLoss> originalelementsdefinitions;
 
 
    vector<int> originalelementsfortheoreticalspectra;
 
 
    vector<string> peakidtodesc;
 
 
    vector<string> isotopeformulaidtodesc;
 
 
    map<string, int> pchemresults;
 
 
    int defaultmaxx;
 
 
    int defaultmaxy;
 
 
    int defaultpixelsizex;
 
 
    int defaultpixelsizey;
 
 
    eVendorType vendor;
 
 
    cParameters();
 
 
    void clear();
 
 
    int checkAndPrepare(bool& terminatecomputation);
 
 
    int prepareLossesAndCompounds(bool& terminatecomputation);
 
 
    bool checkModifications(cSequence& sequence, int& startmodifid, int& endmodifid, int& middlemodifid, string& errormessage);
 
 
    string printToString();
 
 
    void setOutputStream(cMainThread& os);
 
 
    void updateFragmentDefinitions();
 
 
    int calculateNeutralLosses(bool& terminatecomputation, string& errormessage);
 
 
    int generateCompounds(bool& terminatecomputation, string& errormessage);
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is, int fileversionpart1, int fileversionpart2, int fileversionpart3);
 
 
};
 
 
Q_DECLARE_METATYPE(cParameters);
 
 
struct hintStructure {
 
    double mz;
 
 
    int id;
 
};
 
 
bool compareHints(const hintStructure& a, const hintStructure& b);
 
 
 
void searchHintForDeNovo(double mzratio, vector<hintStructure>& experimentalpeaks, double fragmentmasserrortolerance, set<int>& hintset);
 
 
#endif