cSummaryFormula.h

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#ifndef _CSUMMARYFORMULA_H
#define _CSUMMARYFORMULA_H
 
#include <string>
#include <fstream>
#include "core/cFragmentIons.h"
 
 
using namespace std;
using namespace boost;
 
 
class cPeaksList;
class cPeakListSeries;
class cBricksDatabase;
 
 
void reduceMapToStringFormula(map<string, int>& atoms, string& formula);
 
 
void addStringFormulaToMap(string& formula, map<string, int>& atoms);
 
 
void mergeMaps(map<string, int>& source, map<string, int>& target);
 
 
void rechargeMap(int charge, map<string, int>& atoms);
 
 
class cSummaryFormula {
 
    bool partial;
 
    string formula;
 
    void combineAtoms(cPeakListSeries& peaklistseries, int peaklistseriessize, vector<int>& peaklistseriessizes, cPeaksList& isotopeprofile, vector<int>& depthvector, int depth, double mass, double intensity, double charge, double minimumabsoluteintensity, double& localmaximumintensity, double minimumrelativeintensity);
 
    double getIntensity(cBricksDatabase& bricksprobabilities, vector<int>& combarray, int mostintenseid, int mostintenseatomscount, int isotopecount);
 
    void getIsotopeSummary(string& description, cBricksDatabase& bricks, vector<int>& combarray, int mostintenseid, int mostintenseatomscount, int isotopecount, bool positive);
 
    void reduceIsotopeProfile(cPeaksList& isotopeprofile, cPeaksList& reducedprofile, double fwhm);
 
public:
 
 
    cSummaryFormula();
 
 
    cSummaryFormula(string& formula, bool partial = false);
 
 
    void clear();
 
 
    void setFormula(const string& formula, bool partial = false);
 
 
    string getSummary();
 
 
    string getFancySummary(int charge);
 
 
    bool isPartial();
 
 
    void setPartial(bool partial);
 
 
    void addFormula(string& formula, bool remove = false);
 
 
    void setFromMap(map<string, int>& atoms, bool partial);
 
    
    bool isValid(string& errormessage);
 
 
    bool isEmpty();
 
 
    bool hasAllElementsPositive();
 
 
    double getMass();
 
 
    cPeaksList getIsotopePattern(double fwhm, int charge, bool positive, int maxchangedatoms, bool writedescription);
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is);
 
 
    bool equals(cSummaryFormula& secondformula);
 
};
 
 
#endif