cPeaksList.h

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#ifndef _CPEAKSLIST_H
#define _CPEAKSLIST_H
 
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <algorithm>
 
#include "core/cPeak.h"
#include "core/cMzML.h"
#include "core/cImzML.h"
 
 
using namespace std;
 
 
class cMainThread;
 
 
bool compareRelativePeakIntensitiesDesc(const cPeak& a, const cPeak& b);
 
 
bool isInPpmMassErrorTolerance(double experimentalmass, double theoreticalmass, double tolerance);
 
 
double ppmError(double experimentalmass, double theoreticalmass);
 
 
bool searchHint(double mzratio, cPeaksList& experimentalpeaks, double fragmentmasserrortolerance);
 
 
class cPeaksList {
 
    vector<cPeak> peaks;
 
    double rt;
 
    int rtunit;
 
    int x, y;
 
    string title;
 
public:
 
 
    cPeaksList();
 
 
    cPeaksList(const cPeaksList& peakslist);
 
 
    cPeaksList& operator=(const cPeaksList& peakslist);
 
 
    void clear();
 
 
    void attach(cPeaksList& peaklist);
 
 
    void add(cPeak& peak);
 
 
    void loadFromPlainTextStream(ifstream &stream);
 
 
    void loadFromBAFStream(ifstream &stream);
 
 
    void loadFromIBDStream(cImzMLItem& imzmlitem, ifstream &ibdstream, bool use_64bit_float_mz_precision, bool use_64bit_float_intensity_precision);
 
 
    void storeToIBDStream(ofstream &ibdstream, bool use_64bit_float_mz_precision, bool use_64bit_float_intensity_precision);
 
 
    void loadFromMGFStream(ifstream &stream, int timeunit);
 
 
    int size();
 
 
    string print(bool htmlterminatelines = false, bool printgroupid = false);
 
 
    void sortbyMass(int limit = -1);
 
 
    void sortbyRelativeIntensityDesc();
 
 
    void sortbyAbsoluteIntensityDesc();
 
 
    void sortbyGroupId();
 
 
    void sortbyOrderId();
 
 
    int normalizeIntenzity();
 
 
    void normalizeIntenzityByValue(double value);
 
 
    void cropRelativeIntenzity(double minimumrelativeintensitythreshold);
 
 
    void cropAbsoluteIntenzity(unsigned minimumabsoluteintensitythreshold);
 
 
    void cropMinimumMZRatio(double minimummz, double errortolerance);
 
 
    void cropMaximumMZRatio(double maximummz, double errortolerance);
 
 
    cPeak& operator[](int position);
 
 
    void resize(int size);
 
 
    double getMinimumMZRatio();
 
 
    double getMaximumMZRatio();
 
 
    void removeIsotopes(int maximumcharge, double fragmentmasserrortolerance, cMainThread* os = 0);
 
 
    int find(double mzratio, double fragmentmasserrortolerance);
 
 
    void remove(int position);
 
 
    void removeChargeVariants(int maximumcharge, double fragmentmasserrortolerance);
 
 
    void removeNeutralLoss(double loss, int maximumcharge, double fragmentmasserrortolerance);
 
 
    void removeObsolete();
 
 
    void maxHighestPeaksInWindow(int maximumnumberofpeaksinwindow, double windowsize);
 
 
    double getMaximumRelativeIntensityFromMZInterval(double minmz, double maxmz, bool hidematched, bool hideunmatched, ePeptideType peptidetype, bool hidescrambled);
 
 
    double getMaximumAbsoluteIntensityFromMZInterval(double minmz, double maxmz, bool hidematched, bool hideunmatched, ePeptideType peptidetype, bool hidescrambled);
 
 
    double getMaximumRelativeIntensity();
 
 
    double getMaximumAbsoluteIntensity();
 
 
    void setRetentionTime(double rt);
 
 
    double getRetentionTime();
 
 
    void setRetentionTimeUnit(int unit);
 
 
    int getRetentionTimeUnit();
 
 
    void setCoordinates(int x, int y);
 
 
    int getCoordinateX();
 
 
    int getCoordinateY();
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is, int fileversionpart1, int fileversionpart2, int fileversionpart3);
 
 
    string& getTitle();
 
 
    void setTitle(string& title);
 
 
    void reducePeakDescriptions(unordered_map<string, int>& peakdesctoid);
 
 
    void reduceIsotopeFormulaDescriptions(unordered_map<string, int>& isotopeformuladesctoid);
 
 
    void fillOrderIDs();
 
 
    void setIsotopeFlags(bool value);
 
 
    void markIsotopes();
 
 
    bool equals(cPeaksList& secondpeaklist);
 
};
 
 
Q_DECLARE_METATYPE(cPeaksList);
 
#endif