cBricksDatabase.h

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#ifndef _CBRICKSDATABASE_H
#define _CBRICKSDATABASE_H
 
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <algorithm>
#include <iomanip>
 
#include "core/utilities.h"
#include "core/cBrick.h"
#include "core/cSummaryFormula.h"
 
 
using namespace std;
 
 
class cMainThread;
 
 
bool compareBrickMasses(const cBrick& a, const cBrick& b);
 
 
void getNameOfCompositionFromIntVector(string& composition, vector<int>& combarray);
 
 
string& getReversedNameOfCompositionFromStringVector(string& composition, vector<string>& stringcomposition);
 
 
void generateBricksPermutations(vector<string>& bricks, vector<string>& currentpermutation, vector<string>& permutations);
 
 
class cBricksDatabase {
 
    vector<cBrick> bricks;
 
    map<string, int> lossorders;
 
    vector<double> lossmasses;
    vector<string> losssummaries;
    vector< map<string, int> > lossmaps;
    
    void addLossToMap(string& lossstr, vector<int>& lossids);
 
    double getMassFromCombCounts(vector<int>& combcounts, vector<double>& combmasses);
 
 
public:
    
    
    bool nextCombination(vector<int>& combarray, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass);
 
 
    bool nextCombinationFast(vector<int>& combarray, vector<int>& combcounts, vector<double>& combmasses, double& mass, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass);
 
 
    bool nextCombinationFastLimited(vector<int>& combarray, vector<int>& combcounts, vector<int>& comblimits, vector<double>& combmasses, double& mass, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass);
 
 
    cBricksDatabase();
 
 
    int loadFromPlainTextStream(ifstream &stream, string& errormessage, bool ignoreerrors, bool skiph2blocks);
 
 
    void storeToPlainTextStream(ofstream &stream);
 
 
    int size();
 
 
    void print(/*ostream &stream*/);
 
 
    void sortbyMass();
 
 
    cBrick& operator[](int position);
 
 
    double getMassOfComposition(vector<int>& combarray, int numberofbasicbricks);
 
 
    string getRealName(string& composition);
 
 
    string getAcronymName(string& composition, bool useHTMLReferences);
 
 
    string getTagName(string& composition);
 
 
    string getAcronymNameOfTPeptide(const string& tcomposition, bool useHTMLReferences);
 
 
    string getTagNameOfTPeptide(string& tcomposition);
 
 
    void clear();
 
 
    bool replaceAcronymsByIDs(string& sequence, string& errormessage);
 
 
    void push_back(cBrick& brick);
 
 
    void removeLastBrick();
 
 
    string calculateSummaryFromComposition(int brickid);
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is);
 
 
    bool checkKetideBlocks(cBrick& brickseries, bool regularblocksorder);
 
 
    double getMassOfNeutralLosses(vector<int>& lossids);
 
 
    string getSummaryFormulaOfNeutralLosses(vector<int>& lossids);
 
 
    void getMapOfNeutralLosses(vector<int>& lossids, map<string, int>& summarymap);
 
};
 
 
#endif