cSequence.h

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#ifndef _CSEQUENCE_H
#define _CSEQUENCE_H
 
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include "core/utilities.h"
#include "core/cFragmentIons.h"
#include "core/cSummaryFormula.h"
 
 
using namespace std;
using namespace boost;
 
 
class cSequence {
 
    ePeptideType peptidetype;
    string sequence;
    string nterminalmodification;
    string cterminalmodification;
    string branchmodification;
    string name;
    cSummaryFormula summary;
    string reference;
    double rtmin;
    double rtmax;
    bool decoy;
 
public:
 
 
    cSequence();
 
 
    void clear();
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is, int fileversionpart1, int fileversionpart2, int fileversionpart3);
 
 
    ePeptideType getPeptideType();
 
 
    string& getSequence();
 
 
    string& getName();
 
 
    double getMinimumRetentionTime();
 
 
    double getMaximumRetentionTime();
 
 
    string& getReference();
 
 
    void setPeptideType(ePeptideType peptidetype);
 
 
    void setSequence(const string& sequence);
 
 
    void setName(const string& name);
 
 
    void setRetentionTime(double rtmin, double rtmax);
 
 
    void setReference(const string& reference);
 
 
    void setNTterminalModification(const string& modification);
 
 
    void setCTterminalModification(const string& modification);
 
 
    void setBranchModification(const string& modification);
 
 
    string& getNTterminalModification();
 
 
    string& getCTterminalModification();
 
 
    string& getBranchModification();
 
 
    string getNameWithReferenceAsHTMLString();
 
 
    void setSummaryFormula(const string& formula);
 
 
    string getSummaryFormula();
 
 
    bool isDecoy();
 
 
    void setDecoy(bool decoy);
 
};
 
 
#endif