BioProteinSecondaryStructurePrediction.h

Go to the documentation of this file.

#ifndef BIOPROTEINSECONDARYSTRUCTUREPREDICTION_H 
#define BIOPROTEINSECONDARYSTRUCTUREPREDICTION_H 



#include "BioRaw.h"
#include "BioSwissProt.h"
#include "BioFasta.h"
#include "BioProteinSequence.h"
#include "BioPostScript.h"
#include <ostream>
#include <string>

class BioProteinSecondaryStructurePrediction
{
  private :
             string sequence_;
             int helWin_,helnum_;
             int sheetWin_,sheetnum_;
             float helExt_,sheetExt_;
             string predictedSeq_;
             
             bool PREDICT;
             vector<int> helix,sheet,turn;
             void predict(void);
        friend bool operator >(const BioProteinSecondaryStructurePrediction& , const BioProteinSecondaryStructurePrediction&);
        friend bool operator <(const BioProteinSecondaryStructurePrediction& , const BioProteinSecondaryStructurePrediction&);
        friend bool operator ==(const BioProteinSecondaryStructurePrediction& , const BioProteinSecondaryStructurePrediction&);
  public  :
            BioProteinSecondaryStructurePrediction(){}
            BioProteinSecondaryStructurePrediction(BioRaw&);
            BioProteinSecondaryStructurePrediction(BioFasta&);
            BioProteinSecondaryStructurePrediction(BioProteinSequence&);
            BioProteinSecondaryStructurePrediction(BioSwissProt&);
            BioProteinSecondaryStructurePrediction(const string&);

            void showPrediction(ostream& = cout);                                
            void showHelixPrediction(ostream& = cout);
            void showStrandPrediction(ostream& = cout);
            void showTurnPrediction(ostream& = cout);

            int getNumberOfHelices();
            int getNumberOfStrands();
            int getNumberOfTurns();
       //     void setPredictedSequence(string&);
            string getPredictedSequence();

            string getHelix(int i);
            string getStrand(int i);
            string getTurn(int i);

         void setHelixNucleationParameters(int window,int num);
         void setSheetNucleationParameters(int window,int num);
         void setHelixExtensionParameter(float param);
         void setSheetExtensionParamater(float param);

            void showPrediction(BioPostScript& ps,float startx=50,float starty=800,float width=475);
            void showHelixPrediction(BioPostScript& ps,float startx=50,float starty=800,float width=475);
            void showStrandPrediction(BioPostScript& ps,float startx=50,float starty=800,float width=475);
            void showTurnPrediction(BioPostScript& ps,float startx=50,float starty=800,float width=475);



};


#endif