BioProteinSequence.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : The Biologist's Programming Language 
Version 1.0 (19th December 2001)
Prasad, B.V.L.S.
Contact: burrashiva@yahoo.com
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIOPROTEINSEQUENCE_H
#define BIOPROTEINSEQUENCE_H

#include "BioSequence.h"
#include <string>

class BioProteinSequence : public BioSequence
{
        public: 
                BioProteinSequence(const string&); 
                BioProteinSequence();
          BioProteinSequence(const string& seqnam, const string& seq);
    
                bool checkProteinSequence(); 
    void setSequence(const string& seqnam, const string& seq);
                double getMolecularWeight();
    string  getAminoAcid(const long&);
        double getMolarExtinctionCoefficient();
        double getExtinctionCoefficient();
        double getProteinConcentration(double absorption);

        int getNumberOfBasicAminoAcids();
        int getNumberOfAcidicAminoAcids();
        int getNumberOfPolarAminoAcids();
        int getNumberOfNonPolarAminoAcids();

        vector <long >  getPositionsOfBasicAminoAcids();
        vector <long >  getPositionsOfAcidicAminoAcids();
        vector <long >  getPositionsOfPolarAminoAcids();
        vector <long >  getPositionsOfNonPolarAminoAcids();

        
        void  showPositionsOfBasicAminoAcids(ostream& os = cout);
        void  showPositionsOfAcidicAminoAcids(ostream& os = cout);
        void  showPositionsOfPolarAminoAcids(ostream& os = cout);
        void  showPositionsOfNonPolarAminoAcids(ostream& os = cout);

        void showHydropathyPlot(const int& windowSize, BioPostScript& ps);
};

BioProteinSequence BioGetRandomProteinSequence(const int& seqLength);
#endif