BioProteinSequenceRepeatAlignment.h

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#ifndef BIOPROTEINSEQUENCEREPEATALIGNMENT_H
#define BIOPROTEINSEQUENCEREPEATALIGNMENT_H

#include <string>
#include <vector>
#include "BioProteinSequence.h"
#include "BioSwissProt.h"
#include "BioFasta.h"
#include "BioProteinSequenceAlignment.h"
#include "BioPostScript.h"

class BioProteinSequenceRepeatAlignment : public BioProteinSequenceAlignment
{
        friend bool operator >(const BioProteinSequenceRepeatAlignment& , const BioProteinSequenceRepeatAlignment&);
        friend bool operator <(const BioProteinSequenceRepeatAlignment& , const BioProteinSequenceRepeatAlignment&);
        friend bool operator ==(const BioProteinSequenceRepeatAlignment& , const BioProteinSequenceRepeatAlignment&);

        int reapPerIden,threshold;

        int nogs;
        
        BioLenPos lenpos;

        void formAccumulationMatrix();

        void backTrack();

        int reap(int, int);

        void show(ostream & = cout);
        
        void init();        
 public:
       BioProteinSequenceRepeatAlignment();

                 BioProteinSequenceRepeatAlignment(BioProteinSequence,BioProteinSequence,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinSequenceRepeatAlignment(BioProteinSequence,BioProteinSequence,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinSequenceRepeatAlignment(BioProteinSequence,BioProteinSequence,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinSequenceRepeatAlignment(BioProteinSequence,string,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinSequenceRepeatAlignment(BioProteinSequence,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinSequenceRepeatAlignment(BioProteinSequence,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);

     
         BioProteinSequenceRepeatAlignment(BioSwissProt,BioSwissProt,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioSwissProt,BioSwissProt,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioSwissProt,BioSwissProt,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioSwissProt,string,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioSwissProt,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioSwissProt,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);

         BioProteinSequenceRepeatAlignment(BioFasta,BioFasta,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioFasta,BioFasta,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
             BioProteinSequenceRepeatAlignment(BioFasta,BioFasta,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioFasta,string,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(BioFasta,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
             BioProteinSequenceRepeatAlignment(BioFasta,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);

         BioProteinSequenceRepeatAlignment(string,string,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
         BioProteinSequenceRepeatAlignment(string,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
            BioProteinSequenceRepeatAlignment(string,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);
                
        void setThreshold(int);
        void setRepeatIdentity(int);
        void setGaps(int);

        void showAccumulationMatrix(ostream & = cout);
        void showAlignment(ostream & = cout);

         long getNumberOfRepeats();
        long getRepeatStartingPosition(long);
        long getRepeatEndingPosition(long);
        BioSequence getRepeat(long);
        string getAlignedRepeat(long);
        void showAlignment(BioPostScript& ps,float=100,float=650,float=450);

            long getNumberOfIdentities();
            long getNumberOfSimilarities();
    float getIdentity(int);
    int getRepeatScore(int);
    float getScore();

    string getAlignedSequence1();
    string getAlignedSequence2();
        
        
};

#endif