BioDnaSequenceRepeatAlignment.h

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#ifndef BIODNASEQUENCEREPEATALIGNMENT_H
#define BIODNASEQUENCEREPEATALIGNMENT_H

#include "BioDnaSequenceAlignment.h"
#include "BioPostScript.h"
#include "BioLenPos.h"

class BioDnaSequenceRepeatAlignment : public BioDnaSequenceAlignment
{
        friend bool operator >(const BioDnaSequenceRepeatAlignment& , const BioDnaSequenceRepeatAlignment&);
        friend bool operator <(const BioDnaSequenceRepeatAlignment& , const BioDnaSequenceRepeatAlignment&);
        friend bool operator ==(const BioDnaSequenceRepeatAlignment& , const BioDnaSequenceRepeatAlignment&);
        int reapPerIden,threshold;

        int nogs;
        
        BioLenPos lenpos;

        void formAccumulationMatrix();

        void backTrack();

        int reap(int, int);

        void show(ostream & = cout);           

        void init();        
    
 public:
        BioDnaSequenceRepeatAlignment();
        BioDnaSequenceRepeatAlignment(BioDnaSequence,BioDnaSequence,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioDnaSequence,string,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioDnaSequence,BioDnaSequence,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioDnaSequence,string,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioDnaSequence,BioDnaSequence,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioDnaSequence,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);

        BioDnaSequenceRepeatAlignment(BioFasta,BioFasta,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioFasta,string,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioFasta,BioFasta,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioFasta,string,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioFasta,BioFasta,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(BioFasta,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);

        BioDnaSequenceRepeatAlignment(string,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(string,string,string matName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaSequenceRepeatAlignment(string,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);

        void setThreshold(int);
        void setRepeatIdentity(int);
        void setGaps(int);

        void showAccumulationMatrix(ostream & = cout);

        long getNumberOfRepeats();
        long getRepeatStartingPosition(long);
        long getRepeatEndingPosition(long);
        BioSequence getRepeat(long);
        string getAlignedRepeat(long);
        long getNumberOfIdentities();
        float getIdentity(int);
        int getRepeatScore(int);    
        
        void showAlignment(ostream & = cout);
        void showAlignment(BioPostScript& ps,float=100,float=650,float=450);

    string getAlignedSequence1();
    string getAlignedSequence2();
    float getScore();
      

};

#endif