Overlap/BioProteinSequenceAlignment.h

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#ifndef BIOPROTEINSEQUENCEALIGNMENT_H
#define BIOPROTEINSEQUENCEALIGNMENT_H

#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include "BioUtilities.h"
#include "BioProteinSequence.h"
#include "BioSwissProt.h"
#include "BioFasta.h"
#include "BioProteinSubstitutionMatrix.h"
#include "BioMultipleFasta.h"
#include "BioLenPos.h"
#include "BioMatrix.h"

class BioProteinSequenceAlignment
{
protected:
                /*VARIABLES*/
                string seq1_,seq2_; /* These variables holds the sequences to be aligned*/
    
                string outSeq1_,outSeq2_;  /* These varables holds the ouput aligned sequences*/
   
      string seqName1_,seqName2_; /* These variables holds the Sequence Names */
      
                static string aminoAcidSeq_; /* This String Holds the AminoAcid names in a most comman way of its usage*/
    
                int gapPenalty; /* This varible is used to Set the Gap Penality in sequnce alignment process (in substitution matrix) */
    
                int gapExtn; /* This variable is used to set the Gap Extention Penality in seqquence alignment process*/
    
                BioMatrix substitutionMatrix; /* This 2D array holds the Substitutionmatrix elements used for the currrent alignment*/
//              vector < vector < int > > tempMatrix; /* This is a temporary 2D variable used for most convenetianal way data transfer*/
                BioMatrix scoringMatrix;
                //int** accumMatrix;
      int status;
    
        /*FUNCTIONS*/
                void formScoringMatrix();
    
      int getAccValMov(long,long,int);

      void init();
      
      BioProteinSequenceAlignment();
//      ~BioProteinSequenceAlignment(){ delete seq1_, seq2_, outSeq1_, outSeq2_, seqName1_, seqName2_; };
    
                BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,string mat="BLOSUM62",int GP=-11,int extn=-9999);
                BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,string,string,int GP=-11,int extn=-9999);
                BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,int MS,int MMS,int GP=-11,int extn=-9999);
                BioProteinSequenceAlignment(BioProteinSequence,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
                BioProteinSequenceAlignment(BioProteinSequence,string,string,string,int GP=-11,int extn=-9999);
                BioProteinSequenceAlignment(BioProteinSequence,string,int MS,int MMS,int GP=-11,int extn=-9999);

     BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,string mat="BLOSUM62",int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,string,string,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,int MS,int MMS,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioSwissProt,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioSwissProt,string,string,string,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioSwissProt,string,int MS,int MMS,int GP=-11,int extn=-9999);

        
     BioProteinSequenceAlignment(const BioFasta&,const BioFasta&,const string& mat="BLOSUM62",const int& GP=-11,const int& extn=-9999);
     BioProteinSequenceAlignment(BioFasta,BioFasta,string,string,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioFasta,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioFasta,string,string,string,int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999);

        
     BioProteinSequenceAlignment(const string&,const string&,const string& mat="BLOSUM62",int GP=-11,int extn=-9999);
     BioProteinSequenceAlignment(const string&,const string&,const string&,const string&,int GP=-11,int extn=-9999);
        BioProteinSequenceAlignment(const string&,const string&,int MS,int MMS,int GP=-11,int extn=-9999);
                
public:
   void setSequence1(BioProteinSequence);
   void setSequence2(BioProteinSequence);

        void setSequence1(BioSwissProt);
        void setSequence2(BioSwissProt);

   void setSequence1(BioFasta);
        void setSequence2(BioFasta);

        void setSequence1(const string&);
   void setSequence2(const string&);

   void setGapPenalty(int GP=-11,int extn=-9999);
        void setSubstitutionMatrix(const string&);
        void setSubstitutionMatrix(const string&,const string&);
        void setMatchMisMatchScore(int MS=1,int MMS=0);

        void showScoringMatrix(ostream & = cout);

};

#endif