Repeats/BioDnaSequenceAlignment.h

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#ifndef BIODNASEQUENCEALIGNMENT_H
#define BIODNASEQUENCEALIGNMENT_H

#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <vector>
#include "BioUtilities.h"
#include "BioDnaSequence.h"
#include "BioGenBank.h"
#include "BioFasta.h"
#include "BioEmbl.h"
#include "BioDnaSubstitutionMatrix.h"


class BioDnaSequenceAlignment
{
  protected:
  /* CHANGED BY HARI ON 13 MAR 2005 TO GIVE ACCESS TO seq1_ and seq2_ variables to be used in BioDnaSequenceRepeat's showAlignment(ps);*/
  
  /*VARIABLES*/
  
    string seq1_,seq2_; /* These variables hold the sequences to be aligned*/
    
    string outSeq1_,outSeq2_;
    
    string seqName1_,seqName2_; /* These variables hold the Sequence Names */
    
    static string nucleicAcidSeq; /* This String Holds the nucleic acid single letter codes */
    
    int gapPenalty; /* This varible is used to Set the Gap Penalty in sequence alignment process (in substitution matrix) */
    
    int gapExtn; /* This variable is used to set the Gap Extention Penalty in sequence alignment process*/
    
    BioMatrix substitutionMatrix; /* This 2D array holds the Substitutionmatrix elements used for the currrent alignment*/
    
    /* This is a temporary 2D variable used for creating scoring  matrix and accumulation matrix.*/
        vector< vector <int> > tempMatrix; 
    int status;
    
  /*FUNCTIONS*/
  
    void formScoringMatrix();
    int getAccValMov(long,long,int);

    BioDnaSequenceAlignment();
    BioDnaSequenceAlignment(BioDnaSequence,BioDnaSequence,string,string MatName,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioDnaSequence,string,string,string MatName,int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioDnaSequence,BioDnaSequence,string mat="IDENTITY",int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioDnaSequence,string,string mat="IDENTITY",int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioDnaSequence,BioDnaSequence,int MS,int MMS,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioDnaSequence,string,int MS,int MMS,int GP=-11,int extn=-9999);
                    
    BioDnaSequenceAlignment(BioGenBank,BioGenBank,string,string MatName,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioGenBank,string,string,string MatName,int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioGenBank,BioGenBank,string mat="IDENTITY",int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioGenBank,string,string mat="IDENTITY",int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioGenBank,BioGenBank,int MS,int MMS,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioGenBank,string,int MS,int MMS,int GP=-11,int extn=-9999);    

    BioDnaSequenceAlignment(BioFasta,BioFasta,string,string MatName,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioFasta,string,string,string MatName,int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioFasta,BioFasta,string mat="IDENTITY",int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioFasta,string,string mat="IDENTITY",int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999);
    
    BioDnaSequenceAlignment(BioEmbl,BioEmbl,string,string MatName,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioEmbl,string,string,string MatName,int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioEmbl,BioEmbl,string mat="IDENTITY",int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioEmbl,string,string mat="IDENTITY",int GP=-11,int extn=-9999);    
    BioDnaSequenceAlignment(BioEmbl,BioEmbl,int MS,int MMS,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(BioEmbl,string,int MS,int MMS,int GP=-11,int extn=-9999);    

    BioDnaSequenceAlignment(string,string,string,string,int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(string,string,string mat="IDENTITY",int GP=-11,int extn=-9999);
    BioDnaSequenceAlignment(string,string,int MS,int MMS,int GP=-11,int extn=-9999);
        
public:                
    void setSequence1(BioDnaSequence);
    void setSequence2(BioDnaSequence);
    void setSequence1(BioGenBank);
    void setSequence2(BioGenBank);
    void setSequence1(BioFasta);
    void setSequence2(BioFasta);
    void setSequence1(BioEmbl);
    void setSequence2(BioEmbl);
    void setSequence1(string);
    void setSequence2(string);

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

    void showScoringMatrix(ostream & = cout);
};

#endif