BioProteinSecondaryStructureAlignment.h

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#ifndef BIOPROTEINSECONDARYSTRUCTUREALIGNMENT_H
#define BIOPROTEINSECONDARYSTRUCTUREALIGNMENT_H

#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include "BioUtilities.h"
#include "BioMatrix.h"

class BioProteinSecondaryStructureAlignment
{
 private:
          string seq1_,seq2_; 

                string outSeq1_,outSeq2_;

         int gapPenalty;

         BioMatrix substitutionMatrix;

       static string secstr;

      vector < vector < int > > tempMatrix;

      int status;

      void formScoringMatrix();

      void setSubstitutionMatrix();

      int getAccValMov(long,long,int);

      void init();         

         void formAccumulationMatrix();

         void backTrack();

         void show(ostream & = cout);
 public:
      BioProteinSecondaryStructureAlignment();

      BioProteinSecondaryStructureAlignment(string,string,int GP=-11);

      void setSequence1(string);
      void setSequence2(string);      

      void showAlignment(ostream & = cout);

      void setGapPenalty(int GP =-11);

       float getIdentity();       
};

#endif