BioProteinMultiPatternAlignment.h

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#ifndef BIOPROTEINMULTIPATTERNALIGNMENT_H
#define BIOPROTEINMULTIPATTERNALIGNMENT_H

#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <vector>

#include "BioUtilities.h"
#include "BioProteinSequence.h"
#include "BioSwissProt.h"
#include "BioFasta.h"
#include "BioProteinSequenceRepeatAlignment.h"
#include "BioPostScript.h"

using namespace std;

class BioProteinMultiPatternAlignment
{
        friend bool operator >(const BioProteinMultiPatternAlignment& , const BioProteinMultiPatternAlignment&);
       friend bool operator <(const BioProteinMultiPatternAlignment& , const BioProteinMultiPatternAlignment&);
       friend bool operator ==(const BioProteinMultiPatternAlignment& , const BioProteinMultiPatternAlignment&);
   
   vector <BioProteinSequenceRepeatAlignment> reapAligns;
    
    string fileName,substitutionMatrix;

    int match,misMatch;
    
    string querySequence;

    string outSeq1_,outSeq2_;

    vector <int> offsetStart;
    vector <int> offsetEnd;

    vector < vector <int> > finalstposs;
    vector < vector <int> > finaledposs;

    BioMatrix tMatrix;    

    vector <int> scores;

    int status;

    void tempMatrix(string,string);
    
    vector<string> processInputPattern(string);

    vector<int> processStringForPatterns(string );

    bool checkInt(string);

    void showAlign(ostream & = cout);

    void makeAlign();
    
    void init();
    
public: 
       BioProteinMultiPatternAlignment();
        ~BioProteinMultiPatternAlignment();
                 BioProteinMultiPatternAlignment(BioProteinSequence,string,string="BLOSUM62",int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinMultiPatternAlignment(BioProteinSequence,string,string,string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);
                 BioProteinMultiPatternAlignment(BioProteinSequence,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=20);


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

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

      void setSequence(BioProteinSequence);
      void setSequence(BioFasta);
      void setSequence(string);
          
      void addPattern(string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=20);

      void setSubstitutionMatrix(string);
      void setSubstitutionMatrix(string,string);
      void setMatchMisMatchScore(int MS=1,int MMS=0);
          
      void setGapPenalty(int GP=-11,int extn=-9999, int index = -1);
      void setRepeatIdentity(int identity,int index=-1);
      void setThreshold(int,int index = -1);
      void setOffsetRange(int st, int ed,int index=-1);
      void setOrder(string);
      void setGaps(int cou,int index=-1);

      void showAlignment(ostream & = cout);
      void showAlignment(BioPostScript& ps,float=100,float=650,float=450);
      
      int getRepeatStartingPosition(int);

      int getRepeatEndingPosition(int);

      int getNumberOfRepeats();

      int getScore(int);
      string getRepeat(int);
      string getAlignedRepeat(int);
      
};

#endif