BioDnaMultiPatternAlignment.h

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#ifndef BIODNAMULTIPATTERNALIGNMENT_H
#define BIODNAMULTIPATTERNALIGNMENT_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 "BioDnaSequenceRepeatAlignment.h"
#include "BioPostScript.h"

using namespace std;

class BioDnaMultiPatternAlignment
{
        friend bool operator >(const BioDnaMultiPatternAlignment& , const BioDnaMultiPatternAlignment&);
       friend bool operator <(const BioDnaMultiPatternAlignment& , const BioDnaMultiPatternAlignment&);
       friend bool operator ==(const BioDnaMultiPatternAlignment& , const BioDnaMultiPatternAlignment&);
    
    vector <BioDnaSequenceRepeatAlignment> 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: 
        ~BioDnaMultiPatternAlignment();
        BioDnaMultiPatternAlignment();
        BioDnaMultiPatternAlignment(BioDnaSequence,string,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaMultiPatternAlignment(BioDnaSequence,string,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
                
        BioDnaMultiPatternAlignment(BioDnaSequence,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);
        BioDnaMultiPatternAlignment(BioFasta,string,string,string MatName,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaMultiPatternAlignment(BioFasta,string,string MatName="IDENTITY",int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);
        BioDnaMultiPatternAlignment(BioFasta,string,int ReapIden,int MS,int MMS,int GP=-50,int extn=-9999,int TH=10);

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

      void setSequence(BioDnaSequence);
      void setSequence(BioFasta);
      void setSequence(string);
          
      void addPattern(string,int ReapIden=100,int GP=-50,int extn=-9999,int TH=10);

      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