BioDnaSequence.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : A Programming Language for Biologist
Version 1.0 (19th December 2001)
Dr. Prasad, B.V.L.S.
Contact: prasadbvls@helixgenomics.com
Version 1.1 (23th January 2003)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIODNASEQUENCE_H
#define BIODNASEQUENCE_H

#include "BioSequence.h"
#include "BioPostScript.h"
#include "BioHtml.h"
#include <string>

class BioDnaSequence : public BioSequence
{
  void drawORFTable(const vector <string> & vst, BioHtml & os);
  string  markRegion(string  st1, BioHtml & os);
  string reverseMarkRegion(string  st1, BioHtml & os);
  string fillColor(string & st,string & ext);
  void drawOrfs(int,int,int,int,int,BioPostScript&);//private function
        public: 
                BioDnaSequence(const string& ); 
                BioDnaSequence();
          BioDnaSequence(const string& seqnam, const string& seq);
          ~BioDnaSequence();


    bool checkDnaSequence();
    
        void setSequence(const string& seqnam, const string& seq);
        void setSequenceName(const string& seqnam);
        void setSequence(const string& seq);

                string getTranslatedSequence(const int& frameNumber );
                string getTranslatedSequence(const long& ,const long& , const int& frameNumber );

    void showTranslatedSequences(ostream &  os = cout);
    void showTranslatedSequences(const long&,const long&,ostream& os = cout);
    void showTranslatedSequences(BioHtml & );
    void showTranslatedSequences(BioPostScript&,int startX=75,int startY=200,int len=400);
                string getmRnaSequence();
                string getComplementarySequence();
                string getmRnaSequence(const long&, const long&);
                string getComplementarySequence(const long&, const long&);

    string getBase(const long&);

                double getMolecularWeight();
                double getPercentGC();
                double getPercentAT();
                double getTm();
                // Melting Temperature
                // %GC content
                // Tm = 59.9 + 0.41*(%GC) - 600/length
                // Tm = 81.5 + 16.6* log[Na] + 0.41*(%GC) - 675/length - 0.65*(%formamide) - (%mismatch)


};

BioDnaSequence BioGetRandomDnaSequence(const int& seqLength);
vector <string > BioGetDnaSequences(const string& ambiguousSequence);

#endif