SequenceTransform.h

#ifndef SEQUENCETRANSFORM_H
#define SEQUENCETRANSFORM_H

#include"TypeDefBase.h"
//handling sequence transformation between ACGT(Char) and 0123(Digital).
class SequenceTransform_T
{
public:
	static void char2FileDigitalSeq( Str& in, Str& seq );
	static Str digital2CharSeq( Str& seq );
	class ToOppRule_T
	{
	public:
		void operator ()( char& c )
		{
				switch( c )
				{
					case '0' : c = '3'; break;
					case '1' : c = '2'; break;
					case '2' : c = '1'; break;
					case '3' : c = '0'; break;
//					default  : assert("Unexpected Character!");
				}
		}
	};
	static Str char2DigitalSeq( Str& seq );
//private:
	SequenceTransform_T()
	{
	}
	static char char2digital( char resourse );
};

Str getDNAInOppositeStrand(Str s);
vector<pair<Str, Str> > readInFast(Str file);
Str get_rev_comp(Str s );
Str get_comp(Str s );
Str get_rev_comp_dig(Str s );
Str toAminoSeq( const char* seq, int startPos, int endPosition);

#endif// SEQUENCETRANSFORM_H