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//////////////////////////////////////////////////////////////////////
// Sequence.h
//
// Class for manipulating single sequences.
//////////////////////////////////////////////////////////////////////
#ifndef SEQUENCE_H
#define SEQUENCE_H
#include <map>
#include "AlignedFragment.h"
//////////////////////////////////////////////////////////////////////
// Sequence object
//////////////////////////////////////////////////////////////////////
class Sequence {
char *data;
char *name;
int length;
int id;
int *align; //number of sequences aligned to a given position
int *position; //original position used for tracking after erasing fragments
public:
void ClearAlignPosition();
int GetAlign(int i) const;
void SubStr(int begin, int end);
int SetID(int newid);
void Clip(int begin, int end);
void PrintAlign(FILE *f);
void EraseCluster(int start, int end, int n);
int OriginPosition(int current);
void EraseFragment(int begin, int end);
void AddAlignPosition(int begin, int end);
// constructors
Sequence (char *data, char *name, int length, int id);
Sequence (const Sequence &rhs);
// assignment operator
const Sequence& operator= (const Sequence &rhs);
// destructor
~Sequence ();
// getters
const char *GetData () const;
const char *GetName () const;
const int GetLength () const;
const int GetID () const;
// setters
void SetData (char *data);
// compute mapping from letter to positions in sequence
int *ComputeMapping () const;
};
#endif
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