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//////////////////////////////////////////////////////////////////////
// MultiSequence.h
//
// This file contains the routines needed for the creation,
// maintenance, and use of a MultiSequence object which contains all
// of the data associated with a set of sequences.
//////////////////////////////////////////////////////////////////////
#ifndef MULTISEQUENCE_H
#define MULTISEQUENCE_H
#include "Sequence.h"
#include "Block.h"
#include <stdio.h>
//////////////////////////////////////////////////////////////////////
// MultiSequence object
//////////////////////////////////////////////////////////////////////
class MultiSequence {
Sequence **sequences;
int numSequences;
// I/O helper routines
const int AutoDetectFileFormat (const char *filename) const;
void LoadMFA (const char *filename, bool compressGaps);
void LoadPILEUP (const char *filename, bool compressGaps);
void LoadData (const char *filename, bool compressGaps);
const char ComputeAnnotation (const char *data, const int size) const;
public:
//Block operations
void FindBlock(Block &block, int &start, int &end, int minlength = 20);
void AddAlignPosition(Fragment * frag);
void ClearAlignPosition();
// constructors
MultiSequence();
MultiSequence (const MultiSequence &rhs);
// assignment operator
const MultiSequence& operator= (const MultiSequence &rhs);
// destructor
~MultiSequence();
// getters
const int GetNumSequences() const;
const int GetLength() const;
const Sequence &GetSequence (int index) const;
Sequence * GetSequencePtr(int index);
// add sequences
void AddSequence (Sequence *seq);
// sort sequences by id
void Sort();
// input
void LoadSequences (const char *filename);
void LoadAlignment (const char *filename);
// output
void WriteMFA (FILE *file) const;
void WriteCLUSTALW (FILE *file) const;
//Block output
void WriteFASTA(FILE *file,Block *block, MultiSequence *result, int start, int end);
void WriteCLUSTALW(FILE *file, int start, int end);
};
#endif
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