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//////////////////////////////////////////////////////////////////////
// Block.h
//
// Interface for block class
//////////////////////////////////////////////////////////////////////
#ifndef BLOCK_H
#define BLOCK_H
#include <vector>
#include "Types.h"
class MultiSequence;
class Block
{
std::vector<Fragment> frags;
public:
int part;
Fragment seed;
//Remove fragments already present in blocks
int AdjustAFragmentList(AVECT &fragments, Matrix *similarity=NULL, float threshold=0);
int AdjustAFragmentList(AVECT &fragments, int numSeq, Matrix *similarity=NULL, float threshold=0);
//Add a fragment to block
void AddFragment(Fragment &fr);
//Getters
int GetLength();
int size();
//Printing utility
void PrintBlock(FILE *f, MultiSequence *seqs, int compare = 0);
//Block operator
Fragment& operator [](int i);
Block& operator=(const Block &bl);
//Constructors
Block();
Block(std::vector<AlignedFragment>& afrags, MultiSequence *seqs,
bool enableTransitivity, Block *prohibited = NULL);
virtual ~Block();
};
#endif
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