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//////////////////////////////////////////////////////////////////////
// AlignedFragment.h
//
// Class for a pairwise local alignment
//////////////////////////////////////////////////////////////////////
#ifndef ALIGNFRAGMENT_H
#define ALIGNFRAGMENT_H
#include <cstdio>
#include <vector>
#include <fstream>
class Fragment;
class AlignedFragment;
typedef std::vector<AlignedFragment> AVECT;
class AlignedFragment
{
public:
void Print(FILE *file);
int ProcessRepeat(AVECT &fragments, int minlength);
//Getters
int GetEnd(int i);
int GetBegin(int i);
int GetID(int i);
std::pair<int, int> *GetAlignPos(int seq, int pos, int &second);
int GetLength();
Fragment * GetFragment(int i);
Fragment * GetAlignFragment(Fragment &fr);
//
void Adjust(Fragment& fr1, Fragment& fr2, AlignedFragment &rfr1, AlignedFragment &rfr2);
void Prune();
AlignedFragment * SubFragment(int begin0,int end0, int begin1, int end1);
void ShiftRight(int offset1, int offset2);
//Constructors
AlignedFragment(int d1, int d2, int beg1, int beg2, int e1, int e2, int *s1, int *s2);
AlignedFragment& operator =(const AlignedFragment af);
AlignedFragment(const AlignedFragment& af);
AlignedFragment();
virtual ~AlignedFragment();
int id[2];
int begin[2];
int end[2];
float similarity;
int *seq[2];
};
class Fragment{
public:
Fragment();
Fragment(int start, int e, int mul, int sid)
{ begin = start; end = e; multiply = mul; id = sid; length = end - begin + 1;}
Fragment (const Fragment& fr)
{ begin = fr.begin; end = fr.end; length = fr.length; multiply = fr.multiply; id = fr.id;}
Fragment& operator =(const Fragment f)
{begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;}
int Overlap(Fragment& fr);
int begin;
int length;
int multiply; // number of sequences aligned to the fragment
int id;
int end;
};
#endif
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