alignment.h File Reference

#include <iostream>
#include <vector>
#include <string>
#include <map>
#include <algorithm>
#include <stdint.h>
#include "track.h"
#include "sequence.h"
#include "seqTools.h"

Go to the source code of this file.

Classes
class	StochHMM::cell
class	StochHMM::alignment

Namespaces
namespace	StochHMM
	traceback_path.h

Typedefs
typedef std::vector < std::vector< double > >	StochHMM::mmMatrix

Enumerations
enum	StochHMM::tracebackDirection { StochHMM::NONE, StochHMM::DIAGONAL, StochHMM::LEFT, StochHMM::UP }
enum	StochHMM::alignment_type { StochHMM::cGlobal, StochHMM::cLocal, StochHMM::cGlocal }