#ifndef ALGO_ALIGN_UTIL_BLAST_TABULAR__HPP
#define ALGO_ALIGN_UTIL_BLAST_TABULAR__HPP
#include <corelib/ncbistd.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <algo/align/util/align_shadow.hpp>
BEGIN_NCBI_SCOPE
class NCBI_XALGOALIGN_EXPORT CBlastTabular: public CAlignShadow
{
public:
typedef CAlignShadow TParent;
typedef TParent::TCoord TCoord;
CBlastTabular(void) {};
CBlastTabular(const objects::CSeq_align& seq_align, bool save_xcript = false);
CBlastTabular(const TId& idquery, TCoord qstart, bool qstrand,
const TId& idsubj, TCoord sstart, bool sstrand,
const string& xcript);
CBlastTabular(const char* m8, bool force_local_ids = false);
typedef int (*SCORE_FUNC)(const CRef<objects::CSeq_id>& id);
CBlastTabular(const char* m8, SCORE_FUNC score_func);
void SetLength(TCoord length);
TCoord GetLength(void) const;
void SetMismatches(TCoord mismatches);
TCoord GetMismatches(void) const;
void SetGaps(TCoord gaps);
TCoord GetGaps(void) const;
void SetRawScore(TCoord score);
TCoord GetRawScore(void) const;
void SetEValue(double evalue);
double GetEValue(void) const;
void SetIdentity(float identity);
float GetIdentity(void) const;
void SetScore(float score);
float GetScore(void) const;
virtual void Modify(Uint1 where, TCoord new_pos);
protected:
TCoord m_Length;
TCoord m_Mismatches;
TCoord m_Gaps;
TCoord m_RawScore;
double m_EValue;
float m_Identity;
float m_Score;
template <class F>
void x_Deserialize(const char* m8, F seq_id_extractor);
virtual void x_PartialSerialize(CNcbiOstream& os) const;
virtual void x_PartialDeserialize(const char* m8);
static void sx_MineSegment(size_t where, const objects::CStd_seg::TLoc & locs,
TSeqPos * delta, TSeqPos * prev);
};
END_NCBI_SCOPE
#endif
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