1 #ifndef ALGO_ALIGN_UTIL_BLAST_TABULAR__HPP
2 #define ALGO_ALIGN_UTIL_BLAST_TABULAR__HPP
53 CBlastTabular(
const objects::CSeq_align& seq_align,
bool save_xcript =
false);
56 const TId& idsubj,
TCoord sstart,
bool sstrand,
57 const string& xcript);
67 void SetLength(
TCoord length);
70 void SetMismatches(
TCoord mismatches);
74 TCoord GetGaps(
void)
const;
76 void SetRawScore(
TCoord score);
77 TCoord GetRawScore(
void)
const;
79 void SetEValue(
double evalue);
80 double GetEValue(
void)
const;
82 void SetIdentity(
float identity);
83 float GetIdentity(
void)
const;
85 void SetScore(
float score);
86 float GetScore(
void)
const;
101 void x_Deserialize(
const char* m8,
F seq_id_extractor);
104 virtual void x_PartialDeserialize(
const char* m8);
106 static void sx_MineSegment(
size_t where,
const objects::CStd_seg::TLoc & locs,
virtual void Modify(Uint1 point, TCoord new_pos)
virtual void x_PartialSerialize(CNcbiOstream &os) const
CBlastTabular(const objects::CSeq_align &seq_align, bool save_xcript=false)
Include a standard set of the NCBI C++ Toolkit most basic headers.
static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)
unsigned int TSeqPos
Type for sequence locations and lengths.
TSeqPos GetLength(const CSeq_id &id, CScope *scope)
Get sequence length if scope not null, else return max possible TSeqPos.
uint8_t Uint1
1-byte (8-bit) unsigned integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
#define NCBI_XALGOALIGN_EXPORT
unsigned int
A callback function used to compare two keys in a database.
#define F(x)
Make a parametrized function appear to have only one variable.
Int4 delta(size_t dimension_, const Int4 *score_)