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50 unsigned intsub_size)
78 "Unrecognised standard scoring matrix name");
103 unsigned intnum_res,
105: m_NumResidues(num_res)
127: m_NumResidues((unsigned
int)sqrt((double)vals.
size()))
144 for(
unsigned i=0;
i< vals.size();
i++) {
187 "Score matrix index out of bounds");
197 "Score matrix does not contain residue order information");
200 unsigned i= 0, j = 0;
213(
string)
"Residue "+ residue
214+
" not in score matrix alphabet");
222(
string)
"Residue "+ residue
223+
" not in score matrix alphabet");
Exceptions for CGeneralScoreMatrix.
Score matrix that can take any value.
const char * GetResidueOrder(void) const
Get order of residues in the score matrix.
Int4 GetScore(Uint4 i, Uint4 j) const
Get score matrix entry for at specified position.
~CGeneralScoreMatrix()
Destructor.
unsigned int m_NumResidues
EScoreMatrixName
Names of standard scoring matrices.
CGeneralScoreMatrix(EScoreMatrixName type, unsigned int sub_size=25)
Creates a standard score matrix.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
int32_t Int4
4-byte (32-bit) signed integer
uint32_t Uint4
4-byte (32-bit) unsigned integer
unsigned int
A callback function used to compare two keys in a database.
const struct ncbi::grid::netcache::search::fields::SIZE size
const SNCBIPackedScoreMatrix NCBISM_Pam30
const SNCBIPackedScoreMatrix NCBISM_Blosum62
const SNCBIPackedScoreMatrix NCBISM_Pam250
const SNCBIPackedScoreMatrix NCBISM_Blosum80
void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)
Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...
const SNCBIPackedScoreMatrix NCBISM_Pam70
const SNCBIPackedScoreMatrix NCBISM_Blosum45
The standard matrices.
const char * symbols
order of residues
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