;
72 string& sequence_data)
84 static unsigned char*
86 unsigned intquery_length)
98 return input.GetNumAlignedSequences();
Definitions which are dependant on the NCBI C++ Object Manager.
_PSISequenceWeights * _PSISequenceWeightsFree(_PSISequenceWeights *seq_weights)
Deallocates the _PSISequenceWeights structure.
_PSIInternalPssmData * _PSIInternalPssmDataFree(_PSIInternalPssmData *pssm_data)
Deallocates the _PSIInternalPssmData structure.
_PSIMsa * _PSIMsaFree(_PSIMsa *msa)
Deallocates the _PSIMsa data structure.
_PSIAlignedBlock * _PSIAlignedBlockFree(_PSIAlignedBlock *aligned_blocks)
Deallocates the _PSIAlignedBlock structure.
_PSIPackedMsa * _PSIPackedMsaFree(_PSIPackedMsa *msa)
Deallocates the _PSIMsa data structure.
Private interface for Position Iterated BLAST API, contains the PSSM generation engine.
Utilities initialize/setup BLAST.
Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.
This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST alg...
This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine.
static unsigned int GetNumAlignedSequences(const CPsiBlastInputData &input)
Accesses CPsiBlastInputData private method.
static string x_ErrorCodeToString(int error_code)
Gets error strings from a CPssmEngine private method.
static unsigned char * x_GuardProteinQuery(const unsigned char *query, unsigned int query_length)
Accesses CPssmEngine private method.
static void x_GetSubjectSequence(const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
Gets Subject sequence from a CPsiBlastInputData private method.
Include a standard set of the NCBI C++ Toolkit most basic headers.
static unsigned char * x_GuardProteinQuery(const unsigned char *query, unsigned int query_length)
Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence...
static std::string x_ErrorCodeToString(int error_code)
Convert a PSSM return status into a string.
static void x_GetSubjectSequence(const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg.
uint32_t Uint4
4-byte (32-bit) unsigned integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Magic spell ;-) needed for some weird compilers... very empiric.
Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.
C++ API for the PSI-BLAST PSSM engine.
Defines interface for a sequence alignment processor that can populate a multiple alignment data stru...
BlastScoreBlk * InitializeBlastScoreBlk(const unsigned char *query, Uint4 query_size)
Structure used for scoring calculations.
static void Delete(_PSIAlignedBlock *p)
static void Delete(_PSIInternalPssmData *p)
static void Delete(_PSIMsa *p)
static void Delete(_PSIPackedMsa *p)
static void Delete(_PSISequenceWeights *p)
Functor template for deleting object.
This structure keeps track of the regions aligned between the query sequence and those that were not ...
Internal representation of a PSSM in various stages of its creation and its dimensions.
Internal multiple alignment data structure used by the PSSM engine.
Compact version of PSIMsa structure.
Internal data structure to keep computed sequence weights.
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