34 #ifndef ALGO_BLAST_CORE__BLAST_RPS__H
35 #define ALGO_BLAST_CORE__BLAST_RPS__H
43 #define RPS_MAGIC_NUM 0x1e16
44 #define RPS_MAGIC_NUM_28 0x1e17
45 #define NUM_EXPANSION_WORDS 3
83 #define FREQ_RATIO_SCALE 1000000000
#define NUM_EXPANSION_WORDS
Intentionally unused words in .loo file.
struct BlastRPSLookupFileHeader BlastRPSLookupFileHeader
header of RPS blast '.loo' file
struct BlastRPSFreqRatiosHeader BlastRPSFreqRatiosHeader
struct BlastRPSInfo BlastRPSInfo
The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...
struct BlastRPSAuxInfo BlastRPSAuxInfo
information derived from RPS blast '.aux' file
struct BlastRPSProfileHeader BlastRPSProfileHeader
header of RPS blast '.rps' file
int32_t Int4
4-byte (32-bit) signed integer
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
information derived from RPS blast '.aux' file
double ungapped_k
ungapped Karlin value for orig_score_matrix (not used)
Int4 gap_extend_penalty
gap extend penalty used in deriving PSSMs
double * karlin_k
one Karlin value for each DB sequence
Int4 max_db_seq_length
maximum DB sequence length (not used)
double ungapped_h
ungapped Karlin value for orig_score_matrix (not used)
double scale_factor
the PSSMs are scaled by this amount, and so all scores and all cutoff values must be similarly scaled...
Int4 gap_open_penalty
gap open penalty used in deriving PSSMs
char * orig_score_matrix
score matrix used to derive PSSMs
Int4 db_length
RPS DB search space (not used)
The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...
BlastRPSProfileHeader * profile_header
for '.rps' file
BlastRPSProfileHeader * obsr_header
for '.obsr' file
BlastRPSAuxInfo aux_info
for '.aux' file
BlastRPSFreqRatiosHeader * freq_ratios_header
for '.freq' file
BlastRPSLookupFileHeader * lookup_header
for '.loo' file
BlastRPSProfileHeader * freq_header
for '.wcounts' file