int
PSICreatePssmFromFrequencyRatios(const Uint1* query,
Uint4 query_length,
BlastScoreBlk* sbp,
double** freq_ratios,
double impala_scaling_factor,
PSIMatrix** pssm)
{
int status = PSI_SUCCESS;
double* std_prob = NULL;
_PSIInternalPssmData* internal_pssm = NULL;
std_prob = BLAST_GetStandardAaProbabilities();
*pssm = PSIMatrixNew(query_length, (Uint4) sbp->alphabet_size);
internal_pssm = _PSIInternalPssmDataNew(query_length, sbp->alphabet_size);
if ( !std_prob || !*pssm || !internal_pssm ) {
s_PSICreatePssmFromFrequencyRatiosCleanUp(pssm, internal_pssm,
std_prob);
return PSIERR_OUTOFMEM;
}
_PSICopyMatrix_double(internal_pssm->freq_ratios, freq_ratios,
internal_pssm->ncols, internal_pssm->nrows);
status = _PSICreateAndScalePssmFromFrequencyRatios(internal_pssm,
query, query_length,
std_prob, sbp,
impala_scaling_factor);
if (status != PSI_SUCCESS) {
s_PSICreatePssmFromFrequencyRatiosCleanUp(pssm, internal_pssm,
std_prob);
return status;
}
/*** Save the pssm outgoing parameter ***/
s_PSISavePssm(internal_pssm, sbp, *pssm);
s_PSICreatePssmFromFrequencyRatiosCleanUp(NULL, internal_pssm, std_prob);
return status;
}
Kappa_compactSearchItems*
Kappa_compactSearchItemsNew(const Uint1* query, unsigned int queryLength,
BlastScoreBlk* sbp)
{
Kappa_compactSearchItems* retval = NULL;
ASSERT(sbp);
ASSERT(query);
retval = (Kappa_compactSearchItems*)
calloc(1, sizeof(Kappa_compactSearchItems));
if ( !retval ) {
return NULL;
}
retval->standardProb = BLAST_GetStandardAaProbabilities();
if ( !retval->standardProb ) {
return Kappa_compactSearchItemsFree(retval);
}
ASSERT(sbp->alphabet_code == BLASTAA_SEQ_CODE);
ASSERT(sbp->protein_alphabet == TRUE);
ASSERT(sbp->alphabet_size == BLASTAA_SIZE);
ASSERT(sbp->matrix);
retval->query = (Uint1*) query;
retval->qlength = queryLength;
retval->alphabetSize = BLASTAA_SIZE;
retval->matrix = sbp->matrix->data;
retval->kbp_std = sbp->kbp_std;
retval->kbp_psi = sbp->kbp_psi;
retval->kbp_gap_std = sbp->kbp_gap_std;
retval->kbp_gap_psi = sbp->kbp_gap_psi;
retval->lambda_ideal = sbp->kbp_ideal->Lambda;
retval->K_ideal = sbp->kbp_ideal->K;
return retval;
}
double GetStandardProbability(char ch)
{
typedef map < char, double > CharDoubleMap;
static CharDoubleMap standardProbabilities;
if (standardProbabilities.size() == 0) { // initialize static stuff
if (BLASTAA_SIZE != 28) {
ERROR_MESSAGE("GetStandardProbability() - confused by BLASTAA_SIZE != 28");
return 0.0;
}
double *probs = BLAST_GetStandardAaProbabilities();
for (unsigned int i=0; i<28; ++i) {
standardProbabilities[LookupCharacterFromNCBIStdaaNumber(i)] = probs[i];
// TRACE_MESSAGE("standard probability " << LookupCharacterFromNCBIStdaaNumber(i) << " : " << probs[i]);
}
sfree(probs);
}
CharDoubleMap::const_iterator f = standardProbabilities.find(toupper((unsigned char) ch));
if (f != standardProbabilities.end())
return f->second;
WARNING_MESSAGE("GetStandardProbability() - unknown residue character " << ch);
return 0.0;
}
