diff options
Diffstat (limited to 'algo/blast/core/blast_psi_priv.c')
| -rw-r--r-- | algo/blast/core/blast_psi_priv.c | 49 |
1 files changed, 41 insertions, 8 deletions
diff --git a/algo/blast/core/blast_psi_priv.c b/algo/blast/core/blast_psi_priv.c index 92dfb1a7..1062ac8a 100644 --- a/algo/blast/core/blast_psi_priv.c +++ b/algo/blast/core/blast_psi_priv.c @@ -1,6 +1,6 @@ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = - "$Id: blast_psi_priv.c,v 1.53 2005/04/21 20:26:57 camacho Exp $"; + "$Id: blast_psi_priv.c,v 1.57 2005/11/18 20:09:45 camacho Exp $"; #endif /* SKIP_DOXYGEN_PROCESSING */ /* =========================================================================== * @@ -454,7 +454,7 @@ _PSISequenceWeightsFree(_PSISequenceWeights* seq_weights) } #ifdef _DEBUG -static char getRes(char input) +char GetResidue(char input) { switch (input) { case 0: return ('-'); @@ -502,7 +502,7 @@ __printMsa(const char* filename, const _PSIMsa* msa) /*fprintf(fp, "%3d\t", i);*/ for (j = 0; j < msa->dimensions->query_length; j++) { if (msa->cell[i][j].is_aligned) { - fprintf(fp, "%c", getRes(msa->cell[i][j].letter)); + fprintf(fp, "%c", GetResidue(msa->cell[i][j].letter)); } else { fprintf(fp, "."); } @@ -1637,6 +1637,15 @@ _PSISpreadGapWeights(const _PSIMsa* msa, } } +/** The following define enables/disables the _PSICheckSequenceWeights + * function's abort statement in the case when the sequence weights are not + * being checked. When this is enabled, abort() will be invoked if none of the + * sequence weights are checked to be in the proper range. The C toolkit code + * silently ignores this situation, so it's implemented that way here for + * backwards compatibility. + */ +#define SEQUENCE_WEIGHTS_CHECK__ABORT_ON_FAILURE 0 + /* Verifies that each column of the match_weights field in the seq_weights * structure adds up to 1. */ static int @@ -1646,9 +1655,12 @@ _PSICheckSequenceWeights(const _PSIMsa* msa, { const Uint1 kXResidue = AMINOACID_TO_NCBISTDAA['X']; Uint4 pos = 0; /* residue position (ie: column number) */ - Boolean check_performed = FALSE; /* were there any sequences checked? */ const Uint4 kExpectedNumMatchingSeqs = nsg_compatibility_mode ? 0 : 1; +#if SEQUENCE_WEIGHTS_CHECK__ABORT_ON_FAILURE + Boolean check_performed = FALSE; /* were there any sequences checked? */ +#endif + ASSERT(msa); ASSERT(seq_weights); @@ -1659,6 +1671,9 @@ _PSICheckSequenceWeights(const _PSIMsa* msa, if (msa->num_matching_seqs[pos] <= kExpectedNumMatchingSeqs || msa->cell[kQueryIndex][pos].letter == kXResidue) { + /* N.B.: the following statement allows for the sequence weights to + * go unchecked. To allow more strict checking, enable the + * SEQUENCE_WEIGHTS_CHECK__ABORT_ON_FAILURE #define above */ continue; } @@ -1669,15 +1684,19 @@ _PSICheckSequenceWeights(const _PSIMsa* msa, if (running_total < 0.99 || running_total > 1.01) { return PSIERR_BADSEQWEIGHTS; } +#if SEQUENCE_WEIGHTS_CHECK__ABORT_ON_FAILURE check_performed = TRUE; +#endif } +#if SEQUENCE_WEIGHTS_CHECK__ABORT_ON_FAILURE /* This condition should never happen because it means that no sequences * were selected to calculate the sequence weights! */ if ( !check_performed && !nsg_compatibility_mode ) { /* old code didn't check for this... */ assert(!"Did not perform sequence weights check"); } +#endif return PSI_SUCCESS; } @@ -1923,7 +1942,7 @@ _PSIConvertFreqRatiosToPSSM(_PSIInternalPssmData* internal_pssm, internal_pssm->pssm[i][j] = sbp->matrix->data[kResidue][j]; - if (sbp->matrix->data[kResidue][j] != BLAST_SCORE_MIN) { + if (freq_ratios->data[kResidue][j] != 0.0) { double tmp = kPSIScaleFactor * freq_ratios->bit_scale_factor * log(freq_ratios->data[kResidue][j])/NCBIMATH_LN2; @@ -1959,8 +1978,8 @@ _PSIScaleMatrix(const Uint1* query, int** scaled_pssm = NULL; int** pssm = NULL; double factor; - double factor_low = 0.0; - double factor_high = 0.0; + double factor_low = 1.0; + double factor_high = 1.0; double ideal_lambda = 0.0; /* ideal value of ungapped lambda for underlying scoring matrix */ double new_lambda = 0.0; /* Karlin-Altschul parameter calculated @@ -2004,6 +2023,7 @@ _PSIScaleMatrix(const Uint1* query, if (first_time) { factor_high = 1.0 + kPositScalingPercent; factor = factor_high; + factor_low = 1.0; too_high = TRUE; first_time = FALSE; } else { @@ -2188,7 +2208,7 @@ _PSIComputeScoreProbabilities(const int** pssm, /* [in] */ } ASSERT(score_freqs->score_avg == 0.0); - for (s = min_score; s < max_score; s++) { + for (s = min_score; s <= max_score; s++) { score_freqs->score_avg += (s * score_freqs->sprob[s]); } @@ -2358,6 +2378,19 @@ _PSISaveDiagnostics(const _PSIMsa* msa, /* * =========================================================================== * $Log: blast_psi_priv.c,v $ + * Revision 1.57 2005/11/18 20:09:45 camacho + * Fixes for backwards compatibility with C toolkit PSSM engine for certain corner + * cases. + * + * Revision 1.56 2005/10/17 18:34:54 camacho + * Remove abort() call when sequence weights are not checked + * + * Revision 1.55 2005/10/05 14:09:30 camacho + * Port change in revision 6.76 of posit.c + * + * Revision 1.54 2005/10/03 20:42:41 camacho + * Minor + * * Revision 1.53 2005/04/21 20:26:57 camacho * Relax validation in s_PSIValidateAlignedColumns so that query sequence can be * the only aligned sequence for a given column of the multiple sequence |