void stat_calcUngapKarlinParameters(double *dbCharProb, double *queryCharProb, int scoringMatrix[16][16])
{
int4 scoreProbSize, highest, lowest;
double * scoreProb;
int i, j;
lowest = stat_scoreBlock.mismatch;
highest = stat_scoreBlock.match;
scoreProbSize = highest-lowest+1;
scoreProb = (double *) calloc(scoreProbSize, sizeof(double));
for (i=0; i<16; i++) {
for (j=0; j<16; j++) {
scoreProb[scoringMatrix[i][j] - lowest] += dbCharProb[i] * queryCharProb[j];
}
}
// calculate the Karlin parameters, refer to karlin.c
BlastKarlinBlkCalc(scoreProb-lowest, lowest, highest);
stat_ungapH = BlastKarlin_H;
stat_ungapK = BlastKarlin_K;
stat_ungapLambda = BlastKarlin_lambda;
if (stat_ungapK <= 0.001)
{
fprintf(stderr,"ERROR: unable to calculate the KARLIN statistic for the given scoring scheme.\n");
exit(-1);
}
free(scoreProb);
}
void statistics_calculateUngappedKarlinParameters(struct PSSMatrix PSSMatrix)
{
int4 highest, lowest;
double* scoreProbabilities;
int4 queryPosition;
unsigned char subjectCode;
double probability, sum = 0;
int4 score;
int4 numRegularLettersInQuery = 0;
static float* alphabetFrequencies;
if (encoding_alphabetType == encoding_nucleotide)
{
alphabetFrequencies = Nucleotide_prob;
}
else
{
// Use Robinson&Robinson frequencies for protein alphabet
alphabetFrequencies = Robinson_prob;
}
highest = PSSMatrix.highestValue;
lowest = PSSMatrix.lowestValue;
// Initialize array to hold probability values for range of possible scores
scoreProbabilities = (double*)global_malloc(sizeof(double) * (highest - lowest + 1));
scoreProbabilities -= lowest;
score = lowest;
while (score <= highest)
{
scoreProbabilities[score] = 0.0;
score++;
}
// Determine the number of regular letters (ie. non-ambigious codes) in the query
queryPosition = 0;
while (queryPosition < statistics_querySize)
{
// if (PSSMatrix.queryCodes[queryPosition] < encoding_numRegularLetters)
if (PSSMatrix.queryCodes[queryPosition] != encoding_numRegularLetters)
{
numRegularLettersInQuery++;
}
queryPosition++;
}
// For each position in the query PSSMatrix that does not represent an ambigious code
queryPosition = 0;
while (queryPosition < statistics_querySize)
{
// if (PSSMatrix.queryCodes[queryPosition] < encoding_numRegularLetters)
if (PSSMatrix.queryCodes[queryPosition] != encoding_numRegularLetters)
{
// For each regular amino-acid subject code
subjectCode = 0;
while (subjectCode < encoding_numRegularLetters)
{
// Calculate probability that, if a residue was randomly chosen from the subject database
// and a position was randomly chosen from query, they would be subjectCode and queryPosition
// respectively
probability = alphabetFrequencies[subjectCode] / (float)numRegularLettersInQuery;
// Calculate score of aligning query position to this subject residue
score = PSSMatrix.matrix[queryPosition][subjectCode];
// Add to set of probabilities
scoreProbabilities[score] += probability;
subjectCode++;
}
}
queryPosition++;
}
// Calculate residue frequency normalizing value
subjectCode = 0;
while (subjectCode < encoding_numRegularLetters)
{
sum += alphabetFrequencies[subjectCode];
subjectCode++;
}
// Normalized probabilities by dividing them by the sum of the robinson frequency values
score = lowest;
while (score <= highest)
{
scoreProbabilities[score] /= sum;
score++;
}
// Calculate the Lambda, H and K values for these score probabilities
// See karlin.c for implementation
BlastKarlinBlkCalc(scoreProbabilities, lowest, highest);
statistics_ungappedH = BlastKarlin_H;
statistics_ungappedK = BlastKarlin_K;
statistics_ungappedLambda = BlastKarlin_lambda;
if (statistics_ungappedK <= 0.0001)
{
fprintf(stderr, "Error: unable to calculate statistical significance for given scoring scheme\n");
fflush(stderr);
exit(-1);
}
scoreProbabilities += lowest;
free(scoreProbabilities);
}
