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| double statistics_gappedCalculateEvalue | ( | float | normalizedScore | ) |
Definition at line 197 of file statistics.c.
References statistics_searchSpaceSize.
Referenced by fasterGappedExtension_score(), gappedExtension_score(), and print_gappedAlignmentsBrief().
00198 { 00199 return statistics_searchSpaceSize / pow(2, normalizedScore); 00200 }
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| int4 statistics_gappedEvalue2nominal | ( | double | evalue | ) |
Definition at line 203 of file statistics.c.
References statisticalParameters::lambda, statistics_gappedLogK, statistics_gappedParams, statistics_log2, and statistics_searchSpaceSize.
Referenced by blast_search().
00204 { 00205 double normalizedScore; 00206 00207 normalizedScore = log(statistics_searchSpaceSize / evalue) / (double)statistics_log2; 00208 00209 // printf("[%f,%f,%f,%f, %f]\n", normalizedScore, statistics_log2 * normalizedScore, statistics_log2 * normalizedScore + statistics_gappedLogK,(statistics_log2 * normalizedScore + statistics_gappedLogK) 00210 // / (double)statistics_gappedParams.lambda, statistics_gappedParams.lambda); 00211 00212 return ceil((statistics_log2 * normalizedScore + statistics_gappedLogK) 00213 / statistics_gappedParams.lambda); 00214 }
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| float statistics_gappedNominal2normalized | ( | int4 | nominalScore | ) |
Definition at line 179 of file statistics.c.
References statisticalParameters::lambda, statistics_gappedLogK, statistics_gappedParams, and statistics_log2.
Referenced by fasterGappedExtension_score(), gappedExtension_score(), and print_gappedAlignmentsBrief().
00180 { 00181 float normalizedScore; 00182 00183 normalizedScore = (((float)nominalScore * statistics_gappedParams.lambda) 00184 - statistics_gappedLogK) / statistics_log2; 00185 00186 return normalizedScore; 00187 }
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| void statistics_initialize | ( | struct PSSMatrix | PSSMatrix, | |
| uint8 | databaseSize, | |||
| int4 | numberOfSequences | |||
| ) |
Definition at line 45 of file statistics.c.
References statisticalParameters::alpha, statisticalParameters::beta, encoding_alphabetType, encoding_protein, statisticalParameters::H, statisticalParameters::K, statisticalParameters::lambda, PSSMatrix::length, parameters_databaseSize, parameters_extendGap, parameters_gappedFinalNormalizedDropoff, parameters_gappedNormalizedDropoff, parameters_numberOfSequences, parameters_scoringMatrix, parameters_startGap, parameters_ungappedNormalizedDropoff, statistics_calcLengthAdjust(), statistics_calcLengthAdjustNew(), statistics_calculateUngappedKarlinParameters(), statistics_databaseSize, statistics_effectiveDatabaseSize, statistics_effectiveQuerySize, statistics_gappedFinalNominalDropoff, statistics_gappedLogK, statistics_gappedNominalDropoff, statistics_gappedParams, statistics_lengthAdjust, statistics_log2, statistics_lookupPrecomputedParams(), statistics_numberOfSequences, statistics_querySize, statistics_searchSpaceSize, statistics_ungappedH, statistics_ungappedK, statistics_ungappedLambda, statistics_ungappedLogK, statistics_ungappedNominalDropoff, and PSSMatrix::strandLength.
Referenced by blast_search().
00046 { 00047 // Record the size (number of letters) of query and subject database 00048 if (PSSMatrix.strandLength == 0) 00049 statistics_querySize = PSSMatrix.length; 00050 else 00051 statistics_querySize = PSSMatrix.strandLength; 00052 00053 // Use command-line parameter for database size if given 00054 if (parameters_databaseSize == 0) 00055 statistics_databaseSize = databaseSize; 00056 else 00057 statistics_databaseSize = parameters_databaseSize; 00058 00059 statistics_numberOfSequences = numberOfSequences; 00060 00061 // Use command-line parameter for number of sequences if given 00062 if (parameters_numberOfSequences != 0) 00063 numberOfSequences = parameters_numberOfSequences; 00064 00065 // Calculate ungapped karlin-atschul parameters lambda, K and H for given 00066 // query matrix, and average residue compositions for the subject database 00067 statistics_calculateUngappedKarlinParameters(PSSMatrix); 00068 00069 if (encoding_alphabetType == encoding_protein) 00070 { 00071 // Lookup precomputed gapped lambda, K, H, alpha and beta values based on 00072 // scoring matrix and gap penalties 00073 statistics_gappedParams = statistics_lookupPrecomputedParams( 00074 parameters_scoringMatrix, parameters_startGap, parameters_extendGap); 00075 } 00076 else 00077 { 00078 // For nucleotide, use ungapped parameters for gapped alignment 00079 statistics_gappedParams.lambda = statistics_ungappedLambda; 00080 statistics_gappedParams.K = statistics_ungappedK; 00081 statistics_gappedParams.H = statistics_ungappedH; 00082 statistics_gappedParams.alpha = 0; 00083 statistics_gappedParams.beta = 0; 00084 } 00085 00086 // Log of K (for gapped and ungapped extension) and log of 2 00087 statistics_ungappedLogK = log(statistics_ungappedK); 00088 statistics_gappedLogK = log(statistics_gappedParams.K); 00089 statistics_log2 = log(2.0); 00090 00091 // Calculate nominal dropoff for ungapped extension using normalized dropoff 00092 statistics_ungappedNominalDropoff = ceil(parameters_ungappedNormalizedDropoff * 00093 statistics_log2 / statistics_ungappedLambda); 00094 00095 // Same for initial and final gapped extension dropoffs 00096 statistics_gappedNominalDropoff = floor(parameters_gappedNormalizedDropoff * 00097 statistics_log2 / statistics_gappedParams.lambda); 00098 statistics_gappedFinalNominalDropoff = floor(parameters_gappedFinalNormalizedDropoff * 00099 statistics_log2 / statistics_gappedParams.lambda); 00100 00101 // Calculate length adjust for query and subject sequences 00102 if (encoding_alphabetType == encoding_protein) 00103 { 00104 // Round lengthAdjust value down 00105 statistics_lengthAdjust = floor(statistics_calcLengthAdjustNew(numberOfSequences)); 00106 } 00107 else 00108 { 00109 statistics_lengthAdjust = floor(statistics_calcLengthAdjust(numberOfSequences)); 00110 } 00111 00112 // Using length adjustment, calculate effective query, database length and search space 00113 statistics_effectiveQuerySize 00114 = statistics_querySize - statistics_lengthAdjust; 00115 statistics_effectiveDatabaseSize 00116 = statistics_databaseSize - numberOfSequences * statistics_lengthAdjust; 00117 statistics_searchSpaceSize 00118 = statistics_effectiveQuerySize * statistics_effectiveDatabaseSize; 00119 }
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| int4 statistics_ungappedNormalized2nominal | ( | float | normalizedScore | ) |
Definition at line 142 of file statistics.c.
References statistics_log2, statistics_ungappedLambda, and statistics_ungappedLogK.
Referenced by blast_search().
00143 { 00144 float nominalScore; 00145 00146 nominalScore = (normalizedScore * statistics_log2 + statistics_ungappedLogK) / statistics_ungappedLambda; 00147 00148 return floor(nominalScore); 00149 }
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| int4 statistics_ungappedNucleotideTrigger | ( | struct PSSMatrix | PSSMatrix | ) |
Definition at line 217 of file statistics.c.
References int4, PSSMatrix::length, statistics_databaseSize, statistics_log2, statistics_numberOfSequences, statistics_ungappedLambda, and statistics_ungappedLogK.
Referenced by blast_search().
00218 { 00219 double evalue, normalizedScore; 00220 int4 averageSubjectLength; 00221 00222 evalue = 0.025; 00223 averageSubjectLength = statistics_databaseSize / statistics_numberOfSequences; 00224 00225 if (averageSubjectLength > PSSMatrix.length) 00226 { 00227 normalizedScore = log(PSSMatrix.length * averageSubjectLength / evalue) 00228 / (double)statistics_log2; 00229 } 00230 else 00231 { 00232 normalizedScore = log(averageSubjectLength * averageSubjectLength / evalue) 00233 / (double)statistics_log2; 00234 } 00235 00236 return ceil((statistics_log2 * normalizedScore + statistics_ungappedLogK) 00237 / statistics_ungappedLambda); 00238 }
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| uint8 statistics_databaseSize |
Definition at line 18 of file statistics.c.
Referenced by blast_search(), print_XMLfooter(), statistics_calcLengthAdjust(), statistics_calcLengthAdjustNew(), statistics_initialize(), and statistics_ungappedNucleotideTrigger().
Definition at line 19 of file statistics.c.
Referenced by blast_search(), and statistics_initialize().
Definition at line 17 of file statistics.c.
Referenced by blast_search(), and statistics_initialize().
Definition at line 36 of file statistics.c.
Referenced by alignments_checkForJoin(), alignments_getTracebacks(), alignments_regularGappedAlignment(), blast_search(), gappedExtension_dpBeforeSeed(), statistics_initialize(), and unpack_getRegions().
| float statistics_gappedLogK |
Definition at line 13 of file statistics.c.
Referenced by statistics_calcLengthAdjustNew(), statistics_gappedEvalue2nominal(), statistics_gappedNominal2normalized(), statistics_gappedNormalized2nominal(), and statistics_initialize().
Definition at line 35 of file statistics.c.
Referenced by alignments_findGoodAlignments(), alignments_regularGappedAlignment(), blast_search(), and statistics_initialize().
Definition at line 31 of file statistics.c.
Referenced by blast_search(), print_XMLfooter(), statistics_calcLengthAdjustNew(), statistics_gappedEvalue2nominal(), statistics_gappedNominal2normalized(), statistics_gappedNormalized2nominal(), and statistics_initialize().
Definition at line 21 of file statistics.c.
Referenced by blast_search(), print_XMLfooter(), and statistics_initialize().
| float statistics_log2 |
Definition at line 12 of file statistics.c.
Referenced by statistics_gappedEvalue2nominal(), statistics_gappedNominal2normalized(), statistics_gappedNormalized2nominal(), statistics_initialize(), statistics_ungappedEvalue2nominal(), statistics_ungappedNominal2normalized(), statistics_ungappedNormalized2nominal(), and statistics_ungappedNucleotideTrigger().
| int4 statistics_querySize |
Definition at line 16 of file statistics.c.
Referenced by blast_search(), statistics_calcLengthAdjust(), statistics_calcLengthAdjustNew(), statistics_calculateUngappedKarlinParameters(), and statistics_initialize().
Definition at line 20 of file statistics.c.
Referenced by blast_search(), print_XMLfooter(), statistics_gappedCalculateEvalue(), statistics_gappedEvalue2nominal(), statistics_initialize(), statistics_ungappedCalculateEvalue(), and statistics_ungappedEvalue2nominal().
| float statistics_ungappedH |
Definition at line 26 of file statistics.c.
Referenced by blast_search(), statistics_calcLengthAdjust(), statistics_calculateUngappedKarlinParameters(), and statistics_initialize().
| float statistics_ungappedK |
Definition at line 27 of file statistics.c.
Referenced by blast_search(), statistics_calcLengthAdjust(), statistics_calculateUngappedKarlinParameters(), and statistics_initialize().
Definition at line 25 of file statistics.c.
Referenced by blast_search(), statistics_calculateUngappedKarlinParameters(), statistics_initialize(), statistics_ungappedEvalue2nominal(), statistics_ungappedNominal2normalized(), statistics_ungappedNormalized2nominal(), and statistics_ungappedNucleotideTrigger().
| float statistics_ungappedLogK |
Definition at line 28 of file statistics.c.
Referenced by statistics_calcLengthAdjust(), statistics_initialize(), statistics_ungappedEvalue2nominal(), statistics_ungappedNominal2normalized(), statistics_ungappedNormalized2nominal(), and statistics_ungappedNucleotideTrigger().
Definition at line 34 of file statistics.c.
Referenced by blast_search(), statistics_initialize(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), and ungappedExtension_oneHitExtend().
1.5.2