Mercurial > repos > clustalomega > clustalomega
diff clustalomega/clustal-omega-1.0.2/src/squid/vectorops.c @ 1:bc707542e5de
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author | clustalomega |
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date | Thu, 21 Jul 2011 13:35:08 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalomega/clustal-omega-1.0.2/src/squid/vectorops.c Thu Jul 21 13:35:08 2011 -0400 @@ -0,0 +1,297 @@ +/* vectorops.c + * Operations on vectors of floats or doubles. + * + * DSet(), FSet() - set all items in vector to value. + * DScale(), FScale() - multiply all items in vector by scale + * DSum(), FSum() - return sum of values in vector + * DAdd(), FAdd() - add vec2 to vec1. + * DCopy(), FCopy() - set vec1 to be same as vec2. + * DDot(), FDot() - return dot product of two vectors. + * DMax(), FMax() - return value of maximum element in vector + * DMin(), FMin() - return value of minimum element in vector + * DArgMax(), FArgMax() - return index of maximum element in vector + * DArgMin(), FArgMin() - return index of minimum element in vector + * + * DNorm(), FNorm() - normalize a probability vector of length n. + * DLog(), FLog() - convert to log probabilities + * DExp(), FExp() - convert log p's back to probabilities + * DLogSum(), FLogSum() - given vector of log p's; return log of summed p's. + * + * SRE, Tue Oct 1 15:23:25 2002 [St. Louis] + * CVS $Id: vectorops.c,v 1.1 2002/10/09 14:26:09 eddy Exp) + */ + +#include <stdlib.h> +#include <math.h> +#include <float.h> +#include "vectorops.h" + +void +DSet(double *vec, int n, double value) +{ + int x; + for (x = 0; x < n; x++) vec[x] = value; +} + +void +FSet(float *vec, int n, float value) +{ + int x; + for (x = 0; x < n; x++) vec[x] = value; +} + +void +DScale(double *vec, int n, double scale) +{ + int x; + for (x = 0; x < n; x++) vec[x] *= scale; +} + +void +FScale(float *vec, int n, float scale) +{ + int x; + for (x = 0; x < n; x++) vec[x] *= scale; +} + +double +DSum(double *vec, int n) +{ + double sum = 0.; + int x; + for (x = 0; x < n; x++) sum += vec[x]; + return sum; +} + +float +FSum(float *vec, int n) +{ + float sum = 0.; + int x; + for (x = 0; x < n; x++) sum += vec[x]; + return sum; +} + +void +DAdd(double *vec1, double *vec2, int n) +{ + int x; + for (x = 0; x < n; x++) vec1[x] += vec2[x]; +} + +void +FAdd(float *vec1, float *vec2, int n) +{ + int x; + for (x = 0; x < n; x++) vec1[x] += vec2[x]; +} + +void +DCopy(double *vec1, double *vec2, int n) +{ + int x; + for (x = 0; x < n; x++) vec1[x] = vec2[x]; +} + +void +FCopy(float *vec1, float *vec2, int n) +{ + int x; + for (x = 0; x < n; x++) vec1[x] = vec2[x]; +} + +double +DDot(double *vec1, double *vec2, int n) +{ + double result = 0.; + int x; + for (x = 0; x < n; x++) result += vec1[x] * vec2[x]; + return result; +} + +float +FDot(float *vec1, float *vec2, int n) +{ + float result = 0.; + int x; + for (x = 0; x < n; x++) result += vec1[x] * vec2[x]; + return result; +} + +double +DMax(double *vec, int n) +{ + int i; + double best; + + best = vec[0]; + for (i = 1; i < n; i++) + if (vec[i] > best) best = vec[i]; + return best; +} + +float +FMax(float *vec, int n) +{ + int i; + float best; + + best = vec[0]; + for (i = 1; i < n; i++) + if (vec[i] > best) best = vec[i]; + return best; +} + +double +DMin(double *vec, int n) +{ + int i; + double best; + + best = vec[0]; + for (i = 1; i < n; i++) + if (vec[i] < best) best = vec[i]; + return best; +} + +float +FMin(float *vec, int n) +{ + int i; + float best; + + best = vec[0]; + for (i = 1; i < n; i++) + if (vec[i] < best) best = vec[i]; + return best; +} + +double +DArgMax(double *vec, int n) +{ + int i; + int best = 0; + + for (i = 1; i < n; i++) + if (vec[i] > vec[best]) best = i; + return best; +} + +float +FArgMax(float *vec, int n) +{ + int i; + int best = 0; + + for (i = 1; i < n; i++) + if (vec[i] > vec[best]) best = i; + return best; +} + +double +DArgMin(double *vec, int n) +{ + int i; + int best = 0; + for (i = 1; i < n; i++) + if (vec[i] < vec[best]) best = i; + return best; +} + +float +FArgMin(float *vec, int n) +{ + int i; + int best = 0; + + for (i = 1; i < n; i++) + if (vec[i] < vec[best]) best = i; + return best; +} + +void +DNorm(double *vec, int n) +{ + int x; + double sum; + + sum = DSum(vec, n); + if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum; + else for (x = 0; x < n; x++) vec[x] = 1. / (double) n; +} + +void +FNorm(float *vec, int n) +{ + int x; + float sum; + + sum = FSum(vec, n); + if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum; + else for (x = 0; x < n; x++) vec[x] = 1. / (float) n; +} + +void +DLog(double *vec, int n) +{ + int x; + for (x = 0; x < n; x++) + if (vec[x] > 0.) vec[x] = log(vec[x]); + else vec[x] = -DBL_MAX; +} + +void +FLog(float *vec, int n) +{ + int x; + for (x = 0; x < n; x++) + if (vec[x] > 0.) vec[x] = log(vec[x]); + else vec[x] = -FLT_MAX; +} + +void +DExp(double *vec, int n) +{ + int x; + for (x = 0; x < n; x++) vec[x] = exp(vec[x]); +} + +void +FExp(float *vec, int n) +{ + int x; + for (x = 0; x < n; x++) vec[x] = exp(vec[x]); +} + +float +DLogSum(double *vec, int n) +{ + int x; + double max, sum; + + max = DMax(vec, n); + sum = 0.0; + for (x = 0; x < n; x++) + if (vec[x] > max - 50.) + sum += exp(vec[x] - max); + sum = log(sum) + max; + return sum; +} + +float +FLogSum(float *vec, int n) +{ + int x; + float max, sum; + + max = FMax(vec, n); + sum = 0.0; + for (x = 0; x < n; x++) + if (vec[x] > max - 50.) + sum += exp(vec[x] - max); + sum = log(sum) + max; + return sum; +} + + +