Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / squid / vectorops.c

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/vectorops.c b/website/archive/binaries/mac/src/clustalo/src/squid/vectorops.c
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/clustalo/src/squid/vectorops.c
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+/* 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;
+}
+
+
+