fixed makefile

[mothur.git] / fisher2.c

diff --git a/fisher2.c b/fisher2.c
index 9e62302bb0e4ba66c916fea6f876cea8f7da76fd..c86183459dcacebb606125fa12bea3ea08d41918 100644 (file)
--- a/fisher2.c
+++ b/fisher2.c
@@ -1,15 +1,6 @@
-#include <stdlib.h>
-#include <stdio.h> 
-#include <math.h>
-//#include "ctest.h" 
+#include "fisher2.h"
 
 
-#include <limits.h> 
-#define SINT_MAX INT_MAX
-
-#define        max(a, b)               ((a) < (b) ? (b) : (a))
-#define        min(a, b)               ((a) > (b) ? (b) : (a))
-
 static void f2xact(int *nrow, int *ncol, double *table, int *ldtabl,
                  double *expect, double *percnt, double *emin, double
                  *prt, double *pre, double *fact, int *ico, int
@@ -34,30 +25,26 @@ static void f6xact(int *nrow, int *irow, int *iflag, int *kyy,
                   int *key, int *ldkey, int *last, int *ipn);
 static void f7xact(int *nrow, int *imax, int *idif, int *k, int *ks,
                   int *iflag);
-static void f8xact(int *irow, int *is, int *i1, int *izero, int *new);
+static void f8xact(int *irow, int *is, int *i1, int *izero, int *myNew);
 static double f9xact(int *n, int *mm, int *ir, double *fact);
 static void f10act(int *nrow, int *irow, int *ncol, int *icol,
                  double *val, int *xmin, double *fact, int *nd,
                  int *ne, int *m);
-static void f11act(int *irow, int *i1, int *i2, int *new);
+static void f11act(int *irow, int *i1, int *i2, int *myNew);
 static void prterr(int icode, char *mes);
 static int iwork(int iwkmax, int *iwkpt, int number, int itype);
 // void fexact(int *nrow, int *ncol, double *table, int *ldtabl,
 //       double *expect, double *percnt, double *emin, double *prt,
-//       double *pre, /* new in C : */ int *workspace);
+//       double *pre, /* myNew in C : */ int *workspace);
  static void isort(int *n, int *ix);
  static double gammds(double *y, double *p, int *ifault);
  static double alogam(double *x, int *ifault);
 
 
-
-
 /* The only public function : */
-void
-fexact(int *nrow, int *ncol, double *table, int *ldtabl,
+void fexact(int *nrow, int *ncol, double *table, int *ldtabl,
        double *expect, double *percnt, double *emin, double *prt,
-       double *pre, /* new in C : */ int *workspace)
-{
+       double *pre, /* myNew in C : */ int *workspace) {
 
 /*
   ALGORITHM 643, COLLECTED ALGORITHMS FROM ACM.
@@ -324,13 +311,13 @@ f2xact(int *nrow, int *ncol, double *table, int *ldtabl,
 {
     /* IMAX is the largest representable int on the machine. */
     const int imax = SINT_MAX;
-//     const int imax = 2147483647; //xx: I DON´T like this, and
+//     const int imax = 2147483647; //xx: I DON¥T like this, and
 // thanks to the hint from Jason Turner I don't do it anymore. (R.D-U).
 
     /* AMISS is a missing value indicator which is returned when the
        probability is not defined. */
     const double amiss = -12345.;
-
+       
     /* TOL is chosen as the square root of the smallest relative spacing. */
 #ifndef Macintosh
     const  static double tol = 3.45254e-7;
@@ -1741,31 +1728,31 @@ f7xact(int *nrow, int *imax, int *idif, int *k, int *ks,
   */
 
 void
-f8xact(int *irow, int *is, int *i1, int *izero, int *new)
+f8xact(int *irow, int *is, int *i1, int *izero, int *myNew)
 {
     int i;
 
     /* Parameter adjustments */
-    --new;
+    --myNew;
     --irow;
 
     /* Function Body */
     for (i = 1; i < *i1; ++i)
-       new[i] = irow[i];
+       myNew[i] = irow[i];
 
     for (i = *i1; i <= *izero - 1; ++i) {
        if (*is >= irow[i + 1])
            break;
-       new[i] = irow[i + 1];
+       myNew[i] = irow[i + 1];
     }
 
-    new[i] = *is;
+    myNew[i] = *is;
 
     for(;;) {
        ++i;
        if (i > *izero)
            return;
-       new[i] = irow[i];
+       myNew[i] = irow[i];
     }
 }
 
@@ -1886,16 +1873,16 @@ f10act(int *nrow, int *irow, int *ncol, int *icol, double *val,
   -----------------------------------------------------------------------
   */
 void
-f11act(int *irow, int *i1, int *i2, int *new)
+f11act(int *irow, int *i1, int *i2, int *myNew)
 {
     int i;
 
     /* Parameter adjustments */
-    --new;
+    --myNew;
     --irow;
 
-    for (i = 1; i <= (*i1 - 1); ++i)   new[i] = irow[i];
-    for (i = *i1; i <= *i2; ++i)       new[i] = irow[i + 1];
+    for (i = 1; i <= (*i1 - 1); ++i)   myNew[i] = irow[i];
+    for (i = *i1; i <= *i2; ++i)       myNew[i] = irow[i + 1];
 
     return;
 }
@@ -2128,7 +2115,7 @@ L10:
 double alogam(double *x, int *ifault)
 {
     /* Initialized data */
-
+       //printf("alogam x = %f\t%d\n",*x,*ifault);
     static double a1 = .918938533204673;
     static double a2 = 5.95238095238e-4;
     static double a3 = 7.93650793651e-4;
@@ -2160,9 +2147,12 @@ L20:
     f = -log(f);
 L30:
     z = 1. / (y * y);
+       
+       //printf("returning %f\n",(f + (y - .5) * log(y) - y + a1 + (((-a2 * z + a3) * z - a4) * z + a5) / y));
     return(f + (y - .5) * log(y) - y + a1 +
           (((-a2 * z + a3) * z - a4) * z + a5) / y);
 }
 
+
 #endif /* not USING_R */