Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / fasta34 / ag_stats.c

diff --git a/website/archive/binaries/mac/src/fasta34/ag_stats.c b/website/archive/binaries/mac/src/fasta34/ag_stats.c
deleted file mode 100644 (file)
index 97c93f2..0000000
--- a/website/archive/binaries/mac/src/fasta34/ag_stats.c
+++ /dev/null
@@ -1,126 +0,0 @@
-/* this procedure implements Altschul's pre-calculated values for lambda, K */
-
-/* $Name: fa_34_26_5 $ - $Id: ag_stats.c,v 1.5 2006/04/12 18:00:01 wrp Exp $ */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-
-#include "alt_parms.h"
-
-static double K, Lambda, H;
-
-int
-ag_parm(char *pam_type, int gdelval, int ggapval)
-{
-  int r_v, t_gdelval, t_ggapval;
-
-#ifdef OLD_FASTA_GAP
-  t_gdelval = gdelval;
-  t_ggapval = ggapval;
-#else
-  t_gdelval = gdelval+ggapval;
-  t_ggapval = ggapval;
-#endif
-
-  if (strcmp(pam_type,"BL50")==0 || strcmp(pam_type,"BLOSUM50")==0)
-      r_v = look_p(bl50_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"BL62")==0 || strcmp(pam_type,"BLOSUM62")==0)
-      r_v = look_p(bl62_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"P250")==0)
-      r_v = look_p(p250_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"P120")==0)
-      r_v = look_p(p120_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"MD_10")==0)
-      r_v = look_p(md10_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"MD_20")==0)
-      r_v = look_p(md20_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"MD_40")==0)
-      r_v = look_p(md40_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else if (strcmp(pam_type,"DNA")==0 || strcmp(pam_type,"+5/-4")==0)
-      r_v = look_p(nt54_p,t_gdelval,t_ggapval,&K,&Lambda,&H);
-  else r_v = 0;
-
-  return r_v;
-}
-
-int
-look_p(struct alt_p parm[], int gap, int ext,
-       double *K, double *Lambda, double *H)
-{
-  int i;
-
-  gap = -gap;
-  ext = -ext;
-
-  if (gap > parm[1].gap) {
-    *K = parm[0].K;
-    *Lambda = parm[0].Lambda;
-    *H = parm[0].H;
-    return 1;
-  }
-
-  for (i=1; parm[i].gap > 0; i++) {
-    if (parm[i].gap > gap) continue;
-    else if (parm[i].gap == gap && parm[i].ext > ext ) continue;
-    else if (parm[i].gap == gap && parm[i].ext == ext) {
-      *K = parm[i].K;
-      *Lambda = parm[i].Lambda;
-      *H = parm[i].H;
-      return 1;
-    }
-    else break;
-  }
-  return 0;
-}
-
-int E1_to_s(double e_val, int n0, int n1) {
-  double mp, np, a_n0, a_n0f, a_n1, a_n1f, u;
-  int score;
-
-  a_n0 = (double)n0;
-  a_n0f = log(a_n0)/H;
-
-  a_n1 = (double)n1;
-  a_n1f = log(a_n1)/H;
-
-  mp = a_n0 - a_n0f - a_n1f;
-  np = a_n1 - a_n0f - a_n1f;
-
-  if (np < 1.0) np = 1.0;
-  if (mp < 1.0) mp = 1.0;
-
-  /*
-  e_val = K * np * mp * exp ( - Lambda * score);
-  log(e_val) = log(K np mp) - Lambda * score;
-  (log(K np mp)-log(e_val)) / Lambda = score;
-  */
-  score = (int)((log( K * mp * np) - log(e_val))/Lambda +0.5);
-  if (score < 0) score = 0;
-  return score;
-}
-
-double s_to_E4(int score, int n0, int  n1)
-{
-  double p_val;
-  double mp, np, a_n0, a_n0f, a_n1, a_n1f, u;
-  
-  a_n0 = (double)n0;
-  a_n0f = log(a_n0)/H;
-
-  a_n1 = (double)n1;
-  a_n1f = log(a_n1)/H;
-
-  mp = a_n0 - a_n0f - a_n1f;
-  np = a_n1 - a_n0f - a_n1f;
-
-  if (np < 1.0) np = 1.0;
-  if (mp < 1.0) mp = 1.0;
-
-  p_val = K * np * mp * exp ( - Lambda * score);
-
-  if (p_val > 0.01) p_val = 1.0 - exp(-p_val);
-
-  return p_val * 10000.0;
-}
-