Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / fasta34 / tatstats.h

diff --git a/website/archive/binaries/mac/src/fasta34/tatstats.h b/website/archive/binaries/mac/src/fasta34/tatstats.h
deleted file mode 100644 (file)
index 1d5173d..0000000
--- a/website/archive/binaries/mac/src/fasta34/tatstats.h
+++ /dev/null
@@ -1,157 +0,0 @@
-#ifndef MAXSQ
-#include "param.h"
-#endif
-
-#ifndef MAXSAV
-#ifdef FASTS
-#define MAXSAV 25
-#else
-#define MAXSAV 10
-#endif
-#endif
-
-#if defined(IBM_AIX) && defined(MAXSEG)
-#undef MAXSEG
-#endif
-#define MAXSEG 30
-
-struct savestr {
-  int     score;               /* pam score with segment optimization */
-  int     score0;              /* pam score of best single segment */
-  int     start0;              /* score from global match */
-  int     dp;                  /* diagonal of match */
-  int     start;               /* start of match in lib seq */
-  int     stop;                 /* end of match in lib seq */
-  int     exact;               /* exact match */
-#if defined(FASTF)
-  int     *used;                /* array of positions in aa0 that were used */
-#endif
-};
-
-struct dstruct {       /* diagonal structure for saving current run */
-   int     score;      /* hash score of current match */
-   int     start;      /* start of current match */
-   int     stop;       /* end of current match */
-   struct savestr *dmax;   /* location in vmax[] where best score data saved */
-};
-
-struct tat_str {
-  double *probs;
-  int lowscore;
-  int highscore;
-};
-
-struct f_struct {
-  struct dstruct *diag;
-  struct savestr *vmax;        /* best matches saved for one sequence */
-  struct savestr **vptr;
-  struct slink *sarr;
-  struct savestr *lowmax;
-  int maxsav;  /* max number of peptide alignments saved in search */
-  int maxsav_w;        /* max number of peptide alignments saved in alignment */
-  int shuff_cnt;
-  int nsave;
-  int ndo;
-  int noff;
-  int nm0;             /* number of fragments */
-#if defined(FASTS) || defined(FASTM)
-  int *nmoff;          /* offset number, start */
-  int *nm_u;
-  int *aa0b;           /* beginning of each segment */
-  int *aa0e;           /* end of each segment */
-  int *aa0i;           /* index of each segment */
-  int *aa0s;           /* max score of each segment */
-  int *aa0l;           /* longest possible peptide match */
-#else
-  int nmoff;           /* offset number, start */
-  unsigned char *aa0;
-  int aa0ix;
-#endif
-  unsigned char *aa0t; /* temp location for peptides */
-  int *aa0ti;          /* temp index for peptides */
-  int hmask;                   /* hash constants */
-  int *pamh1;                  /* pam based array */
-  int *pamh2;                  /* pam based kfact array */
-#if defined(FASTS) || defined(FASTM)
-  int *link, *harr, *l_end;            /* hash arrays */
-#else
-  struct hlstr *link, *harr;            /* hash arrays */
-#endif
-  int kshft;                   /* shift width */
-  int nsav, lowscor;           /* number of saved runs, worst saved run */
-  unsigned char *aa1x;         /* contains translated codons 111222333 */
-  unsigned char *aa1y;         /* contains translated codons 123123123 */
-  int n10;
-  int *waa;
-  int *res;
-  int max_res;
-  double *priors;
-#if defined(FASTS) || defined(FASTM)
-  struct tat_str **tatprobs;          /* array of pointers to tat structs */
-  double **intprobs;                  /* array of integrated tatprobs */
-#endif
-  int dotat;
-  double spacefactor;
-};
-
-struct slink {
-  int     score;
-  double  tatprob;
-  struct tat_str *tat;
-  struct tat_str *newtat;
-  struct savestr *vp;
-  struct slink *next;
-  struct slink *prev;
-};
-
-struct segstr {
-  double tatprob;
-  int length;
-};
-
-void generate_tatprobs(const unsigned char *query,
-                      int begin,
-                      int end,
-                      double *priors,
-                      int **pam2,
-                      int nsq,
-                      struct tat_str **tatarg, struct tat_str *oldtat);
-
-double
-calc_tatusov ( struct slink *last,
-              struct slink *this,
-              const unsigned char *aa0, int n0,
-              const unsigned char *aa1, int n1,
-              int **pam2, int nsq,
-              struct f_struct *f_str,
-              int pseudocts,
-              int do_opt,
-              int zsflag
-              );
-
-double seg_tatprob(struct slink *start,
-                  const unsigned char *aa0,
-                  int n0,
-                  const unsigned char *aa1,
-                  int n1,
-                  struct f_struct *f_str,
-                  struct pstruct *ppst,
-                  int do_opt);
-
-void calc_priors(double *priors,
-                struct pstruct *ppst,
-                struct f_struct *f_str,
-                const unsigned char *aa1,
-                int n1, int pseudocts);
-
-double factorial (int a, int b);
-
-int max_score(int *scores, int nsq);
-
-int min_score(int *scores, int nsq);
-
-double calc_spacefactor(struct f_struct *f_str);
-
-void linreg(double *lnx, double *x, double *lny,
-           int n,
-           double *a, double *b, double *c, int start);