Mac binaries

[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
new file mode 100644 (file)
index 0000000..1d5173d
--- /dev/null
+++ b/website/archive/binaries/mac/src/fasta34/tatstats.h
@@ -0,0 +1,157 @@
+#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);