Mac binaries

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

diff --git a/website/archive/binaries/mac/src/fasta34/dropnfa.h b/website/archive/binaries/mac/src/fasta34/dropnfa.h
new file mode 100644 (file)
index 0000000..b7082c0
--- /dev/null
+++ b/website/archive/binaries/mac/src/fasta34/dropnfa.h
@@ -0,0 +1,74 @@
+
+/* global definitions shared by dropnfa.c and altivec.c */
+
+#ifndef MAXSAV
+#define MAXSAV 10
+#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 savestr
+{
+   int     score;              /* pam score with segment optimization */
+   int     score0;             /* pam score of best single segment */
+   int     gscore;             /* 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 */
+};
+
+struct bdstr { int CC, DD, CP, DP;};
+
+struct f_struct {
+  struct dstruct *diag;
+  struct savestr vmax[MAXSAV]; /* best matches saved for one sequence */
+  struct savestr *vptr[MAXSAV];
+  struct savestr *lowmax;
+  int ndo;
+  int noff;
+  int hmask;                   /* hash constants */
+  int *pamh1;                  /* pam based array */
+  int *pamh2;                  /* pam based kfact array */
+  int *link, *harr;            /* hash arrays */
+  int kshft;                   /* shift width */
+  int nsav, lowscor;           /* number of saved runs, worst saved run */
+#ifdef TFASTA
+  unsigned char *aa1x;
+  int n10;
+#endif
+  struct bdstr *bss;
+  struct swstr *ss;
+  struct swstr *f_ss, *r_ss;
+  int *waa0;
+  int *waa1;
+  int *res;
+  int max_res;
+  double aa0_f[MAXSQ];
+  double *kar_p;
+ 
+#ifdef FA_ALTIVEC
+  int vec_len;
+  vecInt **vec_matrix;
+  vector signed ALTIVEC_SIZE *vec_HH;
+  vector signed ALTIVEC_SIZE *vec_EE;
+
+  int vec_len2;
+  vecInt2 **vec_matrix2;
+  vector signed ALTIVEC_SIZE2 *vec_HH2;
+  vector signed ALTIVEC_SIZE2 *vec_EE2;
+#endif
+};
+
+static int
+FLOCAL_ALIGN(const unsigned char *A, const unsigned char *B,
+            int M, int N, int low, int up,
+            int **W, int G,int H, int MW,
+            struct f_struct *f_str);