Mac binaries

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

diff --git a/website/archive/binaries/mac/src/fasta34/drop_func.h b/website/archive/binaries/mac/src/fasta34/drop_func.h
new file mode 100644 (file)
index 0000000..d55763a
--- /dev/null
+++ b/website/archive/binaries/mac/src/fasta34/drop_func.h
@@ -0,0 +1,143 @@
+/* drop_func.h */
+
+/* $Name: fa_34_26_5 $ - $Id: drop_func.h,v 1.7 2006/05/31 15:31:45 wrp Exp $ */
+
+/* functions provided by each of the drop files */
+
+/* Copyright (c) 2005 William R. Pearson and the University of Virginia */
+
+
+void   /* initializes f_struct **f_arg */
+init_work (unsigned char *aa0, int n0,
+          struct pstruct *ppst,
+#ifndef DROP_INTERN
+          void **f_arg
+#else
+          struct f_struct **f_arg
+#endif
+);
+
+
+void   /* frees memory allocated in f_struct */
+close_work (const unsigned char *aa0, int n0,
+           struct pstruct *ppst,
+#ifndef DROP_INTERN
+          void **f_arg
+#else
+          struct f_struct **f_arg
+#endif
+);
+
+void   /* documents search function, parameters */
+get_param (struct pstruct *pstr, char *pstring1, char *pstring2);
+
+void   /* calculates alignment score(s), returns them in rst */
+do_work (const unsigned char *aa0, int n0,
+        const unsigned char *aa1, int n1,
+        int frame,
+        struct pstruct *ppst,
+#ifndef DROP_INTERN
+        void *f_arg,
+#else
+        struct f_struct *f_arg,
+#endif
+        int qr_flg, struct rstruct *rst);
+
+void   /* calculates optimal alignment score */
+do_opt (const unsigned char *aa0, int n0,
+       const unsigned char *aa1, int n1,
+       int frame,
+       struct pstruct *ppst,
+#ifndef DROP_INTERN
+       void *f_arg,
+#else
+       struct f_struct *f_arg,
+#endif
+       struct rstruct *rst
+       );
+
+int    /* produces encoding of alignment */
+do_walign (const unsigned char *aa0, int n0,
+          const unsigned char *aa1, int n1,
+          int frame,
+          struct pstruct *ppst, 
+#ifndef DROP_INTERN
+          void *f_arg,
+#else
+          struct f_struct *f_arg,
+#endif
+          struct a_res_str *a_res,
+          int *have_ares);
+
+void
+pre_cons(const unsigned char *aa, int n, int frame, 
+#ifndef DROP_INTERN
+          void *f_arg
+#else
+          struct f_struct *f_arg
+#endif
+       );
+
+void 
+aln_func_vals(int frame, struct a_struct *aln);
+
+int    /* takes aa0, aa1, a_res, and produces seqc0, seqc1 */
+calcons(const unsigned char *aa0, int n0,
+       const unsigned char *aa1, int n1,
+       int *nc,
+       struct a_struct *aln,           /* seqc0/seqc1 coordinates */
+       struct a_res_str a_res,         /* aa0,aa1, coord, inc. res, nres */
+       struct pstruct pst,
+       char *seqc0, char *seqc1, char *seqca,
+#ifndef DROP_INTERN
+       void *f_arg
+#else
+       struct f_struct *f_arg
+#endif
+       );
+
+/* calcons_a - takes aa0, aa1, a_res, and produces seqc0, seqc1, 
+ *             and seqc0a, seqc1a - the annotated sequences 
+ */
+int
+calcons_a(const unsigned char *aa0, unsigned char *aa0a, int n0,
+         const unsigned char *aa1, int n1,
+         int *nc,
+         struct a_struct *aln,
+         struct a_res_str a_res,
+         struct pstruct pst,
+         char *seqc0, char *seqc0a, char *seqc1, char *seqca,
+         char *ann_arr,
+#ifndef DROP_INTERN
+         void *f_arg
+#else
+         struct f_struct *f_arg
+#endif
+         );
+
+int    /* returns lenc - length of aligment */
+calc_code(const unsigned char *aa0, int n0,
+         const unsigned char *aa1, int n1,
+         struct a_struct *aln,
+         struct a_res_str a_res,
+         struct pstruct pst,
+         char *al_str, int al_str_n,
+#ifndef DROP_INTERN
+         void *f_arg
+#else
+         struct f_struct *f_arg
+#endif
+         );
+
+int    /* returns lenc - length of alignment */
+calc_id(const unsigned char *aa0, int n0,
+       const unsigned char *aa1, int n1,
+       struct a_struct *aln, 
+       struct a_res_str a_res,
+       struct pstruct pst,
+#ifndef DROP_INTERN
+       void *f_arg
+#else
+       struct f_struct *f_arg
+#endif
+       );