Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/fasta34/param.h b/website/archive/binaries/mac/src/fasta34/param.h
deleted file mode 100644 (file)
index cdc4690..0000000
--- a/website/archive/binaries/mac/src/fasta34/param.h
+++ /dev/null
@@ -1,151 +0,0 @@
-/* $Name: fa_34_26_5 $ - $Id: param.h,v 1.41 2007/04/26 18:37:19 wrp Exp $ */
-
-
-#ifndef P_STRUCT
-#define P_STRUCT
-
-#define MAXSQ 50
-
-
-/* Concurrent read version */
-
-struct fastr {
-  int ktup;
-  int cgap;
-  int pgap;
-  int pamfact;
-  int scfact;
-  int bestoff;
-  int bestscale;
-  int bkfact;
-  int bktup;
-  int bestmax;
-  int altflag;
-  int optflag;
-  int iniflag;
-  int optcut;
-  int optcut_set;
-  int optwid;
-};
-
-struct prostr {
-    int gopen;
-    int gextend;
-    int width;
-};
-
-struct pstruct         /* parameters */
-{
-  int n0;      /* length of query sequence, used for statistics */
-  int gdelval; /* value gap open (-10) */
-  int ggapval; /* value for additional residues in gap (-2) */
-  int gshift;  /* frameshift for fastx, fasty */
-  int gsubs;   /* nt substitution in fasty */
-  int p_d_mat; /* dna match penalty */
-  int p_d_mis; /* dna mismatch penalty */
-  int p_d_set; /* using match/mismatch */
-  int score_ix;        /* index to sorted score */
-  int zsflag;  /* use scalebest() */
-  int zsflag_f;        /* use scalebest() */
-  int zs_win;
-  int histint;         /* histogram interval */
-  char sq[MAXSQ+1];
-  int hsq[MAXSQ+1];
-  int nsq;             /* length of normal sq */
-  int ext_sq_set;      /* flag for using extended alphabet */
-  char sqx[MAXSQ];
-  int hsqx[MAXSQ+1];
-  int c_nt[MAXSQ+1];
-  int nsqx;    /* length of extended sq */
-  int dnaseq;  /* -1 = not set (protein); 0 = protein; 1 = DNA; 2 = other, 3 RNA */
-  int nt_align;        /* DNA/RNA alignment = 1 */
-  int debug_lib;
-  int tr_type; /* codon table */
-  int sw_flag;
-  char pamfile[120];   /* pam file type */
-  char pgpfile[120];
-  int pgpfile_type;
-  float pamscale;
-  int pam_pssm;
-  int pam_set;
-  int have_pam2;
-  int **pam2[2];
-  int **pam2p[2];
-  int pamoff;  /* offset for pam values */
-  int pam_l, pam_h, pam_xx, pam_xm;    /* lowest, highest pam value */
-  int pam_x_set;
-  int pam_ms;          /* use a Mass Spec pam matrix */
-  int maxlen;
-  long zdb_size; /* force database size */
-  int pgm_id;
-  union {
-    struct fastr fa;
-    struct prostr pr;
-  } param_u;
-  int pseudocts;
-  int shuff_node;
-};
-
-/* Result structure - do not remove */
-struct rstruct
-{
-  int score[3];
-  double comp;
-  double H;
-  double escore;
-  int segnum;
-  int seglen;
-};
-
-#ifndef PCOMPLIB
-struct thr_str {
-  int worker;
-  void *status;
-  int max_work_buf;
-  int qframe;
-  struct pstruct *ppst;
-  int qshuffle;
-  unsigned char *aa0;
-  int n0;
-  int nm0;
-  int max_tot;
-};
-
-#include <sys/types.h>
-
-/* this structure passes library sequences to the worker threads
-   and returns scores */
-
-struct buf_str {
-  int n1;
-  int *n1tot_p;
-  unsigned char *aa1b;
-#ifndef USE_FSEEKO
-  long lseek;
-#else
-  off_t lseek;
-#endif
-  struct lmf_str *m_file_p;
-  int cont;
-  int qframe;
-  int frame;
-  int nsfnum;
-  int sfnum[10];
-  char libstr[20];     /* set to MAX_UID */
-  struct rstruct rst;
-  int r_score, qr_score;
-  double r_escore, qr_escore;
-};
-
-struct buf_head {
-  int buf_cnt;
-  int have_results;
-  unsigned char *start;
-  struct buf_str *buf;
-};
-
-#endif
-
-#endif  /* PSTRUCT */
-
-#include "aln_structs.h"