Mac binaries

[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
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+/* $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"