Mac binaries

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

diff --git a/website/archive/binaries/mac/src/fasta34/structs.h b/website/archive/binaries/mac/src/fasta34/structs.h
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+
+/* $Name: fa_34_26_5 $ - $Id: structs.h,v 1.36 2006/06/22 02:35:05 wrp Exp $ */
+
+#include "aln_structs.h"
+
+struct hist_str {
+  int histflg;
+  int *hist_a;
+  int histint, min_hist, max_hist, maxh;
+  long entries;
+  int z_calls;
+  char stat_info[MAX_STR];
+};
+
+struct db_str {
+  long entries;
+  unsigned long length;
+  int carry;
+};
+
+struct mngmsg          /* Message from host to manager */
+{
+  int n0;              /* Integer returned by hgetseq */
+  int nm0;             /* number of segments */
+  int nmoff;           /* length of fastf segment */
+  unsigned char *aa0a; /* annotation array */
+  char ann_arr[MAX_FN];        /* annotation characters */
+  int ann_flg;         /* have annotation array, characters */
+  char tname[MAX_FN];  /* Query sequence name */
+  int tnamesize;       /* Query name size */
+  int qsfnum[10];
+  int nqsfnum;
+  int qsfnum_n[10];
+  int nqsfnum_n;
+  char lname[MAX_FN];  /* Library  file  name */
+  char *lbnames[MAX_LF]; /* list of library files */
+  struct lmf_str *lb_mfd[MAX_LF];      /* list of opened file pointers */
+
+  int max_tot;         /* function defined total sequence area */
+  int maxn;            /* longest library sequence chunk */
+  int dupn;            /* overlap to use when segmenting sequence (p_comp) */
+  int qoff;            /* overlap when segmenting long query sequence */
+  int loff;            /* overlap when segmenting long library sequences */
+  int maxt3;           /* overlap for tranlated sequences */
+  int qdnaseq;         /* query is protein (0)/dna (1) */
+  int ldnaseq;         /* library is protein (0)/dna (1) */
+  int qframe;          /* number of possible query frames */
+  int nframe;          /* frame for TFASTA */
+  int nitt1;           /* nframe-1 */
+  int thr_fact;                /* fudge factor for threads */
+  int s_int;           /* sampling interval for statistics */
+  int ql_start;                /* starting query sequence */
+  int ql_stop;         /* ending query sequence */
+  int nln;             /* number of library names */
+  int pbuf_siz;                /* buffer size for sequences send in p2_complib */
+  char qtitle[MAX_FN]; /* query title */
+  char ltitle[MAX_FN]; /* library title */
+  char flstr[MAX_FN];  /* FASTLIBS string */
+  char outfile[MAX_FN];
+  char label [MAXLN];  /* Output label */
+  char f_id0[4];       /* function id for markx==10 */
+  char f_id1[4];       /* function id for markx==10 */
+  char sqnam[4];       /* "aa" or "nt" */ 
+  char sqtype[10];     /* "DNA" or "protein" */
+  int long_info;       /* long description flag*/
+  long sq0off, sq1off; /* offset into aa0, aa1 */
+  int markx;           /* alignment display type */
+  int seqnm;           /* query sequence number */
+  int nbr_seq;         /* number of library sequences */
+  int term_code;       /* add termination codes to proteins if absent */
+  int n1_high;         /* upper limit on sequence length */
+  int n1_low;          /* lower limit on sequence length */
+  double e_cut;                /* e_value for display */
+  double e_low;                /* e_value for display */
+  int e_cut_set;       /* e_value deliberately set */
+  int pamd1;           /* 1st dimension of pam matrix */
+  int pamd2;           /* 2nd dimension of pam matrix */
+  int revcomp;         /* flag to do reverse complement */
+  int quiet;           /* quiet option */
+  int nrelv;           /* number of interesting scores */
+  int srelv;           /* number of scores to show in showbest */
+  int arelv;           /* number of scores to show at alignment */
+  int z_bits;          /* z_bits==1: show bit score, ==0 show z-score */
+  char alab[3][24];    /* labels for alignment scores */
+  int nohist;          /* no histogram option */
+  int nshow;
+  int mshow;           /* number of scores to show */
+  int mshow_flg;
+  int ashow;           /* number of alignments to show */
+  int nmlen;           /* length of name label */
+  int show_code;       /* show alignment code in -m 9;  ==1 => identity only, ==2 alignment code*/
+  int self;            /* self comparison */
+  int thold;           /* threshold */
+  int last_calc_flg;   /* needs a last calculation stage */
+  int qshuffle;        /* shuffle the query and do additional comparisons */
+  int shuff_max;       /* number of shuffles to perform */
+  int shuff_node;      /* number of shuffles/worker node */
+  int shuff_wid;
+  int stages;          /* number of stages */
+  double Lambda, K, H; /* Karlin-Altschul parameters */
+  int escore_flg;      /* use escore calculated by do_work() */
+  struct hist_str hist;
+  struct db_str db;
+  void *pstat_void;
+  struct a_struct aln; /* has llen, llnctx, llnctx_flg, showall */
+  struct a_res_str a_res; /* has individual alignment coordinates */
+  char dfile [MAX_FN]; /* file for dumping scores to */
+};
+
+