+++ /dev/null
-
-/* $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 */
-};
-
-