--- /dev/null
+/* doinit.c general and function-specific initializations */
+
+/* copyright (c) 1996, 1997, 1998 William R. Pearson and the U. of Virginia */
+
+/* $Name: fa_34_26_5 $ - $Id: doinit.c,v 1.62 2007/01/08 15:38:46 wrp Exp $ */
+
+/* this file performs general initializations of search parameters
+
+ In addition, it calls several functions in init??.c that provide
+ program-specific initializations:
+
+ f_initenv() - called from initenv()
+ f_getopt() - called from initenv() during a getopt() scan
+ f_getarg() - called from initenv() after the getopt() scan
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "defs.h"
+#include "param.h"
+#include "upam.h" /* required for 'U' option change of nascii */
+
+#include "structs.h"
+
+#define XTERNAL
+#include "uascii.h"
+#undef XTERNAL
+
+extern char *s_optstr;
+extern int optind; /* used by getopt() */
+
+#ifdef PCOMPLIB
+#define PARALLEL
+#include "p_mw.h"
+extern char pgmdir[];
+extern char managepgm[];
+extern char workerpgm[];
+extern int max_buf_cnt;
+#define MAX_WORKERS MAXWRKR
+#endif
+
+char prog_name[MAX_FN];
+
+extern void f_initenv(struct mngmsg *, struct pstruct *, unsigned char **);
+extern void f_lastenv(struct mngmsg *, struct pstruct *);
+extern void f_getopt(char, char *, struct mngmsg *, struct pstruct *);
+extern void f_getarg(int, char **, int, struct mngmsg *, struct pstruct *);
+void ann_ascii(int *qascii, char *ann_arr);
+int set_markx(int markx, int val);
+
+int optcnt;
+int max_workers=MAX_WORKERS;
+#ifdef PCOMPLIB
+int worker_1=0;
+int worker_n=0;
+#endif
+extern char *optarg;
+
+/* initenv () initializes the environment */
+void initenv (int argc, char **argv, struct mngmsg *m_msg,
+ struct pstruct *ppst, unsigned char **aa0)
+{
+ char *cptr, ctmp;
+ int copt, itmp;
+
+ /* options for all search functions */
+ char *g_optstr = "ab:BC:d:DE:F:HiIJ:K:l:Lm:M:N:O:QqR:T:v:V:w:W:X:z:Z:";
+ char optstring[MAX_STR];
+
+/* these initializations will be used by all functions */
+
+ /* prog_name[] is only used for error messages */
+ strncpy(prog_name,argv[0],sizeof(prog_name));
+ prog_name[sizeof(prog_name)-1]='\0';
+
+#ifdef PARALLEL
+ if ((cptr = getenv ("MANAGEPGM")) != NULL) strncpy (managepgm, cptr, 120);
+ if ((cptr = getenv ("WORKERPGM")) != NULL) strncpy (workerpgm, cptr, 120);
+ if ((cptr = getenv ("PGMDIR")) != NULL) strncpy (pgmdir, cptr, 120);
+#endif
+
+ m_msg->ltitle[0] = '\0';
+
+ if ((cptr=getenv("FASTLIBS"))!=NULL) {
+ strncpy(m_msg->flstr,cptr,MAX_FN);
+ m_msg->flstr[MAX_FN-1] = '\0';
+ }
+ else m_msg->flstr[0]='\0';
+
+ m_msg->hist.hist_a = NULL;
+ m_msg->outfile[0] = '\0';
+ m_msg->ldnaseq = SEQT_PROT; /* library is protein */
+ m_msg->n1_low = 0;
+ m_msg->n1_high = BIGNUM;
+ m_msg->ql_start = 1; /* start with first query sequence */
+ m_msg->ql_stop = BIGNUM; /* end with the last query sequence */
+
+ m_msg->pamd1 = MAXSQ;
+ m_msg->pamd2 = MAXSQ;
+
+ m_msg->term_code = 0;
+ ppst->tr_type = 0;
+ ppst->debug_lib = 0;
+ m_msg->nshow = 20;
+#if defined(PCOMPLIB)
+ m_msg->nohist = 1;
+ m_msg->mshow = 20;
+#else
+ m_msg->nohist = 0;
+ m_msg->mshow = 50;
+#endif
+ m_msg->ashow = -1;
+ m_msg->nmlen = DEF_NMLEN;
+ m_msg->z_bits = 1;
+ m_msg->mshow_flg = 0;
+ m_msg->aln.llen = 0;
+ m_msg->aln.llcntx = 30;
+ m_msg->aln.llcntx_flg = 0;
+ m_msg->e_cut = 10.0;
+ m_msg->e_low = 0.0;
+ m_msg->e_cut_set = 0;
+ m_msg->revcomp = 0;
+ m_msg->self = 0;
+ m_msg->long_info = 0;
+ m_msg->maxn = 0;
+ m_msg->dupn = SEQDUP;
+ m_msg->dfile[0] = '\0';
+ m_msg->tname[0] = '\0';
+ m_msg->lname[0] = '\0';
+ m_msg->show_code = 0;
+ m_msg->aln.showall = 0;
+ m_msg->markx = 0;
+ m_msg->sq0off = m_msg->sq1off = 1;
+ strncpy(m_msg->sqnam,"aa",4);
+ strncpy(m_msg->sqtype,"protein",10);
+ m_msg->ann_flg = 0;
+ m_msg->ann_arr[0] = '\0';
+ m_msg->aa0a = NULL;
+
+ ppst->zsflag = ppst->zsflag_f = 1;
+ ppst->zs_win = 0;
+
+ ppst->zdb_size = -1;
+ ppst->dnaseq = SEQT_PROT; /* default is protein */
+ ppst->nt_align = 0;
+
+ f_initenv (m_msg, ppst, aa0);
+
+ strncpy (optstring, g_optstr, sizeof (optstring));
+ strncat (optstring, s_optstr, sizeof (optstring));
+
+ while ((copt = getopt (argc, argv, optstring)) != EOF)
+ {
+ if (strchr (g_optstr, copt) != NULL)
+ {
+ switch (copt) { /* switches for all options */
+ case 'a': m_msg->aln.showall = 1; break;
+ case 'b':
+ if (optarg[0] == '$') {
+ m_msg->mshow = -1;
+ m_msg->e_cut = 10000000.0;
+ break;
+ }
+ else sscanf (optarg, "%d", &m_msg->mshow);
+ m_msg->e_cut = 10000000.0;
+ m_msg->e_cut_set = 1;
+ m_msg->mshow_flg = 1;
+ break;
+ case 'B': m_msg->z_bits = 0; break;
+ case 'C': sscanf(optarg,"%d",&m_msg->nmlen);
+ if (m_msg->nmlen > MAX_UID-1) m_msg->nmlen = MAX_UID-1;
+ break;
+ case 'd': sscanf(optarg,"%d",&m_msg->ashow);
+ if (m_msg->ashow > m_msg->mshow) m_msg->mshow=m_msg->ashow;
+ /* m_msg->ashow_flg = 1; (ashow_flg not in structs.h, not used)*/
+ break;
+ case 'D': ppst->debug_lib = 1;
+ break;
+ case 'E':
+ sscanf(optarg,"%lf",&m_msg->e_cut);
+ m_msg->e_cut_set = 1;
+ break;
+ case 'F':
+ sscanf(optarg,"%lg",&m_msg->e_low);
+ m_msg->e_cut_set = 1;
+ break;
+ case 'H':
+#if defined(PCOMPLIB)
+ m_msg->nohist = 0; break;
+#else
+ m_msg->nohist = 1; break;
+#endif
+ case 'i':
+ m_msg->revcomp = 1; break;
+#ifdef PARALLEL
+ case 'I':
+ m_msg->self = 1; break;
+ case 'J':
+ if (optarg[0]==':') {
+ m_msg->ql_start = 0;
+ sscanf(optarg,":%d",&m_msg->ql_stop);
+ m_msg->ql_stop++;
+ }
+ else if (!strchr(optarg,':')) {
+ m_msg->ql_stop = BIGNUM;
+ sscanf(optarg,"%d",&m_msg->ql_start);
+ }
+ else {
+ sscanf(optarg,"%d:%d",&m_msg->ql_start,&m_msg->ql_stop);
+ m_msg->ql_stop++;
+ }
+ break;
+ case 'K':
+ sscanf(optarg,"%d",&max_buf_cnt);
+ break;
+#endif
+ case 'l':
+ strncpy(m_msg->flstr,optarg,MAX_FN);
+ m_msg->flstr[MAX_FN-1]='\0';
+ break;
+ case 'L':
+ m_msg->long_info = 1; break;
+ case 'm':
+ sscanf(optarg,"%d%c",&itmp,&ctmp);
+ if (itmp==9 && ctmp=='c') {
+ m_msg->show_code = SHOW_CODE_ALIGN;
+ }
+ else if (itmp==9 && ctmp=='i') {
+ m_msg->show_code = SHOW_CODE_ID;
+ }
+ if (itmp > 6 && itmp != 10 && itmp != 9) itmp = 0;
+ m_msg->markx = set_markx(m_msg->markx,itmp);
+ break;
+ case 'M':
+ sscanf(optarg,"%d-%d",&m_msg->n1_low,&m_msg->n1_high);
+ if (m_msg->n1_low < 0) {
+ m_msg->n1_high = -m_msg->n1_low;
+ m_msg->n1_low = 0;
+ }
+ if (m_msg->n1_high == 0) m_msg->n1_high = BIGNUM;
+ if (m_msg->n1_low > m_msg->n1_high) {
+ fprintf(stderr," low cutoff %d greater than high %d\n",
+ m_msg->n1_low, m_msg->n1_high);
+ m_msg->n1_low = 0;
+ m_msg->n1_high = BIGNUM;
+ }
+ break;
+ case 'N':
+ sscanf(optarg,"%d",&m_msg->maxn);
+ break;
+ case 'p':
+ m_msg->qdnaseq = SEQT_PROT;
+ ppst->dnaseq = SEQT_PROT;
+ strncpy(m_msg->sqnam,"aa",4);
+ break;
+ case 'O':
+ strncpy(m_msg->outfile,optarg,MAX_FN);
+ m_msg->outfile[MAX_FN-1]='\0';
+ break;
+ case 'q':
+ case 'Q':
+ m_msg->quiet = 1;
+ break;
+ case 'R':
+ strncpy (m_msg->dfile, optarg, MAX_FN);
+ m_msg->dfile[MAX_FN-1]='\0';
+ break;
+ case 'T':
+#ifdef PCOMPLIB
+ if (strchr(optarg,'-') != NULL) {
+ sscanf(optarg,"%d-%d",&worker_1,&worker_n);
+ if (worker_1 > worker_n) {
+ worker_1 = worker_n = 0;
+ }
+ }
+ else
+#endif
+ sscanf (optarg, "%d", &max_workers);
+ if (max_workers < 0) max_workers=1;
+ break;
+ case 'v':
+ sscanf (optarg,"%d",&ppst->zs_win);
+ break;
+ case 'V':
+ strncpy(m_msg->ann_arr+1,optarg,MAX_FN-2);
+ m_msg->ann_arr[0]='\0';
+ m_msg->ann_arr[MAX_FN-2]='\0';
+ m_msg->ann_flg = 1;
+ ann_ascii(qascii, m_msg->ann_arr);
+ break;
+/*
+ case 'V':
+ fprintf(stderr," -V option not currently supported in parallel\n");
+ break;
+*/
+ case 'w':
+ sscanf (optarg,"%d",&m_msg->aln.llen);
+ if (m_msg->aln.llen < 10) m_msg->aln.llen = 10;
+ if (m_msg->aln.llen > 200) m_msg->aln.llen = 200;
+ if (!m_msg->aln.llcntx_flg) m_msg->aln.llcntx = m_msg->aln.llen/2;
+ break;
+ case 'W':
+ sscanf (optarg,"%d",&m_msg->aln.llcntx);
+ m_msg->aln.llcntx_flg = 1;
+ break;
+ case 'X':
+ sscanf (optarg,"%ld %ld",&m_msg->sq0off,&m_msg->sq1off); break;
+ case 'z':
+ sscanf(optarg,"%d",&ppst->zsflag);
+ break;
+ case 'Z':
+ sscanf(optarg,"%ld",&ppst->zdb_size);
+ break;
+ }
+ }
+ else if (strchr (s_optstr, copt))
+ f_getopt (copt, optarg, m_msg, ppst);
+ }
+ optind--;
+
+ f_lastenv (m_msg, ppst);
+
+ if (argc - optind < 3) return;
+ m_msg->tnamesize = sizeof (m_msg->tname);
+ if (argc - optind > 1) strncpy (m_msg->tname, argv[optind + 1],MAX_FN);
+ if (argc - optind > 2) { strncpy(m_msg->lname, argv[optind + 2],MAX_FN); }
+ f_getarg (argc, argv, optind, m_msg, ppst);
+}
+
+int
+ann_scan(unsigned char *aa0, int n0, struct mngmsg *m_msg, int seqtype)
+{
+ unsigned char *aa0p, *aa0d, *aa0ad;
+ int n_n0;
+
+ /* count how many "real" residues */
+
+ if (seqtype==SEQT_UNK) {
+ for (n_n0=0, aa0p = aa0; aa0p < aa0+n0; aa0p++) {
+ if (*aa0p > '@' || *aa0p == ESS ) n_n0++;
+ }
+ }
+ else {
+ for (n_n0=0, aa0p = aa0; aa0p < aa0+n0; aa0p++) {
+ if (*aa0p < NANN ) n_n0++;
+ }
+ }
+
+ aa0d = aa0;
+ /* n_n0 has the real sequence length */
+ if ((m_msg->aa0a = calloc(n_n0+2, sizeof(char)))==NULL) {
+ fprintf(stderr," cannot allocate annotation sequence: %d\n",n_n0);
+ m_msg->ann_flg = 0;
+ if (seqtype==SEQT_UNK) {
+ for (aa0p = aa0; aa0p < aa0+n0; aa0p++) {
+ if (*aa0p > '@' || *aa0p == ESS) {*aa0d++ = *aa0p;}
+ }
+ }
+ else {
+ for (aa0p = aa0; aa0p < aa0+n0; aa0p++) {
+ if (*aa0p < NANN) {*aa0d++ = *aa0p;}
+ }
+ }
+ *aa0d = '\0';
+ return n_n0;
+ }
+
+ aa0ad = m_msg->aa0a;
+ if (seqtype==SEQT_UNK) {
+ for (aa0p = aa0; aa0p<aa0+n0; aa0p++) {
+ if (*aa0p > '@' || *aa0p == ESS) {*aa0d++ = *aa0p; *aa0ad++='\0';}
+ else if (aa0ad > m_msg->aa0a) { aa0ad[-1] = *aa0p - NANN;}
+ }
+ }
+ else {
+ for (aa0p = aa0; aa0p<aa0+n0; aa0p++) {
+ if (*aa0p < NANN) {*aa0d++ = *aa0p; *aa0ad++='\0';}
+ else if (aa0ad > m_msg->aa0a) { aa0ad[-1] = *aa0p - NANN;}
+ }
+ }
+ *aa0ad = *aa0d = '\0';
+ return n_n0;
+}
+
+void
+ann_ascii(int *qascii, char *ann_arr)
+{
+ char *ann_p;
+ int ann_ix = NANN+1;
+
+ ann_arr[0] = ' ';
+ if (strchr(ann_arr+1,'*')) {qascii['*'] = NA;}
+
+ for (ann_p = ann_arr+1; *ann_p; ann_p++) {
+ if (qascii[*ann_p] == NA) { qascii[*ann_p] = ann_ix++;}
+ }
+}
+
+int
+set_markx(int markx, int val) {
+
+ if (val < 3) {
+ return markx | (MX_ATYPE & val);
+ }
+ else if (val == 3) {
+ markx |= (MX_ATYPE + MX_ASEP);
+ }
+ else if (val == 4) {
+ markx |= (MX_ATYPE + MX_AMAP);
+ }
+ else if (val == 5) {
+ markx |= MX_AMAP;
+ }
+ else if (val == 6) {
+ markx |= (MX_HTML) ;
+ }
+ else if (val == 9) {
+ markx |= MX_M9SUMM;
+ }
+ else if (val == 10) {
+ markx |= MX_M10FORM;
+ }
+
+ return markx;
+}
git://source.jalview.org / jabaws.git / blobdiff