nmgetlib.c

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

/*	if (*lcont==0 && (long)(seqp-seq)!=lm_fd->gcg_len)
	printf("%s read %d of %d\n",libstr,(int)(seqp-seq),lm_fd->gcg_len);
	*/
return (int)(seqp-seq);
}

void
eranlib(char *str,
	int cnt,
	fseek_t seek,
	char *libstr,
	struct lmf_str *lm_fd)
{
  char *bp;
  char id[14];  /* Holds Identifier */

  FSEEK(lm_fd->libf, seek, 0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag) getc(lm_fd->libf);

  sscanf(&lm_fd->lline[5],"%s",id);
  sprintf(str,"%-12.12s ",id);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag) getc(lm_fd->libf);

  while (lm_fd->lline[0]!='D' || lm_fd->lline[1]!='E') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  strncpy(str+12,&lm_fd->lline[5],cnt-11);
  str[cnt-11]='\0';
  if ((bp = strchr(str,'\r'))!=NULL) *bp='\0';
  if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';

  FSEEK(lm_fd->libf,seek,0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag) getc(lm_fd->libf);
}

int
igetlib(unsigned char *seq, int maxs,
	char *libstr,
	int n_libstr,
	fseek_t *libpos,
	int *lcont,
	struct lmf_str *lm_fd,
	long *l_off)
{
	register unsigned char *cp, *seqp;
	register int *ap;
	unsigned char *seqm, *seqm1;
	char *bp;

	*l_off = 1;

	seqp = seq;
	seqm = &seq[maxs-9];
	seqm1 = seqm-1;

	ap = lm_fd->sascii;

	if (*lcont==0) {
		while (lm_fd->lline[0]!=';') {
			lm_fd->lpos = FTELL(lm_fd->libf);
			if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
			}
		*libpos = lm_fd->lpos;
		while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
		strncpy(libstr,lm_fd->lline+1,12);
		libstr[12]='\0';
		if((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
		}

	lm_fd->lline[0]='\0';
	while (seqp<seqm1 && fgets((char *)seqp,(size_t)(seqm-seqp),lm_fd->libf)!=NULL) {
		if (*seqp=='>') goto new;
		if (*seqp==';') {
			if (strchr((char *)seqp,'\n')==NULL) goto cont;
			continue;
			}
		for (cp=seqp; seqp<seqm1; ) {
			if ((*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA &&
		            (*seqp++=ap[*cp++])<NA &&
		            (*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA &&
			    (*seqp++=ap[*cp++])<NA) continue;
			    if (*(--seqp)>NA) break;
			    }
		if (*seqp==ES) goto done;
		lm_fd->lpos = FTELL(lm_fd->libf);
		}
	goto done;
new:	strncpy(lm_fd->lline,(char *)seqp,MAX_STR);
	lm_fd->lline[MAX_STR-1]='\0';
	if (strchr((char *)seqp,'\n')==NULL)
	    fgets(lm_fd->lline,MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
	goto done;

cont:
	fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
	seqm1 = seqp;

done:	if (seqp>=seqm1) {
		(*lcont)++;
		}
	else {
	*lcont=0;
		}


	*seqp = EOSEQ;
	/*	if ((int)(seqp-seq)==0) return 1; */
	return (int)(seqp-seq);
	}

void
iranlib(char *str,
	int cnt,
	fseek_t seek,
	char *libstr,
	struct lmf_str *lm_fd)
{
	char *bp;
	char tline[MAX_FN];

	FSEEK(lm_fd->libf, seek, 0);
	fgets(lm_fd->lline,MAX_STR,lm_fd->libf);

	if (lm_fd->lline[0]=='>' || lm_fd->lline[0]==';') {
		strncpy(tline,lm_fd->lline+1,sizeof(tline));
		tline[sizeof(tline)-1]='\0';
		if ((bp = strchr(tline,'\n'))!=NULL) *bp='\0';
		}
	else {
		tline[0]='\0';
		}

	while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
	if ((bp=strchr(lm_fd->lline,'\n'))!=NULL) *bp=0;
	if ((bp=strchr(lm_fd->lline,' '))!=NULL) *bp=0;
	strncpy(str,lm_fd->lline,cnt);
	str[cnt-1]='\0';
	strncat(str,"  ",cnt-strlen(str)-1);
	strncat(str,tline,cnt-strlen(str)-1);
	
	FSEEK(lm_fd->libf,seek,0);
	fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
	}

int
vgetlib(unsigned char *seq, int maxs,
	char *libstr,
	int n_libstr,
	fseek_t *libpos,
	int *lcont,
	struct lmf_str *lm_fd,
	long *l_off)
{
  int i, ich;
  register unsigned char *cp, *seqp;
  register int *ap;
  unsigned char *seqm, *seqm1;
  char *bp, *tp;

  *l_off = 1;

  seqp = seq;
  seqm = &seq[maxs-9];
  seqm1 = seqm-1;

  ap = lm_fd->sascii;

  if (*lcont==0) {
    while (lm_fd->lline[0]!='>' && lm_fd->lline[0]!=';') {
      lm_fd->lpos = FTELL(lm_fd->libf);
      if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
      if (lm_fd->lfflag) getc(lm_fd->libf);
    }

#ifdef SUPERFAMNUM
    if ((bp=strchr(&lm_fd->lline[1],' ')) &&
	 (bp=strchr(bp+1,SFCHAR))) {
      i=0;
      if ((tp = strtok(bp+1," \t\n"))!=NULL) sfnum[i++] = atoi(tp);
      while ((tp = strtok(NULL," \t")) != NULL) {
	sfnum[i++] = atoi(tp);
	if (i>=10) break;
      }
      sfnum[nsfnum=i]= 0;
      if (nsfnum>1) sf_sort(sfnum,nsfnum);
      else {
	if (nsfnum < 1) fprintf(stderr," found | but no sfnum: %s\n",libstr);
      }
    }
    else sfnum[0]=nsfnum=0;
#endif

    if ((bp=strchr(lm_fd->lline,'\n'))!=NULL) *bp='\0';
    strncpy(libstr,&lm_fd->lline[4],12);
    libstr[12]='\0';
    if ((bp=strchr(libstr,' '))!=NULL) *bp='\0';
    if ((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
    
    fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
    if (lm_fd->lfflag) getc(lm_fd->libf);

    if (n_libstr > 21) {
      strcat(libstr," ");
      strncat(libstr,lm_fd->lline,n_libstr-1-strlen(libstr));
      if ((bp=strchr(libstr,'\n'))!=NULL) *bp='\0';
      libstr[n_libstr-1]='\0';
    }
    *libpos = lm_fd->lpos;
  }

  lm_fd->lline[0]='\0';
  while (seqp<seqm1 && fgets((char *)seqp,(size_t)(seqm-seqp),lm_fd->libf)!=NULL) {
    if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
    if (*seqp=='>') goto new;
    if (*seqp==';') {
      if (strchr((char *)seqp,'\n')==NULL) goto cont;
      continue;
    }
    for (cp=seqp; seqp<seqm1; ) {
      if ((*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA &&
	  (*seqp++=ap[*cp++])<NA) continue;
      if (*(--seqp)>NA) break;
    }
    if (*seqp==ES) goto done;
    lm_fd->lpos = FTELL(lm_fd->libf);
  }
  goto done;
new:
  strncpy(lm_fd->lline,(char *)seqp,MAX_STR);
  lm_fd->lline[MAX_STR-1]='\0';
  if (strchr((char *)seqp,'\n')==NULL) {
    fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
    if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
  }
  goto done;

cont:
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag && (ich=getc(lm_fd->libf))!=LFCHAR) ungetc(ich,lm_fd->libf);
  seqm1 = seqp;

done:
  if (seqp>=seqm1) {
    (*lcont)++;
  }
  else {
    *lcont=0;
  }

  *seqp = EOSEQ;
  /*   if ((int)(seqp-seq)==0) return 1;*/
  return (int)(seqp-seq);
}

void
vranlib(char *str,
	int cnt,
	fseek_t seek,
	char *libstr,
	struct lmf_str *lm_fd)
{
  char *bp, *llp;

  FSEEK(lm_fd->libf, seek, 0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag) getc(lm_fd->libf);

  if (lm_fd->lline[0]=='>'&&(lm_fd->lline[3]==';'||
			     lm_fd->lline[3]=='>')	/* GCG ascii */
      ) {
    strncpy(str,&lm_fd->lline[4],cnt-1);
    str[cnt-1]='\0';

    if (lm_fd->lline[3]=='>' && (bp = strchr(str,' '))!=NULL) *bp='\0';

    if ((bp = strchr(str,':'))!=NULL) *bp='\0';
    if ((bp=strchr(str,'\r'))!=NULL) *bp='\0';
    else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
    else str[cnt-1]='\0';

    fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
    if (lm_fd->lfflag) getc(lm_fd->libf);

    /* skip over redundant stuff */
    for (llp=lm_fd->lline,bp=str; *llp==*bp; llp++,bp++);
    if ((int)(llp-lm_fd->lline)<5) llp = lm_fd->lline;

    if ((bp=strchr(llp,'\r'))!=NULL) *bp=' ';
    if ((bp=strchr(llp,'\n'))!=NULL) *bp='\0';
    strncat(str," ",(size_t)1);
    strncat(str,llp,(size_t)cnt-strlen(str)-1);
  }
  else {
    str[0]='\0';
  }

  FSEEK(lm_fd->libf,seek,0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
  if (lm_fd->lfflag) getc(lm_fd->libf);
}

static int gcg_bton[4]={2,4,1,3};

int
gcg_getlib(unsigned char *seq, int maxs,
	   char *libstr,
	   int n_libstr,
	   fseek_t *libpos,
	   int *lcont,
	   struct lmf_str *lm_fd,
	   long *l_off)
{
  char dummy[20];
  char gcg_date[10];
  register unsigned char *cp, *seqp, stmp;
  register int *ap;
  char gcg_type[10];
  unsigned char *seqm, *seqm1;
  long r_block, b_block;
  char *bp;

  *l_off = 1;

  seqp = seq;
  seqm = &seq[maxs-9];
  seqm1 = seqm-1;

  ap = lm_fd->sascii;

  if (*lcont==0) {
    while (lm_fd->lline[0]!='>' && lm_fd->lline[0]!=';') {
      lm_fd->lpos = FTELL(lm_fd->libf);
      if (fgets(lm_fd->lline,MAX_STR,lm_fd->libf)==NULL) return (-1);
    }
    sscanf(&lm_fd->lline[4],"%s %s %s %s %ld",
	   libstr,gcg_date,gcg_type,dummy,&(lm_fd->gcg_len));

    lm_fd->gcg_binary = (gcg_type[0]=='2');

    fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
    while (strchr((char *)lm_fd->lline,'\n')==NULL) {
      if (strlen(lm_fd->lline)<MAX_STR/2) 
	fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
      else 
      fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf);
    }
    lm_fd->lline[MAX_STR-1]='\0';
    if (n_libstr <= 21) {
      libstr[12]='\0';
    }
    else {
      strncat(libstr," ",1);
      strncat(libstr,lm_fd->lline,n_libstr-1-strlen(libstr));
      if ((bp = strchr(libstr,'\n'))!=NULL) *bp='\0';
      libstr[n_libstr-1]='\0';
    }
    *libpos = lm_fd->lpos;
  }

  lm_fd->lline[0]='\0';

  r_block = b_block = min((size_t)(seqm-seqp),lm_fd->gcg_len);
  if (lm_fd->gcg_binary) { r_block = (r_block+3)/4; }

  fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf);
  if (!lm_fd->gcg_binary) 
    for (cp=seqp; seqp<seq+r_block; ) *seqp++ = ap[*cp++];
  else if (lm_fd->gcg_binary) {
    seqp = seq + r_block;
    cp = seq + 4*r_block;
    while (seqp > seq) {
      stmp = *--seqp;
      *--cp = gcg_bton[stmp&3];
      *--cp = gcg_bton[(stmp >>= 2)&3];
      *--cp = gcg_bton[(stmp >>= 2)&3];
      *--cp = gcg_bton[(stmp >>= 2)&3];
    }
  }
  if (4 * r_block >= lm_fd->gcg_len) {
    fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
    *lcont = 0;
  }
  else {
    if (lm_fd->gcg_binary) b_block = 4*r_block;
    lm_fd->gcg_len -= b_block;
    (*lcont)++;
  }

  seq[b_block] = EOSEQ;
  /*   if (b_block==0) return 1; else */
  return b_block;
}

void
gcg_ranlib(char *str,
	   int cnt,
	   fseek_t seek,
	   char *libstr,
	   struct lmf_str *lm_fd)
{
  char *bp, *bp1, *llp;

  FSEEK(lm_fd->libf, seek, 0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);

  if (lm_fd->lline[0]=='>'&&(lm_fd->lline[3]==';'||lm_fd->lline[3]=='>')) {
    strncpy(str,&lm_fd->lline[4],cnt-1);
    str[cnt-1]='\0';
    if ((bp = strchr(str,' '))!=NULL) *bp='\0';
    else if ((bp=strchr(str,'\r'))!=NULL) *bp='\0';
    else if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
    else str[cnt-1]='\0';

    fgets(lm_fd->lline,MAX_STR,lm_fd->libf);

    /* check beginning of line it is a duplicate */
    for (llp=lm_fd->lline,bp=str; *llp == *bp; llp++,bp++);
    if ((int)(llp-lm_fd->lline)<5) llp = lm_fd->lline;

    /* here we would like to skip over some species stuff */
	/*
    if ((bp1 = strchr(llp,';'))!=NULL && (int)(bp1-llp)<50) {
      if ((bp2 = strchr(bp1+1,';'))!=NULL && (int)(bp2-bp1)<50) {
	*(bp2+1)='\0'; bp1 = bp2+2;
      }
      else {bp1=llp;}
    }
    else if ((bp1=strchr(llp,'.'))!=NULL && *(bp1+1)==' ') {
      *(bp1+1) = '\0'; bp1 += 2;}
    else bp1 = llp;
    */
    
    bp1 = llp;
    if ((bp=strchr(bp1,'\r'))!=NULL) *bp='\0';
    if ((bp=strchr(bp1,'\n'))!=NULL) *bp='\0';
    strncat(str," ",(size_t)1);
    strncat(str,bp1,(size_t)cnt-strlen(str));
    if (bp1!=llp) strncat(str,llp,(size_t)cnt-strlen(str));
  }
  else {
    str[0]='\0';
  }

  FSEEK(lm_fd->libf,seek,0);
  fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
}

void
sf_sort(s,n)
     int *s, n;
{
  int gap, i, j;
  int itmp;

  if (n == 1) return;
	
  for (i=0; i<n-1; i++)
    if (s[i]>s[i+1]) goto l2;
  return;

l2:
  for (gap=n/2; gap>0; gap/=2)
    for (i=gap; i<n; i++)
      for (j=i-gap; j>=0; j -= gap) {
	if (s[j] <= s[j+gap]) break;
	itmp = s[j];
	s[j]=s[j+gap];
	s[j+gap]=itmp;
      }
}

struct sel_acc_str {
  int curr_entry;
  int max_entry;
  char fmt_term;
  char *acc_buff;
  char **acc_list;
  int *gi_list;
  int *acc_hash;
  int *acc_hash_link;
  int hash_mask;
};

/* allocate space, read the accessions from an already open file of
   accessions */

void *sel_acc_libstr_init(FILE *libf, int *acc_off, char fmt_term) {
  struct sel_acc_str *sel_acc_ptr;
  char acc_line[MAX_STR];
  char *bp, *bp1;
  char *acc_buff;
  char *acc_buff_max;	/* end of buffer */
  char *new_buff;	/* reallocated buffer size */
  char *acc_buff_p;
  char **acc_list;
  int acc_cnt, i;
  int new_buff_siz;
  int abuff_siz;		/* allocated buffer size */
  int buff_siz;		/* fread buff_siz */

  if ((sel_acc_ptr = (struct sel_acc_str *)calloc(1,sizeof(struct sel_acc_str)))==NULL) {
    fprintf(stderr, "Cannot allocate struct sel_acc_str\n");
    return NULL;
  }

  /*
  if (fmt && *fmt != '\0') {
    sel_acc_ptr->fmt = (char *)calloc(strlen(fmt)+1,sizeof(char));
    strncpy(sel_acc_ptr->fmt, fmt, strlen(fmt)+1);
    sel_acc_ptr->fmt[strlen(fmt)] = '\0';