/*  $Id: dropfx.c 1280 2014-08-21 00:47:55Z wrp $ */

/* copyright (c) 1998, 1999, 2014 by William R. Pearson and The Rector &
   Vistors of the University of Virginia */

/* Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing,
   software distributed under this License is distributed on an "AS
   IS" BASIS, WITHOUT WRRANTIES OR CONDITIONS OF ANY KIND, either
   express or implied.  See the License for the specific language
   governing permissions and limitations under the License. 
*/

/* implements the fastx algorithm, see:

   W. R. Pearson, T. Wood, Z. Zhang, A W. Miller (1997) "Comparison of
   DNA sequences with protein sequences" Genomics 46:24-36

   see dropnfa.c for better variable descriptions and comments
*/
   
/* 17-Sept-2008 - modified for multiple non-overlapping alignments */

/* 18-Sept-2006 - remove global variables used for alignment */

/* 22-June-2006 - correct incorrect alignment coordinates generated
   after pro_dna() on projected DNA region.  
*/

/* 9-May-2003 -> 3.46 changed lx_band to use projected protein
   boundary end.  this fixes some addressing issues on MacOSX, and
   speeds up alignment on very long proteins
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>

#include "defs.h"
#include "param.h"
#define XTERNAL
#include "upam.h"

/* this must be consistent with upam.h */
#define MAXHASH 32
#define NMAP MAXHASH+1

/* globals for fasta */
#define MAXWINDOW 64

#ifndef MAXSAV
#define MAXSAV 10
#endif

#ifndef ALLOCN0
static char *verstr="3.8 June 2014";
#else
static char *verstr="3.8an0 June 2014";
#endif

struct dstruct		/* diagonal structure for saving current run */
{			
   int     score;	/* hash score of current match */
   int     start;	/* start of current match */
   int     stop;	/* end of current match */
   struct savestr *dmax;   /* location in vmax[] where best score data saved */
};

struct savestr
{
   int     score;		/* pam score with segment optimization */
   int     score0;		/* pam score of best single segment */
   int     gscore;		/* score from global match */
   int     dp;			/* diagonal of match */
   int     start;		/* start of match in lib seq */
   int     stop;		/* end of match in lib seq */
};

struct swstr { int H, E;};
/* struct bdstr { int CC, DD, CP, DP;}; */

#define SGW1 100
#define SGW2 300
struct smgl_str {
  int C[SGW1+1][SGW2+1];
  int st[SGW1+1][SGW2+1];
  int D[SGW2+7], I[SGW2+1];
};

struct update_code_str {
  int p_op_idx;
  int p_op_cnt;
  int show_code;
  int cigar_order;
  int show_ext;
  char *op_map;
};

#ifndef TFAST
static char *ori_code = "-x/=\\+*";	/* FASTX */
static char *cigar_code = "DXFMRI*";
#else
static char *ori_code = "+x/=\\-*";	/* TFASTX */
static char *cigar_code = "IXFMRD*";
#endif

static struct update_code_str *
init_update_data(int show_code);

static void
sprintf_code(char *tmp_str, struct update_code_str *, int op_idx, int op_cnt);

static void 
update_code(char *al_str, int al_str_max, 
	    struct update_code_str *update_data, int op, 
	    int sim_code, unsigned char sp0, unsigned char sp1);

static void
close_update_data(char *al_str, int al_str_max,
		  struct update_code_str *update_data);

void kpsort (struct savestr **v, int n);
extern void *init_stack(int, int);
extern void push_stack(void *, void *);
extern void *pop_stack(void *);
extern void *free_stack(void *);

struct sx_s {int C1, C2, C3, I1, I2, I3, flag; };

struct f_struct {
  struct dstruct *diag;
  int ndo;
  int noff;
  int hmask;			/* hash constants */
  int *pamh1;			/* pam based array */
  int *pamh2;			/* pam based kfact array */
  int *link, *harr;		/* hash arrays */
  int kshft;			/* shift width */
  int nsav;		/* number of saved runs, worst saved run */
#ifndef TFAST
  unsigned char *aa0x;		/* contains translated codons 111222333*/
  unsigned char *aa0y;		/* contains translated codons 123123123*/
#else
  unsigned char *aa1x;		/* contains translated codons 111222333 */
  unsigned char *aa1y;		/* contains translated codons 123123123 */
  int have_yaa;			/* flag if translation is done */
#endif
  struct sx_s *cur;
  int cur_sp_size;
  int *waa0;
  int *waa1;
  struct smgl_str smgl_s;
  int *res;
  int max_res;
};

#define DROP_INTERN
#include "drop_func.h"

int shscore(unsigned char *aa0, int n0, int **pam2);
int saatran(const unsigned char *ntseq, unsigned char *aaseq, int maxs, int frame);
extern int ELK_to_s(double E_join, int n0, int n1, double Lambda, double K, double H);

int savemax (struct dstruct *dptr, int dpos, 
	     struct savestr *vmax, struct savestr **lowmax);

int spam (const unsigned char *aa0, const unsigned char *aa1, 
	  struct savestr *dmax, int **pam2,
	  struct f_struct *f_str);
int sconn (struct savestr **v, int n,int cgap, int pgap, struct f_struct *f_str);
int lx_band(const unsigned char *prot_seq, int len_prot,
	    const unsigned char *dna_prot_seq, int len_dna_prot,
	    int **pam_matrix, int gopen, int gext,
	    int gshift, int start_diag, int width, struct f_struct *f_str);

void fx_walign (const unsigned char *aa0, int n0,
		const unsigned char *xaa, int n1, unsigned char *yaa,
		int frame, int max_res,
		struct pstruct *ppst, 
		struct f_struct *f_str, 
		struct a_res_str *a_res,
		int score_thresh);

struct a_res_str *
merge_ares_chains(struct a_res_str *cur_ares, 
		  struct a_res_str *tmpl_ares,
		  int score_ix, const char *msg);

extern void w_abort (char *p, char *p1);

/* initialize for fasta */

void
init_work (unsigned char *aa0, int n0, 
	   struct pstruct *ppst,
	   struct f_struct **f_arg)
{
   int mhv, phv;
   int hmax;
   int i0, hv;
   int pamfact;
   int btemp;
   struct f_struct *f_str;
   int ktup;		/* word size examined */
   int fact;		/* factor used to scale ktup match value */
   int kt1;		/* ktup-1 */
   int lkt;		/* last ktup - initiall kt1, but can be increased
			   for hsq >= NMAP */

   int maxn0;
   int *pwaa;
   int i, j, q;
   struct swstr *ss, *r_ss;
   int *waa;
   int *res;
   int nsq, ip, *hsq;
#ifndef TFAST
   int last_n0, itemp;
   unsigned char *fd, *fs, *aa0x, *aa0y, *aa0s;
   int n0x, n0x3;
#endif

  if (ppst->ext_sq_set) {
    nsq = ppst->nsqx; ip = 1;
    hsq = ppst->hsqx;
  }
  else {
    nsq = ppst->nsqx; ip = 0;
    hsq = ppst->hsq;
  }

   f_str = (struct f_struct *)calloc(1,sizeof(struct f_struct));

   if (!ppst->param_u.fa.use_E_thresholds) {
     btemp = 2 * ppst->param_u.fa.bestoff / 3 +
       n0 / ppst->param_u.fa.bestscale +
       ppst->param_u.fa.bkfact *
       (ppst->param_u.fa.bktup - ppst->param_u.fa.ktup);
     btemp = min (btemp, ppst->param_u.fa.bestmax);
     if (btemp > 3 * n0) btemp = 3 * shscore(aa0,n0,ppst->pam2[0]) / 5;

     ppst->param_u.fa.cgap = btemp + ppst->param_u.fa.bestoff / 3;
     if (ppst->param_u.fa.optcut_set != 1) {
#ifndef TFAST
       ppst->param_u.fa.optcut = (btemp*5)/4;
#else
       ppst->param_u.fa.optcut = (btemp*4)/3;
#endif
     }
   }

#ifdef OLD_FASTA_GAP
   ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval;
#else
   ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval;
#endif

   ppst->param_u.fa.cgap = max(ppst->param_u.fa.cgap, -ppst->param_u.fa.pgap);

   pamfact = ppst->param_u.fa.pamfact;
   ktup = ppst->param_u.fa.ktup;
   fact = ppst->param_u.fa.scfact * ktup;

   if (pamfact == -1)
      pamfact = 0;
   else if (pamfact == -2)
      pamfact = 1;

   for (i0 = 1, mhv = -1; i0 <=ppst->nsq; i0++)
      if (hsq[i0] < NMAP && hsq[i0] > mhv) mhv = hsq[i0];

   if (mhv <= 0) {
      fprintf (stderr, " maximum hsq <=0 %d\n", mhv);
      exit (1);
   }

   for (f_str->kshft = 0; mhv > 0; mhv /= 2)
      f_str->kshft++;

/*      kshft = 2;	*/
   kt1 = ktup - 1;
   hv = 1;
   for (i0 = 0; i0 < ktup; i0++) {
     hv = hv << f_str->kshft;
   }
   hmax = hv;
   f_str->hmask = (hmax >> f_str->kshft) - 1;

   if ((f_str->harr = (int *) calloc (hmax, sizeof (int))) == NULL) {
     fprintf (stderr, " cannot allocate hash array\n");
     exit (1);
   }
   if ((f_str->pamh1 = (int *) calloc (ppst->nsq+1, sizeof (int))) == NULL) {
     fprintf (stderr, " cannot allocate pamh1 array\n");
     exit (1);
   }
   if ((f_str->pamh2 = (int *) calloc (hmax, sizeof (int))) == NULL) {
     fprintf (stderr, " cannot allocate pamh2 array\n");
     exit (1);
   }
   if ((f_str->link = (int *) calloc (n0, sizeof (int))) == NULL) {
     fprintf (stderr, " cannot allocate hash link array");
     exit (1);
   }

#ifdef TFAST
   if ((f_str->aa1x =(unsigned char *)calloc((size_t)ppst->maxlen+2,
					     sizeof(unsigned char)))
       == NULL) {
     fprintf (stderr, "cannot allocate aa1x array %d\n", ppst->maxlen+2);
     exit (1);
   }
   f_str->aa1x++;

   if ((f_str->aa1y =(unsigned char *)calloc((size_t)ppst->maxlen+2,
					     sizeof(unsigned char)))
       == NULL) {
     fprintf (stderr, "cannot allocate aa1y array %d\n", ppst->maxlen+2);
     exit (1);
   }
   f_str->aa1y++;
#else	/* FASTX */
   maxn0 = n0 + 2;
   if ((aa0x =(unsigned char *)calloc((size_t)maxn0,sizeof(unsigned char)))
       == NULL) {
     fprintf (stderr, "cannot allocate aa0x array %d\n", maxn0);
     exit (1);
   }
   aa0x++;
   f_str->aa0x = aa0x;

   if ((aa0y =(unsigned char *)calloc((size_t)maxn0,sizeof(unsigned char)))
       == NULL) {
     fprintf (stderr, "cannot allocate aa0y array %d\n", maxn0);
     exit (1);
   }
   aa0y++;
   f_str->aa0y = aa0y;

   last_n0 = 0;
   for (itemp=0; itemp<3; itemp++) {
     n0x = saatran(aa0,&aa0x[last_n0],n0,itemp);

     /*
       for (i=0; i<n0x; i++) {
       fprintf(stderr,"%c",aa[aa0x[last_n0+i]]);
       if ((i%60)==59) fprintf(stderr,"\n");
       }
       fprintf(stderr,"\n");
     */
     last_n0 += n0x+1;
   }
   /*
        fprintf(stderr,"\n");
   */
   for (itemp=0, fs=aa0x; itemp <3; itemp++,fs++) {
     for (fd = &aa0y[itemp]; *fs!=EOSEQ; fd += 3, fs++) *fd = *fs;
     *fd=EOSEQ;
   }

   /* now switch aa0 and aa0x for hashing functions */
   /* this seems dangerous in threaded code, but only the pointer is changed,
      not the data itself */

   fs = aa0;
   aa0 = aa0x;
   aa0x = fs;
					 
#endif

   for (i0 = 0; i0 < hmax; i0++)
      f_str->harr[i0] = -1;
   for (i0 = 0; i0 < n0; i0++)
      f_str->link[i0] = -1;

   /* encode the aa0 array */

   phv = hv = 0;
   lkt = kt1;
   for (i0 = 0; i0 < min(lkt,n0); i0++) {
     if (hsq[aa0[i0]] >= NMAP) {hv=phv=0; lkt=i0+ktup; continue;}
     hv = (hv << f_str->kshft) + hsq[aa0[i0]];
     phv += ppst->pam2[ip][aa0[i0]][aa0[i0]] * ktup;
   }

   for (; i0 < n0; i0++) {
     if (hsq[aa0[i0]] >= NMAP) {
       hv=phv=0; 
       lkt = i0+ktup;
       /* restart hv, phv calculation */
       for (; (i0 < lkt || hsq[aa0[i0]]>=NMAP) && i0<n0; i0++) {
	 if (hsq[aa0[i0]] >= NMAP) {hv=phv=0; lkt = i0+ktup; continue;}
	 hv = (hv << f_str->kshft) + hsq[aa0[i0]];
	 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]] * ktup;
       }
     }
     if (i0 >= n0) break;
     hv = ((hv & f_str->hmask) << f_str->kshft) + hsq[aa0[i0]];
     f_str->link[i0] = f_str->harr[hv];
     f_str->harr[hv] = i0;
     if (pamfact) {
       f_str->pamh2[hv] = (phv += ppst->pam2[ip][aa0[i0]][aa0[i0]] * ktup);
       /* this check should always be true, but just in case */
       if (hsq[aa0[i0-kt1]]<NMAP)
	 phv -= ppst->pam2[ip][aa0[i0 - kt1]][aa0[i0 - kt1]] * ktup;
     }
     else f_str->pamh2[hv] = fact * ktup;
   }

#ifndef TFAST
   /* done hashing, now switch aa0, aa0x back */
   fs = aa0;
   aa0 = aa0x;
   aa0x = fs;
#endif

   if (pamfact)
      for (i0 = 1; i0 < ppst->nsq; i0++)
	 f_str->pamh1[i0] = ppst->pam2[ip][i0][i0] * ktup;
   else
      for (i0 = 1; i0 < ppst->nsq; i0++)
	 f_str->pamh1[i0] = fact;

   f_str->ndo = 0;	/* used to save time on diagonals with long queries */

#ifndef ALLOCN0
   if ((f_str->diag = (struct dstruct *) calloc ((size_t)MAXDIAG,
						 sizeof (struct dstruct)))==NULL) {
      fprintf (stderr," cannot allocate diagonal arrays: %ld\n",
	      (long) MAXDIAG *sizeof (struct dstruct));
      exit (1);
     };
#else
   if ((f_str->diag = (struct dstruct *) calloc ((size_t)n0,
					      sizeof (struct dstruct)))==NULL) {
      fprintf (stderr," cannot allocate diagonal arrays: %ld\n",
	      (long)n0*sizeof (struct dstruct));
      exit (1);
     };
#endif


   if ((waa= (int *)malloc (sizeof(int)*(nsq+1)*n0)) == NULL) {
     fprintf(stderr,"cannot allocate waa struct %3d\n",nsq*n0);
     exit(1);
   }

   pwaa = waa;
   for (i=0; i<nsq; i++) {
     for (j=0;j<n0; j++) {
       *pwaa = ppst->pam2[ip][i][aa0[j]];
       pwaa++;
     }
   }
   f_str->waa0 = waa;

   if ((waa= (int *)malloc (sizeof(int)*(nsq+1)*n0)) == NULL) {
     fprintf(stderr,"cannot allocate waa struct %3d\n",nsq*n0);
     exit(1);
   }

   pwaa = waa;
   for (i=0; i<nsq; i++) {
     for (j=0;j<n0; j++) {
       *pwaa = ppst->pam2[0][i][aa0[j]];
       pwaa++;
     }
   }
   f_str->waa1 = waa;

#ifndef TFAST
   maxn0 = max(2*n0,MIN_RES);
#else
   /* maxn0 needs to be large enough to accomodate introns
      for TFASTX.  For all other functions, it will be
      more reasonable. */
   maxn0 = max(4*n0,MIN_RES);
#endif
   if ((res = (int *)calloc((size_t)maxn0,sizeof(int)))==NULL) {
     fprintf(stderr,"cannot allocate alignment results array %d\n",maxn0);
     exit(1);
   }
   f_str->res = res;
   f_str->max_res = maxn0;

   *f_arg = f_str;
}


/* pstring1 is a message to the manager, currently 512 */
/* pstring2 is the same information, but in a markx==10 format */
void
get_param (const struct pstruct *ppst,
	   char **pstring1, char *pstring2,
	   struct score_count_s *s_info)
{
  char options_str1[128];
  char options_str2[128];
#ifndef TFAST
  char *pg_str="FASTX";
#else
  char *pg_str="TFASTX";
#endif

  if (!ppst->param_u.fa.use_E_thresholds) {
    sprintf(options_str1,"join: %d (%.3g), opt: %d (%.3g)",
	    ppst->param_u.fa.cgap, (double)s_info->s_cnt[0]/(double)s_info->tot_scores,
	    ppst->param_u.fa.optcut, (double)s_info->s_cnt[2]/(double)s_info->tot_scores);
    sprintf(options_str2,"pg_join: %d (%.3g)\n; pg_optcut: %d (%.3g)",
	    ppst->param_u.fa.cgap, (double)s_info->s_cnt[0]/(double)s_info->tot_scores,
	    ppst->param_u.fa.optcut, (double)s_info->s_cnt[2]/(double)s_info->tot_scores);
  }
  else {
    sprintf(options_str1,"E-join: %.2g (%.3g), E-opt: %.2g (%.3g)",
	    ppst->param_u.fa.E_join, (double)s_info->s_cnt[0]/(double)s_info->tot_scores,
	    ppst->param_u.fa.E_band_opt, (double)s_info->s_cnt[2]/(double)s_info->tot_scores);
    sprintf(options_str2,"pg_join_E(): %.2g (%.3g)\n; pg_optcut_E(): %.2g (%.3g)",
	    ppst->param_u.fa.E_join, (double)s_info->s_cnt[0]/(double)s_info->tot_scores,
	    ppst->param_u.fa.E_band_opt, (double)s_info->s_cnt[2]/(double)s_info->tot_scores);
  }

  if (!ppst->param_u.fa.optflag) {
    sprintf (pstring1[0], "%s (%s)",pg_str,verstr);
  }
  else {
    sprintf (pstring1[0], "%s (%s) [optimized]",pg_str,verstr);
  }

#ifdef OLD_FASTA_GAP
  sprintf (pstring1[1], "%s matrix (%d:%d)%s, gap-pen: %d/%d, shift: %d\n ktup: %d, %s, width: %3d",
#else
  sprintf (pstring1[1], "%s matrix (%d:%d)%s, open/ext: %d/%d, shift: %d\n ktup: %d, %s, width: %3d",
#endif
	   ppst->pam_name, ppst->pam_h,ppst->pam_l,
	   (ppst->ext_sq_set) ? "xS":"\0",
	   ppst->gdelval, ppst->ggapval, ppst->gshift,
	   ppst->param_u.fa.ktup, options_str1, ppst->param_u.fa.optwid);

  if (ppst->param_u.fa.iniflag) strcat(pstring1[0]," init1");

  if (pstring2 != NULL) {
#ifdef OLD_FASTA_GAP
    sprintf (pstring2, "; pg_name_alg: %s\n; pg_ver_rel: %s\n; pg_matrix: %s (%d:%d)%s\n\
; pg_gap-pen: %d %d\n; pg_ktup: %d\n; %s\n",
#else
     sprintf (pstring2, "; pg_name_alg: %s\n; pg_ver_rel: %s\n; pg_matrix: %s (%d:%d)%s\n\
; pg_open_ext: %d %d\n; pg_ktup: %d\n; %s\n",
#endif
	      pg_str,verstr,ppst->pam_name, ppst->pam_h,ppst->pam_l, 
	      (ppst->ext_sq_set) ? "xS":"\0", ppst->gdelval,
              ppst->ggapval,ppst->param_u.fa.ktup,options_str2);
   }
}

void
close_work (const unsigned char *aa0, int n0,
	    struct pstruct *ppst,
	    struct f_struct **f_arg)
{
  struct f_struct *f_str;

  f_str = *f_arg;

  if (f_str != NULL) {
    if (f_str->cur != NULL) free(f_str->cur);
#ifndef TFAST
    f_str->aa0y--;
    free(f_str->aa0y);
    f_str->aa0x--;
    free(f_str->aa0x);
#else
    f_str->aa1y--;
    free(f_str->aa1y);
    f_str->aa1x--;
    free(f_str->aa1x);
#endif
    free(f_str->res);
    free(f_str->waa1);
    free(f_str->waa0);
    free(f_str->diag);
    free(f_str->link);
    free(f_str->pamh2); 
    free(f_str->pamh1);
    free(f_str->harr);
    free(f_str);
    *f_arg = NULL;
  }
}

/* do_fastx() always compares a (possibly translated) protein query
   sequence to another protein sequence. 

   #ifndef TFAST (e.g. FASTX),
   then the hash table was built from the translated (amino-acid)
   version of the query.

   #ifdef TFAST, then aa0 is already a protein sequence

   Args:
   aa0, n0 query sequence
   aa1, n1 library sequence
   yaa translated DNA sequence (from either aa0 or aa1)
   *ppst -> param struct
   *f_str -> function structure set in init_work()
   *rst -> scores (results struct)
   *hoff -> offset of query in library sequence
 */
void do_fastx (const unsigned char *aa0, int n0,
	       const unsigned char *aa1, int n1,
	       unsigned char *yaa, 	/* translated 123123... */
	       const struct pstruct *ppst, struct f_struct *f_str,
	       struct rstruct *rst, int *hoff, int shuff_flg,
	       struct score_count_s *s_info)
{
   int     nd;		/* diagonal array size */
   int     lhval;
   int     kfact;
   int i;
   int my_hoff;
   int c_gap, opt_cut;
   const unsigned char *aa_prot, *aa_trans_prot;
   int n_aap, n_taap;
   register struct dstruct *dptr;
   struct savestr vmax[MAXSAV];	/* best matches saved for one sequence */
   struct savestr *vptr[MAXSAV];
   struct savestr *lowmax;
   int lowscor;
   register int tscor;

#ifndef ALLOCN0
   register struct dstruct *diagp;
#else
   register int dpos;
   int     lposn0;
#endif
   struct dstruct *dpmax;
   register int lpos;
   int     tpos;
   struct savestr *vmptr;
   int     scor, tmp;
   int     im, ib, nsave;
   int ktup, kt1, ip, lkt, ktup_sq;
   const int *hsq;
   int n0_eff;
#ifndef TFAST
   int n0x31, n0x32;
   n0x31 = (n0-2)/3;
   n0x32 = n0x31+1+(n0-n0x31-1)/2;
#else
   const unsigned char *fs;
   unsigned char *fd;
   int n1x31, n1x32, itemp;
   n1x31 = (n1-2)/3;
   n1x32 = n1x31+1+(n1-n1x31-1)/2;
#endif

   if (ppst->ext_sq_set) {
     ip = 1;
     hsq = ppst->hsqx;
   }
   else {
     ip = 0;
     hsq = ppst->hsq;
   }

   ktup = ppst->param_u.fa.ktup;
   kt1 = ktup-1;
   if (ktup <= 3) {
     ktup_sq = ktup*ktup;
   }
   else {
     ktup_sq = ktup;
   }
   if (ktup == 1) ktup_sq *= 2;

   if (n1 < ktup) {
     rst->score[0] = rst->score[1] = rst->score[2] = 0;
     return;
   }

   if (n0+n1+1 >= MAXDIAG) {
     fprintf(stderr,"n0,n1 too large: %d, %d\n",n0,n1);
     rst->score[0] = rst->score[1] = rst->score[2] = -1;
     return;
   }

   if (ppst->param_u.fa.use_E_thresholds) {
     rst->valid_stat = 0;
     n0_eff = n0;
     if (n0 > 120) n0_eff = (n0+2)/3;
     c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst->pH);
     opt_cut = ELK_to_s(ppst->param_u.fa.E_band_opt*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst->pH);
   }
   else {
     c_gap = ppst->param_u.fa.cgap;
     opt_cut = ppst->param_u.fa.optcut;
     rst->valid_stat = 1;
   }
   /* if (shuff_flg) rst->valid_stat = 1; */

   f_str->noff = n0 - 1;

#ifdef ALLOCN0
   nd = n0;
#endif

#ifndef ALLOCN0
   nd = n0 + n1;
#endif

   dpmax = &f_str->diag[nd];
   for (dptr = &f_str->diag[f_str->ndo]; dptr < dpmax;)
   {
      dptr->stop = -1;
      dptr->dmax = NULL;
      dptr++->score = 0;
   }

   for (vmptr = vmax; vmptr < &vmax[MAXSAV]; vmptr++)
      vmptr->score = 0;
   lowmax = vmax;
   lowscor = 0;

   /* start hashing */
   lhval = 0;
   lkt = kt1;
   for (lpos = 0; (lpos < lkt || hsq[aa1[lpos]]>=NMAP) && lpos<n1; lpos++) {
     if (hsq[aa1[lpos]]>=NMAP) {
       lhval = 0; lkt=lpos+ktup; continue;
#ifdef ALLOCN0		/* reinitialize dptr */
       dptr = &f_str->diag[lpos % nd];
       dptr->stop = -1;
       dptr->dmax = NULL;
       dptr->score = 0;
#endif
     }
     lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
   }

#ifndef ALLOCN0
   diagp = &f_str->diag[f_str->noff + lkt];
   for (; lpos < n1; lpos++, diagp++) {
     /*     if (hsq[aa1[lpos]]>=NMAP) {lhval = 0; continue;} */
     if (hsq[aa1[lpos]]>=NMAP) {
       lpos++ ; diagp++;
       while (lpos < n1 && hsq[aa1[lpos]]>=NMAP) {lpos++; diagp++;}
       if (lpos >= n1) break;
       lhval = 0;
     }
     lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
     for (tpos = f_str->harr[lhval]; tpos >= 0; tpos = f_str->link[tpos]) {
       if ((tscor = (dptr = &diagp[-tpos])->stop) >= 0) {
#else
   lposn0 = f_str->noff + lpos;
   for (; lpos < n1; lpos++, lposn0++) {
     if (hsq[aa1[lpos]]>=NMAP) {lhval = 0; goto loopl;}
     lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
     for (tpos = f_str->harr[lhval]; tpos >= 0; tpos = f_str->link[tpos]) {
       dpos = lposn0 - tpos;
       if ((tscor = (dptr = &f_str->diag[dpos % nd])->stop) >= 0) {
#endif
	 tscor += ktup;
	 if ((tscor -= lpos) <= 0) {	/* better to start over */
	   scor = dptr->score;
	   if ((tscor += (kfact = f_str->pamh2[lhval])) < 0 && lowscor < scor) {
#ifdef ALLOCN0
	     lowscor = savemax (dptr, dpos, vmax, &lowmax);
#else
	     lowscor = savemax (dptr, dptr - f_str->diag, vmax, &lowmax);
#endif
	   }
	   if ((tscor += scor) >= kfact) {
	     dptr->score = tscor;
	     dptr->stop = lpos;
	   }
	   else {
	     dptr->score = kfact;
	     dptr->start = (dptr->stop = lpos) - kt1;
	   }
	 }				/* continue current run in diagonal */
	 else {
	   dptr->score += f_str->pamh1[aa0[tpos]];
	   dptr->stop = lpos;
	 }
       }
       else {
	 dptr->score = f_str->pamh2[lhval];
	 dptr->start = (dptr->stop = lpos) - kt1;
       }
     }				/* end tpos */

#ifdef ALLOCN0
      /* reinitialize diag structure */
   loopl:
     if ((dptr = &f_str->diag[lpos % nd])->score > lowscor) {
       lowscor = savemax (dptr, lpos, vmax, &lowmax);
     }
     dptr->stop = -1;
     dptr->dmax = NULL;
     dptr->score = 0;
#endif
   }				/* end lpos */

#ifdef ALLOCN0
   for (tpos = 0, dpos = f_str->noff + n1 - 1; tpos < n0; tpos++, dpos--) {
     if ((dptr = &f_str->diag[dpos % nd])->score > lowscor) {
       lowscor = savemax (dptr, dpos, vmax, &lowmax);
     }
   }
#else
   for (dptr = f_str->diag; dptr < dpmax;) {
     if (dptr->score > lowscor) {
       lowscor = savemax (dptr, dptr - f_str->diag, vmax, &lowmax);
     }
     dptr->stop = -1;
     dptr->dmax = NULL;
     dptr++->score = 0;
   }
   f_str->ndo = nd;
#endif

/*
        at this point all of the elements of aa1[lpos]
        have been searched for elements of aa0[tpos]
        with the results in diag[dpos]
*/

   for (nsave = 0, vmptr = vmax; vmptr < &vmax[MAXSAV]; vmptr++)
   {
     /*
       fprintf(stderr,"0: %4d-%4d  1: %4d-%4d  dp: %d score: %d\n",
	       f_str->noff+vmptr->start-vmptr->dp,
	       f_str->noff+vmptr->stop-vmptr->dp,
	       vmptr->start,vmptr->stop,
	       vmptr->dp,vmptr->score);
     */
      if (vmptr->score > 0) {
	 vmptr->score = spam (aa0, aa1, vmptr, ppst->pam2[ip], f_str);
	 vptr[nsave++] = vmptr;
      }
   }

   if (nsave <= 0) {
     rst->score[0] = rst->score[1] = rst->score[2] = 0;
     return;
   }
       
#ifndef TFAST
   /* FASTX code here to modify the start, stop points for 
      the three phases of the translated protein sequence
      */
   /*
     fprintf(stderr,"n0x: %d; n0x31:%d; n0x32: %d\n",n0,n0x31,n0x32);
     for (ib=0; ib<nsave; ib++) {
       fprintf(stderr,"0: %4d-%4d  1: %4d-%4d  dp: %d score: %d\n",
	       f_str->noff+vptr[ib]->start-vptr[ib]->dp,
	       f_str->noff+vptr[ib]->stop-vptr[ib]->dp,
	       vptr[ib]->start,vptr[ib]->stop,
	       vptr[ib]->dp,vptr[ib]->score);
     }

     fprintf(stderr,"---\n");
   */
   for (ib=0; ib<nsave; ib++) {
     if (f_str->noff-vptr[ib]->dp+vptr[ib]->start >= n0x32)
       vptr[ib]->dp += n0x32;
     if (f_str->noff-vptr[ib]->dp +vptr[ib]->start >= n0x31)
       vptr[ib]->dp += n0x31;
   }
#else
   /* TFASTX code here to modify the start, stop points for 
      the three phases of the translated protein sequence
      TFASTX modifies library start points, rather than 
      query start points
   */

   for (ib=0; ib<nsave; ib++) {
     if (vptr[ib]->start >= n1x32) {
       vptr[ib]->start -= n1x32;
       vptr[ib]->stop -= n1x32;
       vptr[ib]->dp -= n1x32;
     }
     if (vptr[ib]->start >= n1x31) {
       vptr[ib]->start -= n1x31;
       vptr[ib]->stop -= n1x31;
       vptr[ib]->dp -= n1x31;
     }
   }
	    
#endif /* TFASTX */

   scor = sconn (vptr, nsave, c_gap, 
		 ppst->param_u.fa.pgap, f_str);

   for (vmptr=vptr[0],ib=1; ib<nsave; ib++)
     if (vptr[ib]->score > vmptr->score) vmptr=vptr[ib];

/*  kssort (vptr, nsave); */

   rst->score[1] = vmptr->score;	/* best single score - init1*/
   rst->score[0] = max (scor, vmptr->score);  /* initn */
   rst->score[2] = rst->score[0];		/* initn */

#ifndef TFAST /* FASTX */
   *hoff = my_hoff=f_str->noff - vmptr->dp;
#else
   *hoff = my_hoff = vmptr->dp-f_str->noff;
#endif

   /*
   if (n1 > 5000) {
     fprintf(stderr," Long n1: %d\n",n1);
   }
   */

   s_info->tot_scores++;
   if (rst->score[0] >= c_gap) {s_info->s_cnt[0]++;}
   if (ppst->param_u.fa.optflag) {
#ifdef TFAST
     if ( /* shuff_flg || */ rst->score[0] > opt_cut) {
/* generate f_str->aa1y only if it is not there */
       if ( !f_str->have_yaa ) {
	 for (fs=aa1,itemp=0; itemp <3; itemp++,fs++) {
	   for (fd= yaa+itemp; *fs!=EOSEQ; fd += 3, fs++) {*fd = *fs;}
	   *fd=EOSEQ;
	 }
       }
     }
     aa_prot = aa0;
     n_aap = n0;
     aa_trans_prot= yaa;
     n_taap = n1;
#else 
     aa_prot = aa1;
     n_aap = n1;
     aa_trans_prot= yaa;
     n_taap = n0;
#endif
     if ( /* shuff_flg || */ rst->score[0] > opt_cut) {
       s_info->s_cnt[2]++;
       rst->valid_stat = 1;
       rst->score[2] = lx_band(aa_prot,n_aap,aa_trans_prot,n_taap,
			       ppst->pam2[ip],
			       -ppst->gdelval,
			       -ppst->ggapval,-ppst->gshift,
			       my_hoff-ppst->param_u.fa.optwid/2,ppst->param_u.fa.optwid,
			       f_str);
     }
   }
}

/* returns rst.score[0] - initn
   	   rst.score[1] - init1
	   rst.score[2] - opt
*/

void do_work (const unsigned char *aa0, int n0,
	      const unsigned char *aa1, int n1,
	      int frame,
	      const struct pstruct *ppst, struct f_struct *f_str,
	      int qr_flg, int shuff_flg, struct rstruct *rst,
	      struct score_count_s *s_info)
{
  int hoff;
  int last_n1, itx, itt, n10, i;

#ifdef TFAST
  unsigned char *aa1x;
  /* aa0 has a protein sequence */
  /* aa1 has a raw DNA sequence */

  itt = frame;
  last_n1 = 0;
  aa1x = f_str->aa1x;
  for (itx= itt*3; itx< itt*3+3; itx++) {
    n10  = saatran(aa1,&aa1x[last_n1],n1,itx);
    /*
    fprintf(stderr," itt %d itx: %d\n",itt,itx);
    for (i=0; i<n10; i++) {
      fprintf(stderr,"%c",aa[f_str->aa1x[last_n1+i]]);
      if ((i%60)==59) fprintf(stderr,"\n");
    }
    fprintf(stderr,"\n");
    */
    last_n1 += n10+1;
  }
  n10 = last_n1-1;
  f_str->have_yaa = 0;
#endif

  rst->score[0] = rst->score[1] = rst->score[2] = 0;
  rst->escore = 1.0;
  rst->segnum = rst->seglen = 1;

#ifndef TFAST
  do_fastx (f_str->aa0x, n0, aa1, n1, f_str->aa0y, ppst, f_str, rst, &hoff, shuff_flg, s_info);
#else /* tfastx */
  do_fastx (aa0, n0, f_str->aa1x, n10, f_str->aa1y, ppst, f_str, rst, &hoff, shuff_flg, s_info);
#endif

  rst->comp = rst->H = -1.0;
}

void do_opt (const unsigned char *aa0, int n0,
	     const unsigned char *aa1, int n1,
	     int frame,
	     struct pstruct *ppst,
	     struct f_struct *f_str,
	     struct rstruct *rst)
{
  int optflag, tscore, hoff;
  struct score_count_s s_info;

#ifdef TFAST
  int last_n1, itx, itt, n10, i;
  unsigned char *xaa;

  /* aa0 has a protein sequence */
  /* aa1 has a raw DNA sequence */

  itt = frame;
  last_n1 = 0;
  xaa = f_str->aa1x;
  for (itx= itt*3; itx< itt*3+3; itx++) {
    n10  = saatran(aa1,&xaa[last_n1],n1,itx);
    last_n1 += n10+1;
  }
  n10 = last_n1-1;
  f_str->have_yaa = 0;
#endif

  optflag = ppst->param_u.fa.optflag;
  ppst->param_u.fa.optflag = 1;

#ifndef TFAST
  do_fastx (f_str->aa0x, n0, aa1, n1, f_str->aa0y, ppst, f_str, rst, &hoff, 0, &s_info);
#else	/* TFASTX */
  do_fastx (aa0, n0, xaa, n10, f_str->aa1y, ppst, f_str, rst, &hoff, 0, &s_info);
#endif

  ppst->param_u.fa.optflag = optflag;
}

int
savemax (struct dstruct *dptr, int dpos,
	 struct savestr *vmax, struct savestr **lowmax)
{
   struct savestr *vmptr;
   int i;

/* check to see if this is the continuation of a run that is already saved */

   if ((vmptr = dptr->dmax) != NULL && vmptr->dp == dpos &&
	 vmptr->start == dptr->start) {
      vmptr->stop = dptr->stop;
      if ((i = dptr->score) <= vmptr->score) return (*lowmax)->score;
      vmptr->score = i;
      if (vmptr != (*lowmax)) return (*lowmax)->score;
   }
   else {
     i = (*lowmax)->score = dptr->score;
     (*lowmax)->dp = dpos;
     (*lowmax)->start = dptr->start;
     (*lowmax)->stop = dptr->stop;
     dptr->dmax = (*lowmax);
   }

   for (vmptr = vmax; vmptr < vmax+MAXSAV; vmptr++) {
     if (vmptr->score < i) {
       i = vmptr->score;
       *lowmax = vmptr;
     }
   }
   return i;
}

int spam (const unsigned char *aa0, const unsigned char *aa1,
	  struct savestr *dmax, int **pam2,
	  struct f_struct *f_str)
{
   int     lpos;
   int     tot, mtot;
   struct {
     int     start, stop, score;
   } curv, maxv;
   const unsigned char *aa0p, *aa1p;

   aa1p = &aa1[lpos = dmax->start];
   aa0p = &aa0[lpos - dmax->dp + f_str->noff];
   curv.start = lpos;

   tot = curv.score = maxv.score = 0;
   for (; lpos <= dmax->stop; lpos++) {
     tot += pam2[*aa0p++][*aa1p++];
     if (tot > curv.score) {
       curv.stop = lpos;
       curv.score = tot;
      }
      else if (tot < 0) {
	if (curv.score > maxv.score) {
	  maxv.start = curv.start;
	  maxv.stop = curv.stop;
	  maxv.score = curv.score;
	}
	tot = curv.score = 0;
	curv.start = lpos+1;
      }
   }

   if (curv.score > maxv.score) {
     maxv.start = curv.start;
     maxv.stop = curv.stop;
     maxv.score = curv.score;
   }

/*	if (maxv.start != dmax->start || maxv.stop != dmax->stop)
		printf(" new region: %3d %3d %3d %3d\n",maxv.start,
			dmax->start,maxv.stop,dmax->stop);
*/
   dmax->start = maxv.start;
   dmax->stop = maxv.stop;

   return maxv.score;
}

#define XFACT 10

int sconn (struct savestr **v, int n, 
       int cgap, int pgap, struct f_struct *f_str)
{
  int     i, si;
  struct slink {
    int     score;
    struct savestr *vp;
    struct slink *next;
  }      *start, *sl, *sj, *so, sarr[MAXSAV];
  int     lstart, tstart, plstop, ptstop;

/*	sort the score left to right in lib pos */

  kpsort (v, n);

  start = NULL;

/*	for the remaining runs, see if they fit */

   for (i = 0, si = 0; i < n; i++)
   {

/*	if the score is less than the gap penalty, it never helps */
      if (v[i]->score < cgap)
	 continue;
      lstart = v[i]->start;
      tstart = lstart - v[i]->dp + f_str->noff;

/*	put the run in the group */
      sarr[si].vp = v[i];
      sarr[si].score = v[i]->score;
      sarr[si].next = NULL;

/* 	if it fits, then increase the score */
      for (sl = start; sl != NULL; sl = sl->next)
      {
	 plstop = sl->vp->stop;
	 ptstop = plstop - sl->vp->dp + f_str->noff;
	 if (plstop < lstart+XFACT && ptstop < tstart+XFACT) {
	   sarr[si].score = sl->score + v[i]->score + pgap;
	   break;
	 }
      }

/*	now recalculate where the score fits */
      if (start == NULL)
	 start = &sarr[si];
      else
	 for (sj = start, so = NULL; sj != NULL; sj = sj->next)
	 {
	    if (sarr[si].score > sj->score)
	    {
	       sarr[si].next = sj;
	       if (so != NULL)
		  so->next = &sarr[si];
	       else
		  start = &sarr[si];
	       break;
	    }
	    so = sj;
	 }
      si++;
   }

   if (start != NULL)
      return (start->score);
   else
      return (0);
}

void
kssort (v, n)
struct savestr *v[];
int     n;
{
   int     gap, i, j;
   struct savestr *tmp;

   for (gap = n / 2; gap > 0; gap /= 2)
      for (i = gap; i < n; i++)
	 for (j = i - gap; j >= 0; j -= gap)
	 {
	    if (v[j]->score >= v[j + gap]->score)
	       break;
	    tmp = v[j];
	    v[j] = v[j + gap];
	    v[j + gap] = tmp;
	 }
}

void
kpsort (struct savestr **v, int n) {
  int gap, i, j, k;
  int incs[4] = { 21, 7, 3, 1 };
  struct savestr *tmp;
  int v_start;

  for ( k = 0; k < 4; k++) {
    gap = incs[k];
    for (i = gap; i < n; i++) {
      tmp = v[i];
      j = i;
      v_start = v[i]->start;
      while (j >= gap && v[j - gap]->start > v_start) {
	v[j] = v[j - gap];
	j -= gap;
      }
      v[j] = tmp;
    }
  }
}

static void
init_row(struct sx_s *row, int sp) {
  int i;
  for (i = 0; i < sp; i++) {
      row[i].C1 = row[i].I1 = 0;
      row[i].C2 = row[i].I2 = 0;
      row[i].C3 = row[i].I3 = 0;
      row[i].flag = 0;
  }
}

int
lx_band(const unsigned char *prot_seq,  /* array with protein sequence numbers*/
	int len_prot,    /* length of prot. seq */
	const unsigned char *dna_prot_seq, /* translated DNA sequence numbers*/
	int len_dna_prot,   /* length trans. seq. */
	int **pam_matrix,   /* scoring matrix */
	int gopen, int gext, /* gap open, gap extend penalties */
	int gshift,         /* frame-shift penalty */
	int start_diag,     /* start diagonal of band */
	int width,         /* width for band alignment */
	struct f_struct *f_str)
{
  void *ckalloc();
  int i, j, bd, bd1, x1, sp, p1=0, p2=0, end_prot;
  int sc, del, best = 0, cd,ci, e1, e2, e3, cd1, cd2, cd3, f, gg;
  register int *wt;
  const unsigned char *dp;
  register struct sx_s *ap, *aq;

  sp = width+7;	
  gg = gopen+gext;
  /*  sp = sp/3; */
  if (f_str->cur == NULL) {
    f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp);
    f_str->cur_sp_size = sp;
  }
  else if (f_str->cur_sp_size != sp) {
    free(f_str->cur);
    f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp);
    f_str->cur_sp_size = sp;
  }

  init_row(f_str->cur, sp);

  /*
  if (start_diag %3 !=0) start_diag = start_diag/3-1;
  else start_diag = start_diag/3;
  */

  /*
  if (width % 3 != 0) width = width/3+1;
  else width = width /3;
  */

  /* currently, this code assumes that the DNA sequence is longer than the
     protein sequence. This is not always true.  len_prot in the loop below
     should be decreased to the projection of the DNA on the protein */

  x1 = start_diag; 		/* x1 = lower bound of DNA */

  
  end_prot = max(0,-width-start_diag) + (len_dna_prot+5)/3 + width;
  end_prot = min(end_prot,len_prot);

  /* i counts through protein sequence, x1 through DNAp */

  for (i = max(0, -width-start_diag), x1+=i; i < end_prot; i++, x1++) {
      bd = min(x1+width, len_dna_prot/3);	/* upper bound of band */
      bd1 = max(0,x1);	                /* lower bound of band */
      wt = pam_matrix[prot_seq[i]];
      del = 1-x1;   /*adjustment*/
      bd += del; 
      bd1 +=del;

      ap = &f_str->cur[bd1];
      aq = ap+1;
      e1 = f_str->cur[bd1-1].C3;
      e2 = ap->C1;
      cd1 = cd2= cd3= 0;

      for (dp = &dna_prot_seq[(bd1-del)*3]; ap < &f_str->cur[bd]; ap++) {
	  sc = max(max(e1, (e3=ap->C2))-gshift, e2)+wt[*dp++];
	  if (cd1 > sc) sc = cd1;
	  cd1 -= gext;
	  if ((ci = aq->I1) > 0) {
	      if (sc < ci) { ap->C1 = ci; ap->I1 = ci-gext;}
	      else {
		  ap->C1 = sc;
		  sc -= gg;
		  if (sc > 0) {
		      if (sc > best) best =sc;
		      if (cd1 < sc) cd1 = sc;
		      ap->I1 = max(ci-gext, sc);
		  } else ap->I1 = ci-gext;
	      }
	  } else {
	      if (sc <= 0) {
		  ap->I1 = ap->C1 = 0;
	      } else {
		  ap->C1 = sc; sc-=gg;
		  if (sc >0) {
		      if (sc > best) best =sc;
		      if (cd1 < sc) cd1 = sc;
		      ap->I1 = sc;
		  } else ap->I1 = 0;
	      }
	  }
	  sc = max(max(e2, (e1=ap->C3))-gshift, e3)+wt[*dp++];
	  if (cd2 > sc) sc = cd2;
	  cd2 -= gext;
	  if ((ci = aq->I2) > 0) {
	      if (sc < ci) { ap->C2 = ci; ap->I2 = ci-gext;}
	      else {
		  ap->C2 = sc;
		  sc -= gg;
		  if (sc > 0) {
		      if (sc > best) best =sc;
		      if (cd2 < sc) cd2 = sc;
		      ap->I2 = max(ci-gext, sc);
		  }
	      }
	  } else {
	      if (sc <= 0) {
		  ap->I2 = ap->C2 = 0;
	      } else {
		  ap->C2 = sc; sc-=gg;
		  if (sc >0) {
		      if (sc > best) best =sc;
		      if (cd2 < sc) cd2 = sc;
		      ap->I2 = sc;
		  } else ap->I2 = 0;
	      }
	  }
	  sc = max(max(e3, (e2=aq->C1))-gshift, e1)+wt[*dp++];
	  if (cd3 > sc) sc = cd3;
	  cd3 -= gext;
	  if ((ci = aq++->I3) > 0) {
	      if (sc < ci) { ap->C3 = ci; ap->I3 = ci-gext;}
	      else {
		  ap->C3 = sc;
		  sc -= gg;
		  if (sc > 0) {
		      if (sc > best) best =sc;
		      if (cd3 < sc) cd3 = sc;
		      ap->I3 = max(ci-gext, sc);
		  }
	      }
	  } else {
	      if (sc <= 0) {
		  ap->I3 = ap->C3 = 0;
	      } else {
		  ap->C3 = sc; sc-=gg;
		  if (sc >0) {
		      if (sc > best) best =sc;
		      if (cd3 < sc) cd3 = sc;
		      ap->I3 = sc;
		  } else ap->I3 = 0;
	      }
	  }
      }
  }
  /*  printf("The best score is %d\n", best); */
  return best+gopen+gext;
}

/* ckalloc - allocate space; check for success */
void *ckalloc(size_t amount)
{
  void *p;

  if ((p = (void *)malloc( (size_t)amount)) == NULL)
    w_abort("Ran out of memory.","");
  return(p);
}

/* calculate the 100% identical score */
int
shscore(unsigned char *aa0, int n0, int **pam2)
{
  int i, sum;
  for (i=0,sum=0; i<n0; i++)
    sum += pam2[aa0[i]][aa0[i]];
  return sum;
}

#define WIDTH 60

/* code above is to convert sequence into numbers */

typedef struct mat *match_ptr;

typedef struct mat {
	int i, j, l;
	match_ptr next;
} match_node;

typedef struct {
	int i,j;
} state;

typedef state *state_ptr;

typedef struct st_s { int C, I, D;} *st_ptr;

/* static st_ptr up=NULL, down, tp; */
/* static int *st_up; */
/* static int gop, gext, shift; */

void *ckalloc(size_t);
static match_ptr small_global(), global();
static int local_align(), find_best();
static void init_row2(),  init_ROW();

int
pro_dna(const unsigned char *prot_seq,	/* array with prot. seq. numbers*/
	int len_prot,	 		/* length of prot. seq */
	const unsigned char *dna_prot_seq, /* trans. DNA seq. numbers*/
	int len_dna_prot,		/* length trans. seq. */
	int **pam_matrix,		/* scoring matrix */
	int gopen, int gex,		/* gap open, gap extend penalties */
	int gshift,        		/* frame-shift penalty */
	struct smgl_str *smgl_sp,
	int max_res,
	struct a_res_str *a_res)	/* alignment info */
{
  match_ptr align, ap, aq;
  int x, y, ex, ey, i, score;
  int *alignment;
  st_ptr up, down, tp;

  /* these globals removed */
  /*   gext = gex; gop = gopen; shift = gshift; */

  /* for fastx (but not tfastx), these could be moved into init_work(),
     and done only once */

  up = (st_ptr) ckalloc(sizeof(struct st_s)*(len_dna_prot+10));
  down = (st_ptr) ckalloc(sizeof(struct st_s)*(len_dna_prot+10));
  tp = (st_ptr) ckalloc(sizeof(struct st_s)*(len_dna_prot+10));

  /*local alignment find the best local alignment x (prot) and y (DNA)
    is the starting position of the best local alignment
    and ex (prot) ey (DNA) is the ending position */
  score= local_align(&x, &y, &ex, &ey, pam_matrix,
		     gopen, gex, gshift,
		     dna_prot_seq, len_dna_prot,
		     prot_seq, len_prot, up, down);

  /* this is very strange, since local_align initialized up, down */
  up += 3; down += 3; tp += 3;

  /* x, y - start in prot, dna_prot */
  a_res->min0 = x;	/* prot */
  a_res->max0 = ex;	/* prot */

  a_res->min1 = y;	/* DNA-prot */
  a_res->max1 = ey;	/* DNA-prot */

  align = global(x, y, ex, ey, pam_matrix, gopen, gex, gshift, 
		 dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp,
		 smgl_sp);

  alignment = a_res->res;

  /* from earlier version */
  /* alignment[0] = x; */ /* start of alignment in prot */
  /* alignment[1] = y; */ /* start of alignment in DNA */

  for (ap = align, i= 0; ap; i++) {
    if (i < max_res) {alignment[i] = ap->l;}
    aq = ap->next; free(ap); ap = aq;
  }

  if (i >= max_res) {
    fprintf(stderr," alignment truncated: %d/%d\n", max_res,i);
  }

  up = &up[-3]; down = &down[-3]; tp = &tp[-3];
  free(up); free(tp); free(down);
  /* free(st_up); */ /*  moved into local align */

  a_res->nres = i;	/* i has the length of the alignment */
  return score;
}

static void
swap(void **a, void **b) {
  void *t;

  t = *a;
  *a = *b;
  *b = t;
}

/*
   local alignment find the best local alignment x and y
   is the starting position of the best local alignment
   and ex ey is the ending position 
*/
static int
local_align(int *x, int *y, int *ex, int *ey,
	    int **wgts, int gop, int gext, int shift,
	    const unsigned char *dnap, int ld,
	    const unsigned char *pro,  int lp,
	    st_ptr up, st_ptr down) {

  int i, j,  score, x1,x2,x3,x4, e1, e2 = 0, e3,
    sc, del,  e, best = 0, *wt, cd, ci;
  state_ptr cur_st, last_st, cur_i_st;
  st_ptr cur, last;
  const unsigned char *dp;
  int *st_up, *cur_d_st;

/*      
   Array rowiC store the best scores of alignment ending at a position
   Arrays rowiD, and rowiI store the best scores of alignment ending
                 at a position with a deletion or insrtion
   Arrays sti stores the starting position of the best alignment whose
              score stored in the corresponding row array.
   The program stores two rows to complete the computation, same is
        for the global alignment routine.
*/

  /* for fastx (but not tfastx), this could be moved into init_work(),
     and done only once */
  st_up = (int *) ckalloc(sizeof(int)*(ld+10));
  init_row2(st_up, ld+5);

  ld += 2;
  init_ROW(up, ld+1);	/* set to zero */
  init_ROW(down, ld+1);	/* set to zero */


  cur = up+1;
  last = down+1; 

  /* for fastx (but not tfastx), these could be moved into init_work(),
     and done only once */
  cur_st = (state_ptr) ckalloc(sizeof(state)*(ld+1));
  last_st = (state_ptr) ckalloc(sizeof(state)*(ld+1));
  cur_i_st = (state_ptr) ckalloc(sizeof(state)*(ld+1));

  cur_d_st = st_up; 

  dp = dnap-2;
  for (i = 0; i < lp; i++) {
    wt = &wgts[pro[i]][0];
    for (j = 0; j < 2; j++) {
      cur_st[j].i = i+1;
      cur_st[j].j = j+1;
    }
    for (j = 2; j < ld; j++) {
      score = wt[dp[j]];
      del = -1;
      if (j >= 3) {
	sc = -score;
	e3 = e2-shift; e2 = last[j-3].C;
	e1 = last[j-2].C-shift; 
	if (e1 > sc) {sc = e1; del = 2;}
	if (e2 > sc) {sc = e2; del = 3;}
	if (e3 > sc) {sc = e3; del = 4;} 
      } else {
	sc = e2  = 0;
	if (sc < -score) sc=-score;
	else del = 3;
      }
      sc += score;
      if (sc < (ci=last[j].I)) {
	sc = ci; del = 0;
      }
      if (sc < (cd=cur[j].D)) {
	sc = cd; del = 5;
      }
      cur[j].C = sc;
      e = sc  - gop;
      if (e > cd) {
	cur[j+3].D = e-gext;
	cur_d_st[j+3] = 3;
      } else {
	cur[j+3].D = cd-gext;
	cur_d_st[j+3] = cur_d_st[j]+3;
      }
      switch(del) {
      case 5:
	e1 = cur_d_st[j];
	cur_st[j].i = cur_st[j-e1].i;
	cur_st[j].j = cur_st[j-e1].j;
	break;
      case 0:
	cur_st[j].i = cur_i_st[j].i;
	cur_st[j].j = cur_i_st[j].j;
	break;
      case 2:
      case 3:
      case 4:
	if (i) {
	  if (j-del >= 0) {
	    cur_st[j].i = last_st[j-del].i;
	    cur_st[j].j = last_st[j-del].j;
	  } else {
	    cur_st[j].i = i;
	    cur_st[j].j = 0;
	  }
	} else {
	  cur_st[j].i = 0;
	  cur_st[j].j = max(0, j-del+1);
	}
	break;
      case -1:
	cur_st[j].i = i+1;
	cur_st[j].j = j+1;
	break;
      }
      if (e > ci) {
	cur[j].I  = e -gext;
	cur_i_st[j].i = cur_st[j].i;
	cur_i_st[j].j = cur_st[j].j;
      } else {
	cur[j].I  = ci- gext;
      }
      if (sc > best) {
	x1 = cur_st[j].i;
	x2 = cur_st[j].j;
	best =sc;
	x3 = i;
	x4 = j;
      }
    }
    swap((void **)&last, (void **)&cur);
    swap((void **)&cur_st, (void **)&last_st);
  }
  /*	printf("The best score is %d\n", best); */
  *x = x1; *y = x2; *ex = x3; *ey = x4;
  free(cur_st); free(last_st); free(cur_i_st); 
  free(st_up);
  return best;
}

/* 
   Both global_up and global_down do linear space score only global 
   alignments on subsequence pro[x]...pro[ex], and dna[y]...dna[ey].
   global_up does the algorithm upwards, from row x towards row y.
   global_down does the algorithm downwards, from row y towards x.
*/

static void
global_up(st_ptr *row1, st_ptr *row2,
	  int x, int y, int ex, int ey, 
	  int **wgts, int gop, int gext, int shift,
	  unsigned char *dnap,
	  unsigned char *pro,
	  int N) {
  int i, j, k, sc, e, e1, e2, e3, t, ci, cd, score, *wt;
  st_ptr cur, last;

  cur = *row1; last = *row2;

  sc = -gop-gext;

  for (j = 1; j <= ey-y+1; j++) {
    if (j % 3 == 0) {last[j].C = sc; sc -= gext; last[j].I = sc-gop;}
    else { last[j].I = last[j].C = -10000;}
    cur[j].I = -10000;
  }  

  last[0].C = 0; cur[0].D = cur[1].D = cur[2].D = -10000;
  last[0].D = last[1].D = last[2].D = -10000;

  if (N) last[0].I = -gext;
  else last[0].I = -gop-gext;

  for (i = 1; i <= ex-x+1; i++) {
    wt = &wgts[pro[i+x-1]][0]; e2 = last[0].C; e1 = -10000;
    for (j = 0; j <= ey-y+1; j++) {
      t = j+y;
      sc = -10000; 
      if (t < 3) score = -10000;
      else score = wt[dnap[t-3]]; 
      if (j < 4) {
	if (j == 3) sc = e2;
	else if (j == 2) sc = e2-shift;
      } 
      else {
	e3 = e2; e2 = e1;
	e1 = last[j-2].C;
	sc = max(max(e1, e3)-shift, e2);
      }
      sc += score;
      sc = max(sc, max(ci=last[j].I, cd = cur[j].D));
      cur[j].C = sc;
      cur[j+3].D = max(cd, sc-gop)-gext;
      cur[j].I = max(ci, sc-gop)-gext;
    }
    swap((void **)&last, (void **)&cur);
  }
  for (i = 0; i <= ey-y+1; i++) last[i].I = cur[i].I;
  if (*row1 != last) swap((void **)row1, (void **)row2);
}

static void
global_down(st_ptr *row1, st_ptr *row2,
	    int x, int y, int ex, int ey,
	    int **wgts, int gop, int gext, int shift,
	    unsigned char *dnap, unsigned char *pro,
	    int N) {
  int i, j, k, sc, del, *tmp, e,  t, e1,e2,e3, ci,cd, s1, s2, s3, *wt;
  st_ptr cur, last;

  cur = (*row1); last = *row2;

  sc = -gop-gext;

  for (j = ey-y; j >= 0; j--) {
    if ((ey-y+1-j) % 3) {last[j].C = sc; sc-=gext; last[j].I = sc-gop;}
    else  last[j].I =  last[j].C = -10000;
  } 

  last[ey-y+1].C = 0;
  cur[ey-y+1].D = cur[ey-y].D = cur[ey-y-1].D = -10000;
  last[ey-y+1].D = last[ey-y].D = last[ey-y-1].D = -10000;

  if (N) last[ey-y+1].I = -gext;
  else last[ey-y+1].I = -gop-gext;

  for (i = ex-x; i >= 0; i--) {
    wt = &wgts[pro[i+x]][0]; e2 = last[ey-y+1].C; 
    e1 = s2 = s3 = -10000; 
    for (j = ey-y+1; j >= 0; j--) {
      t = j+y;
      s1 = wt[dnap[t-1]];
      sc = -10000;
      if (t+3 > ey) {
	if (t+2==ey) sc = e2+s2;
	else if (t+1==ey) sc = e2-shift+s1;
      } else {
	e3 = e2; e2 = e1;
	e1 = last[j+2].C;
	sc = max(max(e1+s1, e3+s3)-shift, e2+s2);
      }
      if (sc < (cd= cur[j].D)) {
	sc = cd; 
	cur[j-3].D = cd-gext;
      } else cur[j-3].D =max(cd, sc-gop)-gext;
      if (sc < (ci= last[j].I)) {
	sc = ci; del = 0;
	cur[j].I = ci - gext;
      } else cur[j].I = max(sc-gop,ci)-gext;
      cur[j].C = sc;
      s3 = s2; s2 = s1;
    }
    swap((void **)&last, (void **)&cur);
  }
  for (i = 0; i <= ey-y+1; i++) last[i].I = cur[i].I;
  if (*row1 != last) swap((void **)row1, (void **)row2);
}

static void
init_row2(int *row, int ld) {
  int i;
  for (i = 0; i < ld; i++) row[i] = 0;
}

static void
init_ROW(st_ptr row, int ld) {
  int i;
  for (i = 0; i < ld; i++) row[i].I = row[i].D = row[i].C = 0;
}

static match_ptr
combine(match_ptr x1, match_ptr x2, int st) {
  match_ptr x;

  if (x1 == NULL) return x2;
  for (x = x1; x->next; x = x->next);
  x->next = x2;
  if (st) {
    for (x = x2; x; x = x->next) {
      x->j++;
      if (x->l == 3 || x->l == 4) break;
    }
    x->l--;
  }
  return x1;
}

/*
   global use the two upwards and downwards score only linear
   space global alignment subroutine to recursively build the
   alignment.
*/

match_ptr
global(int x, int y, int ex, int ey, 
       int **wgts, int gop, int gext, int shift,
       unsigned char *dnap, 
       unsigned char *pro,
       int N1, int N2,
       st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp,
       struct smgl_str *smgl_sp
       )
{
  int m;
  int m1, m2;
  match_ptr x1, x2, mm1, mm2;
  /*printf("%d %d %d %d\n", x,y, ex, ey);*/
  /*
    if the space required is limited, we can do a quadratic space
    algorithm to find the alignment.
  */
  if (ex <= x) {
    mm1  = NULL; mm2= NULL;
    for (m = y+3; m <= ey; m+=3) {
      x1 = (match_ptr) ckalloc(sizeof(match_node));
      x1->l = 5; x1->next = mm1; 
      if (mm1== NULL) mm2 = x1;
      mm1 = x1;
    }
    if (ex == x) {
      if ((ey-y) % 3 != 0) {
	x1 = (match_ptr) ckalloc(sizeof(match_node));
	x1->l = ((ey-y) % 3) +1; x1->next = NULL;
	if (mm2) mm2->next = x1;
	else mm1 = x1;
      } else {
	if (mm2) mm2->l = 4;
      }
    }
    return mm1;
  }
  if (ey <= y) {
    mm1  = NULL;
    for (m = x; m <= ex; m++) {
      x1 = (match_ptr) ckalloc(sizeof(match_node));
      x1->l = 0; x1->next = mm1; mm1 = x1;
    }
    return mm1;
  }
  if (ex -x < SGW1-1 && ey-y < SGW2-1) 
    return small_global(x,y,ex,ey,
			wgts, gop, gext, shift,
			dnap, pro, N1, N2, smgl_sp);
  m = (x+ex)/2;
  /*     
	 Do the score only global alignment from row x to row m, m is
	 the middle row of x and ex. Store the information of row m in
	 upC, upD, and upI.
  */
  global_up(up_stp, tp_stp, x, y, m, ey, 
	    wgts, gop, gext, shift,
	    dnap, pro, N1);

  /* 
     Do the score only global alignment downwards from row ex
     to row m+1, store information of row m+1 in downC downI and downD
  */
  global_down(dn_stp, tp_stp,  m+1, y, ex, ey, 
	      wgts, gop, gext, shift,
	      dnap, pro, N2);

  /*
    Use these information of row m and m+1, to find the crossing
    point of the best alignment with the middle row. The crossing
    point is given by m1 and m2. Then we recursively call global
    itself to compute alignments in two smaller regions found by
    the crossing point and combine the two alignments to form a
    whole alignment. Return that alignment.
  */
  if (find_best(*up_stp, *dn_stp, &m1, &m2, ey-y+1, y, gop)) {
    x1 = global(x, y, m, m1, wgts, gop, gext, shift, dnap, pro, N1, 0,
		up_stp, dn_stp, tp_stp, smgl_sp);
    x2 = global(m+1, m2, ex, ey, wgts, gop, gext, shift, dnap, pro, 0, N2,
		up_stp, dn_stp, tp_stp, smgl_sp);
    if (m1 == m2) x1 = combine(x1,x2,1);
    else x1 = combine(x1, x2,0);
  } else {
    x1 = global(x, y, m-1, m1, wgts, gop, gext, shift,  dnap, pro, N1, 1,
		up_stp, dn_stp, tp_stp, smgl_sp);
    x2 = global(m+2, m2, ex, ey, wgts, gop, gext, shift, dnap, pro, 1, N2,
		up_stp, dn_stp, tp_stp, smgl_sp);
    mm1 = (match_ptr) ckalloc(sizeof(match_node));
    mm1->i = m; mm1->l = 0; mm1->j = m1;
    mm2 = (match_ptr) ckalloc(sizeof(match_node));
    mm2->i = m+1; mm2->l = 0; mm2->j = m1;
    mm1->next = mm2; mm2->next = x2;
    x1 = combine(x1, mm1, 0);
  }
  return x1;
}

static int
find_best(st_ptr up, st_ptr down,
	  int *m1, int *m2,
	  int ld, int y, int gop) {
  int i, best = -100000, j = 0, s1, s2, s3, s4, st;
  up++;
  for (i = 1; i < ld; i++) {
    s2 = up[i-1].C + down[i].C;
    s4 = up[i-1].I + down[i].I + gop;
    if (best < s2) {
      best = s2; j = i; st = 1;
    }
    if (best < s4) {
      best = s4; j = i; st = 0;
    }
  }
  *m1 = j-1+y;
  *m2 = j+y;
  /*printf("find best score =%d\n", best);*/
  return st;
} 

/*
   An alignment is represented as a linked list whose element
   is of type match_node. Each element represent an edge in the
   path of the alignment graph. The fields of match_node are
   l ---  gives the type of the edge.
   i, j --- give the end position.
*/

static match_ptr
small_global(int x, int y, int ex, int ey,
	     int **wgts, int gop, int gext, int shift,
	     unsigned char *dnap, unsigned char *pro,
	     int N1, int N2, struct smgl_str *smgl_sp) {

  /* int C[SGW1+1][SGW2+1], st[SGW1+1][SGW2+1], D[SGW2+7], I[SGW2+1]; */

  int i, j, e, sc, score, del, k, t, *wt, ci, cd;
  int *cI, *cD, *cC, *lC, *cst, e2, e3, e4;
  match_ptr mp, first;

  /*printf("small_global %d %d %d %d\n", x, y, ex, ey);*/
  sc = -gop-gext; smgl_sp->C[0][0] = 0;

  cI = smgl_sp->I;
  if (N1) cI[0] = -gext; else cI[0] = sc;
  for (j = 1; j <= ey-y+1; j++) {
    if (j % 3== 0) {
      smgl_sp->C[0][j] = sc;
      sc -= gext;
      cI[j] = sc-gop;
    } 
    else {cI[j] = smgl_sp->C[0][j] = -10000;}
    smgl_sp->st[0][j] = 5;
  }

  lC = &smgl_sp->C[0][0];
  cD = smgl_sp->D; cD[0] = cD[1] = cD[2] = -10000;

  for (i = 1; i <= ex-x+1; i++) {
    cC = &smgl_sp->C[i][0];	
    wt = &wgts[pro[i+x-1]][0]; cst = &smgl_sp->st[i][0];
    for (j = 0; j <=ey-y+1; j++) {
      sc = -10000; del = 0;
      ci = cI[j];
      cd= cD[j];
      t = j+y;
      if (t < 3) score = -10000;
      else score = wt[dnap[t-3]];
      if (j >= 4) {
	e2 = lC[j-2]-shift; sc = lC[j-3]; e4 = lC[j-4]-shift;
	del = 3;
	if (e2 > sc) { sc = e2; del = 2;}
	if (e4 >= sc) { sc = e4; del = 4;}
      } else {
	if (j ==3) {sc= lC[0]; del = 3;}
	else if (j == 2) {sc = lC[0]-shift; del = 2;}
      }
      sc = sc+score;
      if (sc < ci) {
	sc = ci; del = 0; 
      }
      if (sc <= cd) {
	sc = cd;
	del = 5;
      }
      cC[j] = sc;
      sc -= gop;
      if (sc < cd) {
	del += 10;
	cD[j+3] = cd - gext;
      } else cD[j+3] = sc -gext;
      if (sc < ci) {
	del += 20;
	cI[j] = ci-gext;
      } else cI[j] = sc-gext;
      *(cst++) = del;
    }
    lC = cC;
  }
  if (N2 && ci +gop > cC[ey-y+1]) {
    smgl_sp->st[ex-x+1][ey-y+1] = 0;
    /*printf("small score = %d\n", ci+gop);*/
  } /*else printf("small score =%d\n", cC[ey-y+1]);*/
  first = NULL; e = 1;
  for (i = ex+1, j = ey+1; i > x || j > y; i--) {
    mp = (match_ptr) ckalloc(sizeof(match_node));
    mp->i = i-1;
    k  = (t=smgl_sp->st[i-x][j-y])%10;
    mp->j = j-1;
    if (e == 5 && (t/10)%2 == 1) k = 5;
    if (e == 0 && (t/20)== 1) k = 0;
    if (k == 5) { j -= 3; i++; e=5;}
    else {j -= k;if (k==0) e= 0; else e = 1;}
    mp->l = k;
    mp->next = first;
    first = mp;
  }

  /*	for (i = 0; i <= ex-x; i++) {
	for (j = 0; j <= ey-y; j++) 
	printf("%d ", C[i][j]);
	printf("\n");
	}
  */
  return first;	
}

#define XTERNAL
#include "upam.h"

/* this code shows the alignment of the protein with the three phased
   translation of the DNA sequence
 */

extern void
display_alig(int *a, unsigned char *dna_p, unsigned char * pro, int length, int ld)
{
  int len = 0, i, j, x, y, lines, k;
  char line1[100], line2[100], line3[100],
    tmp[10] = "         ";
  unsigned char *dna_p1, c1, c2, c3, *st;

  dna_p1 = ckalloc((size_t)ld);
  for (st = dna_p, i = 0; i < ld; i++, st++) dna_p1[i] = NCBIstdaa[*st];
  line1[0] = line2[0] = line3[0] = '\0'; x= a[0]; y = a[1]-1;
 
  for (len = 0, j = 2, lines = 0; j < length; j++) {
    i = a[j];
    /*printf("%d %d %d\n", i, len, b->j);*/
    if (i > 0 && i < 5) tmp[i-2] = NCBIstdaa[pro[x++]];
    if (i == 5) {
      i = 3; tmp[0] = tmp[1] = tmp[2] = '-';
      if (a[j+1] == 2) tmp[2] = ' ';
    }
    if (i > 0) {
      strncpy(&line1[len], (const char *)&dna_p1[y], i);
      y+=i;
    }
    else {
      line1[len] = '-';
      i = 1;
      tmp[0] = NCBIstdaa[pro[x++]];
    }
    strncpy(&line2[len], tmp, i);
    for (k = 0; k < i; k++) {
      if (tmp[k] != ' ' && tmp[k] != '-') {
	if (k == 2) {tmp[k] = '\\';}
	else if (k == 1) { tmp[k] = '|'; }
	else { tmp[k] = '/'; }
      }
      else { tmp[k] = ' '; }
    }
    if (i == 1) tmp[0] = ' ';
    strncpy(&line3[len], tmp, i); 
    tmp[0] = tmp[1] =  tmp[2] = ' ';
    len += i;
    line1[len] = line2[len] =line3[len]  = '\0'; 
    if (len >= WIDTH) {
      printf("\n%5d", WIDTH*lines++);
      for (k = 10; k <= WIDTH; k+=10) {
	printf("    .    :");
      }
      if (k-5 < WIDTH) { printf("    ."); }
      c1 = line1[WIDTH]; c2 = line2[WIDTH]; c3 = line3[WIDTH];
      line1[WIDTH] = line2[WIDTH] = line3[WIDTH] = '\0';

      printf("\n     %s\n     %s\n     %s\n", line1, line3, line2);

      line1[WIDTH] = c1; line2[WIDTH] = c2; line3[WIDTH] = c3;
      strncpy(line1, &line1[WIDTH], sizeof(line1)-1);
      strncpy(line2, &line2[WIDTH], sizeof(line2)-1);
      strncpy(line3, &line3[WIDTH], sizeof(line3)-1);
      len = len - WIDTH;
    }
  }
  printf("\n%5d", WIDTH*lines);
  for (k = 10; k < len; k+=10) 
    printf("    .    :");
  if (k-5 < len) printf("    .");
  printf("\n     %s\n     %s\n     %s\n", line1, line3, line2);
}

/* alignment store the operation that align the protein and dna sequence.
   The code of the number in the array is as follows:
   0:     delete of an amino acid.
   2:     frame shift, 2 nucleotides match with an amino acid
   3:     match an  amino acid with a codon
   4:     the other type of frame shift
   5:     delete of a codon
   

   Also the first two element of the array stores the starting point 
   in the protein and dna sequences in the local alignment.

   Display looks like where WIDTH is assumed to be divisible by 10.

   -- this alignment is incorrect, protein phases rather than DNA are shown --

    0    .    :    .    :    .    :    .    :    .    :    .    :
     CCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTG
      P  M  I  L  G  Y  W  N  V  R  G  L  T  H  P  I  R  M  L  L 

   60    .    :    .    :    .    :    .    :    .    :    .    :
     GAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTT
      E  Y  T  D  S  S  Y  D  E  K  R  Y  T  M  G  D  A  P  D  F 
*/


/* fatal - print message and die */
void fatal(msg)
char *msg;
{
	fprintf(stderr, "%s\n", msg);
	exit(1);
}

void
fx_walign (const unsigned char *aa0, int n0,
	   const unsigned char *xaa, int n1, unsigned char *yaa,
	   int frame, int max_res,
	   struct pstruct *ppst, 
	   struct f_struct *f_str, 
	   struct a_res_str *a_res,
	   int score_thresh
	   )
{
  unsigned char *local_xaa, *local_yaa;
  int score;
  int i, last_n1, itemp, n10;
  int hoff, l_min, l_max, n_nt, n_aa, w_fact;
  int score_ix, window;
  int aa1_min_s, aa1_max_s;
  unsigned char *fs, *fd;
  struct score_count_s s_info;
  int itx;
  
  memset(&s_info,0,sizeof(s_info));

  score_ix = ppst->score_ix;

  /*  check for large differences in sequence length - if there is a
      large difference, use do_fastx() to get the offset. */

#ifndef TFAST	/* FASTX */
  n_nt = n0;
  n_aa = n1;
#else		/* TFASTX */
  n_nt = n1;
  n_aa = n0;
#endif

  do_fastx(aa0, n0, xaa, n1, yaa, ppst, f_str, &a_res->rst, &hoff,1, &s_info);

  if (a_res->rst.score[score_ix] <= score_thresh) {
    a_res->sw_score = 0;
    a_res->n1 = n1;
    return;
  }

  /* now we will do an alignment, but we need to be certain to do the
     alignment in the region mapped by hoff to include the
     high-scoring region */

  /* if initn > 2 * init1, use wider window */
  if (a_res->rst.score[0] > 2 * a_res->rst.score[1]) {w_fact = 4;} 
  else w_fact = 2;

  /* Here we need to use different strategies depending on whether we
     have DNA or protein.  For a DNA query (protein library, FASTX), the
     strategy is simple -- NULL bound the library protein sequence and
     do the alignment.  For a protein query (TFASTX), things are more complex.
     Moreover, the mapping must be calculated differently in each case.
  */


#ifndef TFAST /* map onto the protein (aa1) sequence */  
  window = min(n1, ppst->param_u.fa.optwid);
  l_min = max(0, -window - hoff);
  l_max = min(n1, n0-hoff+window);

  local_yaa = yaa;
  local_xaa = (unsigned char *)xaa;
  if (l_min > 0 || l_max < n1 -1 ) {
    local_xaa = (unsigned char *)calloc(l_max - l_min+2,sizeof(char));
    local_xaa++;
    memcpy(local_xaa, xaa+l_min, l_max - l_min);
  }
/*
  if (l_min > 0) {
    aa1_min_s = xaa[l_min-1];
    local_xaa[l_min-1] = '\0';
  }
  if (l_max < n1 - 1) {
    aa1_max_s = xaa[l_max];
    xaa[l_max] = '\0';
  }
*/
#else
  window = min(n0, ppst->param_u.fa.optwid);
  l_min = max(0,(hoff-window)*3);
  l_max = min((hoff+window+n0)*3,n_nt);
  local_xaa = (unsigned char *)xaa;
  local_yaa = yaa;
  if (l_min > 0 || l_max <n_nt -1) {
    local_yaa = (unsigned char*)calloc(l_max - l_min + 2,sizeof(unsigned char));
    local_yaa++;
    memcpy(local_yaa, yaa+l_min, l_max - l_min);
  }

  /*
  if (l_min > 0)
    aa1_min_s = yaa[l_min-1];
    yaa[l_min-1] = '\0';
  }
  if (l_max < n_nt-1) {

    aa1_max_s = yaa[l_max];
    yaa[l_max] = '\0';
  }
  */
#endif

  if (a_res->rst.score[ppst->score_ix] <= score_thresh) {
    a_res->sw_score = 0;
    a_res->n1 = n1;
    return;
  }

  /* pro_dna always compares protein to DNA, and returns protein
     coordinates in a_res->min0,max0 */

  a_res->sw_score = 
    pro_dna(
#ifndef TFAST	/* FASTX */
	    local_xaa, l_max - l_min, 	 /* true protein is in aa1/xaa */
	    yaa, n_nt,
#else 		/* TFASTX */
	    aa0, n0, 		/* true protein is in aa0 */
	    local_yaa, l_max - l_min,
#endif
	    ppst->pam2[0],
#ifdef OLD_FASTA_GAP
	    -(ppst->gdelval - ppst->ggapval),
#else
	    -ppst->gdelval,
#endif
	    -ppst->ggapval,
	    -ppst->gshift,
	    &f_str->smgl_s,
	    max_res, a_res);

  /*
  if (a_res->rst.score[0] < a_res->sw_score) {
    a_res->rst.score[0] = a_res->sw_score;
    a_res->rst.score[ppst->score_ix] = a_res->sw_score;
  }
  */

#ifndef TFAST
  if (l_min > 0 || l_max < n1-1) free(--local_xaa);
/*
  if (l_min > 0) {
    xaa[l_min-1] = aa1_min_s;
  }
  if (l_max < n1 - 1) {
    xaa[l_max] = aa1_max_s;
  }
*/
  a_res->min0 += l_min;
  a_res->max0 += l_min;
#else
  if (l_min > 0 || l_max < n1-1) free(--local_yaa);
  /*
  if (l_min > 0) {
    yaa[l_min-1] = aa1_min_s;
  }
  if (l_max < n1 - 1) {
    yaa[l_max] = aa1_max_s;
  }
  */
  a_res->n1 = n1;
  a_res->min1 += l_min;
  a_res->max1 += l_min;
#endif

}

/*
  fx_malign is a recursive interface to fx_walign() that is called
  from do_walign(). fx_malign() first does an alignment, then checks
  to see if the score is greater than the threshold. If so, it tries
  doing a left and right alignment.

  In this implementation, the translation required for f_str->aa1x and
  f_str->aa1y is done at each recursive level. A better implementation
  would do the translation once, and then be more sophisticated about
  the boundaries on f_str->aa1x,y.  This is challenging, however,
  because there is no easy way to subset aa1x [111112222233333],
  though it is possible to subset aa1y cleanly.  The current solution
  is to re-generate xaa from yaa.

  21-Nov-2010 -- like do_walign(), fx_malign() uses a const xaa, to
  ensure that threads do not interfere with each other.  If a
  sub-range is needed, a new sequence is produced.

 */
struct a_res_str *
fx_malign (const unsigned char *aa0, int n0,
	   const unsigned char *xaa, int n1, unsigned char *yaa,
	   int frame, 
	   int score_thresh, int max_res,
	   struct pstruct *ppst,
	   struct f_struct *f_str,
	   struct a_res_str *cur_ares,
	   int first_align)
{
  struct a_res_str *tmpl_ares, *tmpr_ares, *this_ares;
  struct a_res_str *mtmpl_ares, *mtmpr_ares, *mt_next;
  unsigned char *my_xaa;
  unsigned char *local_xaa, *local_yaa;
  int nxyaa;
  int hoff, score_ix;
  int min_alen;
  struct rstruct rst;
  /*   char save_res; */
  int iphase, i;
  unsigned char *fd;
  int max_sub_score = -1;

  score_ix = ppst->score_ix;

  /* now we need alignment storage - get it */
  if ((cur_ares->res = (int *)calloc((size_t)max_res,sizeof(int)))==NULL) {
    fprintf(stderr," *** cannot allocate alignment results array %d\n",max_res);
    exit(1);
  }

  cur_ares->next = NULL;
    
#ifdef TFAST  
  min_alen = min(n0,MIN_LOCAL_LEN)*3;	/* n0 in aa, min_alen in nt */
#else 
  min_alen = min(n0/3,MIN_LOCAL_LEN);	/* no in nt, min_alen in aa */
#endif

#ifdef TFAST
  /* convert yaa to xaa -- cannot use *fs to stop because subset
     does not have '\0' in all three frames */
  my_xaa = (unsigned char *)calloc(n1+2,sizeof(unsigned char));
  my_xaa++;
  for (fd=my_xaa, iphase = 0; iphase < 3; iphase++) {
    for (i=iphase; i<n1; i+=3,fd++) *fd = yaa[i];
  }
  *fd=EOSEQ;
#else
  my_xaa = (unsigned char *)xaa;
#endif

  fx_walign(aa0, n0, my_xaa, n1, yaa, frame, max_res, 
	    ppst, f_str, cur_ares,(first_align ? 1 : score_thresh));

  /* in cur_ares, min0,max0 are always protein, min1,max1 are always
     DNA, but n0 could be protein or DNA, depending on
     FASTX/TFASTX */

  if (!ppst->do_rep || cur_ares->rst.score[ppst->score_ix] <= score_thresh) {
#ifdef TFAST
    free(--my_xaa);
#endif
    return cur_ares;
  }

  /* we are going to do a recursive edit, so we need a local copy of
     xaa (fastx) or yaa (tfastx) */

#ifdef TFAST	/* TFASTX, n1 is nt */
    nxyaa = cur_ares->min1;
#else		/* FASTX n1 is aa */
    nxyaa = cur_ares->min0;
#endif

  if (nxyaa >= min_alen) { /* try the left  */
    /* allocate a_res */	
    tmpl_ares = (struct a_res_str *)calloc(1, sizeof(struct a_res_str));

#ifdef TFAST	/* TFASTX, no xaa */
    local_xaa = my_xaa;	/* my_xaa is calloc'ed for TFAST */
    local_yaa = (unsigned char *)calloc(nxyaa+2, sizeof(unsigned char));
    local_yaa++;  /* skip the initial zero */
    memcpy(local_yaa, yaa, nxyaa);
/*
    save_res = yaa[cur_ares->min1]; 
    yaa[cur_ares->min1] = '\0';
*/
#else
    local_yaa = yaa;
    local_xaa = (unsigned char *)calloc(nxyaa+2, sizeof(unsigned char));
    local_xaa++;  /* skip the initial zero */
    memcpy(local_xaa, xaa, nxyaa);
/*
    save_res = xaa[cur_ares->min0];
    xaa[cur_ares->min0] = '\0';
*/
#endif
    tmpl_ares = fx_malign(aa0, n0, local_xaa, nxyaa,
			  local_yaa,
			  frame, score_thresh, max_res, 
			  ppst, f_str, tmpl_ares, 0);

#ifdef TFAST
    free(--local_yaa);	/* local_yaa, allocated above */
#else
    free(--local_xaa);	/* FASTX - local_xaa allocated above */
#endif

    if (tmpl_ares->rst.score[ppst->score_ix] > score_thresh) {
      max_sub_score = tmpl_ares->rst.score[ppst->score_ix];
    }
    else {
      if (tmpl_ares->res) free(tmpl_ares->res);
      free(tmpl_ares);
      tmpl_ares = NULL;
    }
  }
  else {tmpl_ares = NULL;}

  /* do the right */
#ifdef TFAST	/* TFASTX - n0 is aa, n1 nt */
  nxyaa = n1 - cur_ares->max1 - 1;
#else		/* FASTX - n1 is aa, n0 nt */
  /* this is counter-intuitive, because n1 is the length of the DNA
     sequence in both cases */
  nxyaa = n1 - cur_ares->max0 - 1;
#endif

  if (nxyaa >= min_alen) {    /* try the right  */      
    /* allocate a_res */	
    tmpr_ares = (struct a_res_str *)calloc(1, sizeof(struct a_res_str));

    /* find boundaries */
#ifdef TFAST	/* TFASTX, no xaa */
    local_xaa = my_xaa;
    local_yaa = (unsigned char *)calloc(nxyaa+2, sizeof(unsigned char));
    local_yaa++;  /* skip the initial zero */
    memcpy(local_yaa, yaa+cur_ares->max1+1,nxyaa);
/*
    save_res = yaa[cur_ares->max1];
    yaa[cur_ares->max1] = '\0';
*/
#else
    local_yaa = yaa;
    local_xaa = (unsigned char *)calloc(nxyaa+2, sizeof(unsigned char));
    local_xaa++;  /* skip the initial zero */
    memcpy(local_xaa, xaa+cur_ares->max0+1,nxyaa);
/*
    save_res = xaa[cur_ares->max0];
    xaa[cur_ares->max0] = '\0';
*/
#endif
    tmpr_ares = fx_malign(aa0, n0, 
			  local_xaa, nxyaa, local_yaa,
			  frame,
			  score_thresh, max_res,
			  ppst, f_str, tmpr_ares,0);
#ifdef TFAST	/* TFASTX, no xaa */
    free(--local_yaa);
#else
    free(--local_xaa);
#endif
/*    yaa[cur_ares->max1] = save_res;*/

    if (tmpr_ares->rst.score[ppst->score_ix] > score_thresh) {
      /* adjust the left boundary */
      for (this_ares = tmpr_ares; this_ares; this_ares = this_ares->next) {
#ifdef TFAST
	this_ares->min1 += cur_ares->max1+1;
	this_ares->max1 += cur_ares->max1+1;
#else
	this_ares->min0 += cur_ares->max0+1;
	this_ares->max0 += cur_ares->max0+1;
#endif
      }

      if (tmpr_ares->rst.score[ppst->score_ix] > max_sub_score) {
	max_sub_score = tmpr_ares->rst.score[ppst->score_ix];
      }
    }
    else {
      if (tmpr_ares->res) free(tmpr_ares->res);
      free(tmpr_ares);
      tmpr_ares = NULL;
    }
  }
  else {tmpr_ares = NULL;}

#ifdef TFAST
    free(--my_xaa);
#endif

  if (max_sub_score <= score_thresh) {
    if (tmpl_ares) {
      if (tmpl_ares->res) free(tmpl_ares->res);
      free(tmpl_ares);
    }
    if (tmpr_ares) {
      if (tmpr_ares->res) free(tmpr_ares->res);
      free(tmpr_ares);
    }
    return cur_ares;
  }

  cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left");
  cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right");

  return cur_ares;
}

/* do_walign() can be called with aa0,n0 as nt (FASTX) or 
   aa0,n0 as aa (TFASTX).  if aa0 is nt, then f_str->aa0x,y have the
   translations already.  if aa0 is aa, then f_str->aa1x,y must be
   generated.

   This is the last time that aa0 can be nt or aa; in all lower
   functions (fx_malign, do_fastx, fx_walign), both aa0, n0 and aa1,
   n1 are amino acids; though one or the other may be translated.

   In the lower functions, yaa can be aa0y (FASTX) or aa1y (TFASTX).
   If it is aa1y, there may be no translation available.

   21-Nov-2010 With fasta-36.3.1, do_walign() uses const aa0, aa1.  If aa1 needs
   modification for recursive alignment, a copy is made.
*/

struct a_res_str *
do_walign (const unsigned char *aa0, int n0,
	   const unsigned char *aa1, int n1,
	   int frame, int repeat_thresh,
	   struct pstruct *ppst, 
	   struct f_struct *f_str, 
	   int *have_ares)
{
  int hoff, use_E_thresholds_s, optflag_s, optcut_s, optwid_s, score;
  struct a_res_str *a_res, *tmp_a_res;
  int a_res_index;
  int last_n1, itx, itt, n10, iphase;
  unsigned char *xaa, *fs, *fd;
  struct rstruct rst;
#ifdef DEBUG
  unsigned long adler32_crc;
#endif

  *have_ares = 0x3;	/* set 0x2 bit to indicate local copy */

  if ((a_res = (struct a_res_str *)calloc(1, sizeof(struct a_res_str)))==NULL) {
    fprintf(stderr," [do_walign] Cannot allocate a_res");
    return NULL;
  }

#ifdef DEBUG
  adler32_crc = adler32(1L,aa1,n1);
#endif

  use_E_thresholds_s = ppst->param_u.fa.use_E_thresholds;
  optflag_s = ppst->param_u.fa.optflag;
  optcut_s = ppst->param_u.fa.optcut;
  optwid_s = ppst->param_u.fa.optwid;
  ppst->param_u.fa.use_E_thresholds = 0;
  ppst->param_u.fa.optflag = 1;
  ppst->param_u.fa.optcut = 0;
  if (!ppst->param_u.fa.optwid_set) {
    ppst->param_u.fa.optwid *= 2;
  }

#ifndef TFAST	/* FASTX */
  a_res = fx_malign(f_str->aa0x, n0, aa1, n1, f_str->aa0y, frame,
		    repeat_thresh, f_str->max_res,
		    ppst, f_str, a_res, 1);
#else		/* TFASTX */
  /* aa0 has a protein sequence */
  /* aa1 has a raw DNA sequence */

  itt = frame;
  last_n1 = 0;
  xaa = f_str->aa1x;
  for (itx= itt*3; itx< itt*3+3; itx++) {
    n10  = saatran(aa1,&xaa[last_n1],n1,itx);
    last_n1 += n10+1;
  }
  n10 = last_n1-1;
  /* create aa1y from xaa */
  for (fs=xaa,iphase=0; iphase <3; iphase++,fs++) {
    for (fd= &f_str->aa1y[iphase]; *fs!=EOSEQ; fd += 3, fs++) *fd = *fs;
    *fd=EOSEQ;
  }
  f_str->have_yaa = 1;

  a_res = fx_malign(aa0, n0, xaa, n10, f_str->aa1y, frame,
		    repeat_thresh, f_str->max_res,
		    ppst, f_str, a_res, 1);
#endif
  /*
  if (a_res->res[0] != 3) {
    fprintf(stderr, "*** alignment does not start with match: %d\n",a_res->res[0]);
  }
  */

#ifdef DEBUG
  if (adler32(1L,aa1,n1) != adler32_crc) {
    fprintf(stderr,"[dropfx.c/do_walign] adler32_crc mismatch n1: %d\n",n1);
  }
#endif

  a_res_index = 0;
  for (tmp_a_res=a_res; tmp_a_res; tmp_a_res = tmp_a_res->next) {
    tmp_a_res->index = a_res_index++;
  }

  ppst->param_u.fa.use_E_thresholds = use_E_thresholds_s;
  ppst->param_u.fa.optflag = optflag_s;
  ppst->param_u.fa.optcut = optcut_s;
  ppst->param_u.fa.optwid = optwid_s;
  return a_res;
}

/* aln_func_vals - set up aln.qlfact, qlrev, llfact, llmult, frame, llrev */
/* call from calcons, calc_id, calc_code */
void 
aln_func_vals(int frame, struct a_struct *aln) {

#ifndef TFAST
  aln->llrev = 0;
  aln->llfact = 1;
  aln->llmult = 1;
  aln->qlfact = 3;
  aln->frame = frame;
  if (frame > 0) aln->qlrev = 1;
  else aln->qlrev = 0;
  aln->llrev = 0;
#else	/* TFASTX */
  aln->qlfact = 1;
  aln->qlrev = 0;
  aln->llfact = 3;
  aln->llmult = 1;
  aln->frame = frame;
  if (frame > 0) aln->llrev = 1;
  else aln->llrev = 0;
  aln->qlrev = 0;
#endif	/* TFASTX */
}

/* this function is required for programs like tfastx/y/s that do
   translations on DNA sequences and save them in f_str->aa1??
*/

void
pre_cons(const unsigned char *aa1, int n1, int frame, struct f_struct *f_str) {
#ifdef TFAST
  int i, last_n1, itemp, n10;
  unsigned char *fs, *fd;
  int itx;

  last_n1 = 0;
  for (itx=3*frame; itx<3+3*frame; itx++) {
    n10 = saatran(aa1,&f_str->aa1x[last_n1],n1,itx);
/*
  for (i=0; i<n10; i++) {
  fprintf(stderr,"%c",ppst->sq[aa10[last_n1+i]]);
  if ((i%60)==59) fprintf(stderr,"\n");
  }
  fprintf(stderr,"\n");
*/
    last_n1 += n10+1;
  }
  n10 = last_n1-1;

  /* create aa1y from aa1x */
  for (fs=f_str->aa1x,itemp=0; itemp <3; itemp++,fs++) {
    for (fd= &f_str->aa1y[itemp]; *fs!=EOSEQ; fd += 3, fs++) *fd = *fs;
    *fd=EOSEQ;
  }
  f_str->have_yaa = 1;
#endif
}

/*
   Alignment: store the operation that align the protein and dna sequence.
   The code of the number in the array is as follows:
   0:     delete of an amino acid.
   2:     frame shift, 2 nucleotides match with an amino acid
   3:     match an  amino acid with a codon
   4:     the other type of frame shift
   5:     delete of a codon

   The first two elements of the array stores the starting point 
   in the protein and dna sequences in the local alignment.
*/

#include "a_mark.h"

extern int align_type(int score, char sp0, char sp1, int nt_align, struct a_struct *aln, int pam_x_id_sim);

extern void
process_annot_match(int *itmp, int *pam2aa0v, 
		    long ip, long ia, char *sp1, char *sp1a, const unsigned char *sq,
		    struct annot_entry *annot_arr_p, char **ann_comment,
		    void *annot_stack, int *have_push_features, int *v_delta,
		    int *d_score_p, int *d_ident_p, int *d_alen_p, struct domfeat_link **left_domain_p,
		    long *left_end_p, int init_score);

extern int
next_annot_match(int *itmp, int *pam2aa0v, 
		 long ip, long ia, char *sp1, char *sp1a, const unsigned char *sq,
		 int i_annot, int n_annot, struct annot_entry **annot_arr, char **ann_comment,
		 void *annot_stack, int *have_push_features, int *v_delta,
		 int *d_score_p, int *d_ident_p, int *d_alen_p, struct domfeat_link **left_domain,
		 long *left_domain_end, int init_score);

extern void
close_annot_match (int ia, void *annot_stack, int *have_push_features,
		   int *d_score_p, int *d_ident_p, int *d_alen_p,
		   struct domfeat_link **left_domain_p,
		   long *left_end_p, int init_score);

extern void
comment_var(long i0, char sp0, long i1, char sp1, char o_sp1, char sim_char,
	    const char *ann_comment, struct dyn_string_str *annot_var_dyn,
	    int target, int d_type);

void
display_push_features(void *annot_stack, struct dyn_string_str *annot_var_dyn,
		      long i0_pos, char sp0, long i1_pos, char sp1, char sym, 
		      int score, double comp, int n0, int n1,
		      void *pstat_void, int d_type);

#define DP_FULL_FMT 1	/* Region: score: bits: id: ... */
#define Q_TARGET 0
#define L_TARGET 1

int seq_pos(int pos, int rev, int off);

int
calc_cons_a(const unsigned char *aa0, int n0,
	    const unsigned char *aa1, int n1,
	    int *nc,
	    struct a_struct *aln,
	    struct a_res_str *a_res, 
	    struct pstruct *ppst,
	    char *seqc0, char *seqc1, char *seqca, int *cumm_seq_score,
	    const unsigned char *ann_arr,
	    const unsigned char *aa0a, const struct annot_str *annot0_p, char *seqc0a,
	    const unsigned char *aa1a, const struct annot_str *annot1_p, char *seqc1a,
	    int *score_delta,
	    struct dyn_string_str *annot_var_dyn,
	    struct f_struct *f_str,
	    void *pstat_void)
{
  int i0, i1, i, j;
  int lenc, not_c, itmp, ngap_p, ngap_d, nfs;
  int *i_spa;
  char *sp0, *sp0a, *sp1, *sp1a, *spa, t_spa;
  const unsigned char *sq;

  const unsigned char *ap0, *ap1;
  const unsigned char *ap1a;	/* ap1 always points to protein, and
				   only protein has annotations */
  int *rp, *rpmax;
  int have_ann = 0;

  /* variables for variant changes/region scores */
  char tmp_str[MAX_LSTR];
  void *annot_stack;
  int have_push_features, prev_match;
  char *sim_sym = aln_map_sym[MX_ACC];
  struct annot_entry **s_annot1_arr_p;
  int  i1_annot, v_delta, v_tmp;
  long i0_offset, i1_offset;

  long i1_left_end;
  int d1_score, d1_ident, d1_alen;
  struct domfeat_link *left_domain_list1;

  char *ann_comment;

  *score_delta = 0;
  d1_score = d1_ident = d1_alen = 0;
  i1_left_end = -1;
  left_domain_list1 = NULL;

  NULL_dyn_string(annot_var_dyn);

  if (ppst->ext_sq_set) {sq = ppst->sqx;}
  else {sq = ppst->sq;}

#ifndef TFAST	/* FASTX */
  aln->amin1 = aln->smin1 = a_res->min0;	/* prot */
  aln->amin0 = aln->smin0 = a_res->min1;	/* DNA */

  i0_offset = aln->q_offset;
  i1_offset = aln->l_offset;

  ap0 = f_str->aa0y;	/* translated DNA */
  ap1 = aa1;		/* protein */

  sp0 = seqc0;	/* translated DNA */
  sp1 = seqc1;	/* protein */

  have_ann = (seqc0a !=NULL && aa1a != NULL);
  ap1a = aa1a;
  sp1a = seqc1a;	/* protein library can have annotation */
  sp0a = seqc0a;	/* sp0a is always ' ' - no translated
			   annotation */
#else		/* TFASTX */
  aln->amin0 = aln->smin0 = a_res->min0;	/* DNA */
  aln->amin1 = aln->smin1 = a_res->min1;	/* prot */

  i1_offset = aln->q_offset;
  i0_offset = aln->l_offset;

  ap1 = aa0;		/* aa0 is protein */
  /* with fx_malign(), there is no guarantee that we have a valid f_str->aa1y, so make one */
  pre_cons(aa1,n1,aln->frame, f_str);
  ap0 = f_str->aa1y;	/* aa1 is DNA */
  sp1 = seqc0;		/* sp1 points to protein query */
  sp0 = seqc1;		/* sp0 points to DNA */

  have_ann = (seqc0a !=NULL && aa0a != NULL);
  ap1a = aa0a;
  sp1a = seqc0a;	/* protein query can have annotation */
  sp0a = seqc1a;	/* sp0a is always ' ' - no translated
			   annotation */
#endif
  spa = seqca;
  if (cumm_seq_score) i_spa = cumm_seq_score;

  rp = a_res->res;
  rpmax = &a_res->res[a_res->nres];

  lenc = not_c = aln->nident = aln->nmismatch = aln->nsim = aln->npos = ngap_p = ngap_d = nfs= 0;
  i0 = a_res->min1;
  i1 = a_res->min0;

  v_delta = 0;
  i1_annot = 0;
  annot_stack = NULL;
  s_annot1_arr_p = NULL;
  have_push_features = prev_match = 0;
  if (have_ann) {
    if (annot1_p && annot1_p->n_annot > 0) annot_stack = init_stack(64,64);
    if (annot1_p && annot1_p->n_annot > 0) {
      s_annot1_arr_p = annot1_p->s_annot_arr_p;

      while (i1_annot < annot1_p->n_annot) {
	if (s_annot1_arr_p[i1_annot]->pos >= i1+i1_offset) {break;}
	if (s_annot1_arr_p[i1_annot]->end < i1+i1_offset) {i1_annot++; continue;}

	if (s_annot1_arr_p[i1_annot]->label == '-') {
	  process_annot_match(&itmp, NULL, i1_offset+seq_pos(i1,aln->llrev,0), i0_offset + seq_pos(i0,aln->qlrev,0),
			      sp1, sp1a, sq, s_annot1_arr_p[i1_annot],  &ann_comment, 
			      annot_stack, &have_push_features, &v_delta,
			      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end, 0);
	}
	i1_annot++;
      }
    }
  }

  while (rp < rpmax) {
    /*    fprintf(stderr,"%d %d %d (%c) %d (%c)\n"
	  ,(int)(rp-res),*rp,i0,sq[ap0[i0]],i1,sq[ap1[i1]]);
    */
    switch (*rp++) {
    case 0: 	/* aa insertion */
      *sp0++ = '-';
      *sp1++ = sq[ap1[i1]];
      *spa++ = M_DEL;
      if (cumm_seq_score) {
	if (prev_match) *i_spa = ppst->gdelval;
	*i_spa++ += ppst->ggapval;
      }

      if (have_ann) {
	*sp0a = ' ';
	*sp1a = ann_arr[ap1a[i1]];
	if (s_annot1_arr_p) {
	  if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {

	    i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
					i0_offset+seq_pos(i0,aln->qlrev,0), sp1, sp1a, sq, 
					i1_annot, annot1_p->n_annot, s_annot1_arr_p,
					&ann_comment, annot_stack, &have_push_features, &v_delta,
					&d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,
					ppst->ggapval+ppst->gdelval
					);
	  }

	  if (prev_match) d1_score += ppst->gdelval;
	  d1_score += ppst->ggapval;
	  d1_alen++;
	  prev_match = 0;
	}
	sp0a++; sp1a++;
      }

      if (have_ann && have_push_features) {
	display_push_features(annot_stack, annot_var_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			      sim_sym[*spa], 
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
	have_push_features = 0;
      }

      i1++;
      lenc++;
      ngap_d++;
      break;
    case 2:	/* -1 frameshift, which is treatead as an insertion/match for annotations */
      nfs++;
      /* frameshifts produce a two-character alignment string */
      /* first annotate the frameshift  (first character) */
      *sp0++ = '/';
      i0 -= 1;
      *sp1++ = '-';
      *spa++ = M_DEL;

      if (have_ann) {*sp0a++ = *sp1a++ = ' ';}
      not_c++;

      /* then annotate the match after the frameshift */

      itmp=ppst->pam2[0][ap0[i0]][ap1[i1]];
      *sp0 = sq[ap0[i0]];
      *sp1 = sq[ap1[i1]];

      if (cumm_seq_score) *i_spa++ = ppst->gshift;

      if (have_ann) {
	have_push_features = 0;
	/* this simple strategy works because the coordinate system
	   for the alignment is reversed appropriately */
	*sp1a = ann_arr[ap1a[i1]];
	*sp0a = ' ';
	if (s_annot1_arr_p) {
	  /* coordiates are much more complex for next_annot_match,
	     and comment_var, because they may need to be reversed */

	  if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	    i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
					i0_offset+seq_pos(i0,aln->qlrev,0), sp1, sp1a, sq, 
					i1_annot, annot1_p->n_annot, s_annot1_arr_p,
					&ann_comment, annot_stack, &have_push_features, &v_delta,
					&d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	    if (sq[ap1[i1]] != *sp1) {
	      t_spa = align_type(itmp, *sp0, *sp1, 0, NULL, ppst->pam_x_id_sim);

	      comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			  i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			  sq[ap1[i1]], sim_sym[t_spa], ann_comment,
			  annot_var_dyn,1,1);
	    }
	  }
	  d1_score += ppst->gshift;
	  d1_score += itmp;
	  prev_match = 1;
	}
	sp0a++; sp1a++;
      }

      *spa = align_type(itmp, *sp0, *sp1, 0, aln, ppst->pam_x_id_sim);

      d1_alen++;
      if (*spa == M_IDENT) {d1_ident++;}

      if (have_ann && have_push_features) {
	display_push_features(annot_stack, annot_var_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			      sim_sym[*spa],
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
	have_push_features = 0;
      }

      if (cumm_seq_score) *i_spa++ = itmp;
      i0 += 3;
      i1++;

      sp0++; sp1++; spa++;
      lenc++;
      break;
    case 3:	/* codon/aa match */
      itmp=ppst->pam2[0][ap0[i0]][ap1[i1]];
      *sp0 = sq[ap0[i0]];
      *sp1 = sq[ap1[i1]];

      if (have_ann) {
	*sp1a = ann_arr[ap1a[i1]];
	*sp0a = ' ';
	if (s_annot1_arr_p) {
	  if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	    i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
					i0_offset+seq_pos(i0,aln->qlrev,0), sp1, sp1a, sq, 
					i1_annot, annot1_p->n_annot, s_annot1_arr_p,
					&ann_comment, annot_stack, &have_push_features, &v_delta,
					&d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	    if (sq[ap1[i1]] != *sp1) {
	      t_spa = align_type(itmp, *sp0, *sp1, 0, NULL, ppst->pam_x_id_sim);

	      comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			  i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			  sq[ap1[i1]], sim_sym[t_spa], ann_comment,
			  annot_var_dyn, 1, 1);
	    }
	  }
	  prev_match = 1;
	  d1_score += itmp;
	}
	sp0a++; sp1a++;
      }

      *spa = align_type(itmp, *sp0, *sp1, 0, aln, ppst->pam_x_id_sim);
      d1_alen++;
      if (*spa == M_IDENT) {d1_ident++;}
  
      if (cumm_seq_score) *i_spa++ = itmp;

      if (have_ann && have_push_features) {
	display_push_features(annot_stack, annot_var_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			      sim_sym[*spa],
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
	have_push_features = 0;
      }

      i0 += 3;
      i1++;

      sp0++; sp1++; spa++;
      lenc++;
      break;
    case 4:	/* +1 frameshift */
      nfs++;
      /* frameshift produces two alignment characters */
      /* first frameshift */
      *sp0++ = '\\';
      i0 += 1;
      *sp1++ = '-';
      *spa++ = M_DEL;
      if (cumm_seq_score) *i_spa++ = ppst->gshift;

      if (have_ann) {*sp1a++ = *sp0a++ = ' ';}
      not_c++;

      /* then alignment */
      itmp=ppst->pam2[0][ap0[i0]][ap1[i1]];
      *sp0 = sq[ap0[i0]];
      *sp1 = sq[ap1[i1]];

      if (have_ann) {
	*sp1a = ann_arr[ap1a[i1]];
	*sp0a = ' ';
	if (s_annot1_arr_p) {
	  if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	    i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
					i0_offset+seq_pos(i0,aln->qlrev,0), sp1, sp1a, sq, 
					i1_annot, annot1_p->n_annot, s_annot1_arr_p,
					&ann_comment, annot_stack, &have_push_features, &v_delta,
					&d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	    if (sq[ap1[i1]] != *sp1) {
	      t_spa = align_type(itmp, *sp0, *sp1, 0, NULL, ppst->pam_x_id_sim);

	      comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			  i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			  sq[ap1[i1]], sim_sym[t_spa], ann_comment,
			  annot_var_dyn, 1, DP_FULL_FMT);
	    }
	  }
	  d1_score += ppst->gshift;
	  d1_score += itmp;
	  prev_match = 1;
	}
	sp0a++; sp1a++;
      }

      *spa = align_type(itmp, *sp0, *sp1, 0, aln, ppst->pam_x_id_sim);
      d1_alen++;
      if (*spa == M_IDENT) {d1_ident++;}

      if (cumm_seq_score) *i_spa++ = itmp;

      /* now we have done all the ?modified identity checks, display
	 potential site annotations */
      if (have_ann && have_push_features) {
	display_push_features(annot_stack, annot_var_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			      sim_sym[*spa], 
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
	have_push_features = 0;
      }

      i0 += 3;
      i1++;

      sp0++; sp1++; spa++;
      lenc++;
      break;
    case 5:	/* codon insertion */
      if (have_ann) {
	*sp1a++ = *sp0a++ = ' ';
      }

      if (cumm_seq_score) {
	if (prev_match) *i_spa = ppst->gdelval;
	*i_spa++ = ppst->ggapval;
      }

      if (prev_match) d1_score += ppst->gdelval;
      d1_score += ppst->ggapval;

      prev_match = 0;

      *sp0++ = sq[ap0[i0]];
      i0 += 3;
      *sp1++ = '-';
      *spa++ = M_DEL;
      lenc++;
      ngap_p++;
      break;
    }
  }

  /* done with alignment loop */

  if (have_ann) {
    *sp0a = *sp1a = '\0';
    if (s_annot1_arr_p) {
      have_push_features = 0;

      if (s_annot1_arr_p && i1_left_end > 0) {
	close_annot_match(-1, annot_stack, &have_push_features,
			  &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,
			  0);
      }

      if (have_push_features) {
	display_push_features(annot_stack, annot_var_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), *sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), *sp1,
			      sim_sym[*spa], 
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
	have_push_features = 0;
      }
    }
  }
  *spa = '\0';

#ifndef TFAST
  aln->amax0 = i0;
  aln->amax1 = i1;
  aln->ngap_q = ngap_d;
  aln->ngap_l = ngap_p;
#else
  aln->amax1 = i0;
  aln->amax0 = i1;
  aln->ngap_q = ngap_p;
  aln->ngap_l = ngap_d;
#endif
  aln->calc_last_set = 1;

  aln->nfs = nfs;

  *score_delta = v_delta;

  if (have_ann) {
    *sp0a = *sp1a = '\0';
    have_push_features = 0;
    /* check for left ends after alignment */
    if (annot1_p && i1_left_end > 0) {
      close_annot_match(-1, annot_stack, &have_push_features,
			&d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,
			0);
    }

    if (have_push_features) {
      display_push_features(annot_stack, annot_var_dyn,
			    i0_offset + seq_pos(aln->amax0-1,aln->qlrev,0), *sp0, 
			    i1_offset + seq_pos(aln->amax1-1,aln->llrev,0), *sp1,
			    sim_sym[*spa],
			    a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, DP_FULL_FMT);
    }

    free_stack(annot_stack);
  }

  if (lenc < 0) lenc = 1;
  *nc = lenc;
/*	now we have the middle, get the right end */
  return lenc+not_c;
}

void
calc_astruct(struct a_struct *aln_p, struct a_res_str *a_res_p, struct f_struct *f_str) {

  aln_p->calc_last_set = 0;

#ifndef TFAST	/* FASTX */
  aln_p->amin1 = a_res_p->min0;	/* prot */
  aln_p->amin0 = a_res_p->min1;	/* DNA */
  aln_p->amax1 = a_res_p->max0;	/* prot */
  aln_p->amax0 = a_res_p->max1;	/* DNA */
#else		/* TFASTX */
  aln_p->amin0 = a_res_p->min0;	/* DNA */
  aln_p->amin1 = a_res_p->min1;	/* prot */
  aln_p->amax0 = a_res_p->max0;	/* DNA */
  aln_p->amax1 = a_res_p->max1;	/* prot */
#endif
}

/* build an array of match/ins/del - length strings */

/* modified 10-June-2014 to distinguish matches from mismatches, op=1
   (previously unused) indicates an aligned non-identity */

/* op_codes are:  0 - aa insertion
   		  1 - (now) aligned non-identity
   		  2 - -1 frameshift
   		  3 - aligned identity
   		  4 - +1 frameshift
   		  5 - codon insertion
*/

static struct update_code_str *
init_update_data(show_code) {

  struct update_code_str *update_data_p;

  if ((update_data_p = (struct update_code_str *)calloc(1,sizeof(struct update_code_str)))==NULL) {
    fprintf(stderr,"*** error [%s:%d] - init_update_data(): cannot allocate update_code_str\n",
	      __FILE__, __LINE__);
    return NULL;
  }

  update_data_p->p_op_cnt = 0;
  update_data_p->show_code = show_code;

  if ((show_code & SHOW_CODE_MASK) == SHOW_CODE_CIGAR) {
    update_data_p->op_map = cigar_code;
    update_data_p->cigar_order = 1;
  }
  else {
    update_data_p->op_map = ori_code;
    update_data_p->cigar_order = 0;
  }

  if ((show_code & SHOW_CODE_EXT) == SHOW_CODE_EXT) {
    update_data_p->show_ext = 1;
  }
  else {
    update_data_p->show_ext = 0;
  }

  return update_data_p;
}

static void
close_update_data(char *al_str, int al_str_max, 
		  struct update_code_str *up_dp) {
  char tmp_cnt[MAX_SSTR];

  if (!up_dp) return;
  sprintf_code(tmp_cnt,up_dp, up_dp->p_op_idx, up_dp->p_op_cnt);
  strncat(al_str,tmp_cnt,al_str_max);

  free(up_dp);
}

/* update_indel_code() has been modified to work more correctly with
   ggsearch/glsearch, which, because alignments can start with either
   insertions or deletions, can produce an initial code of "0=".  When
   that happens, it is ignored and no code is added.

   *al_str - alignment string [al_str_max] - not dynamic
   op -- encoded operation, currently 0=match, 1-delete, 2-insert, 3-term-match, 4-mismatch
   op_cnt -- length of run
   show_code -- SHOW_CODE_CIGAR uses cigar_code, otherwise legacy
*/

/* update_indel_code() is called for insertions and deletions
   update_match_code() is called for every match
*/

static void
sprintf_code(char *tmp_str, struct update_code_str *up_dp, int op_idx, int op_cnt) {

  if (op_cnt == 0) return;

  if (up_dp->cigar_order) {
    sprintf(tmp_str,"%d%c",op_cnt,up_dp->op_map[op_idx]);
  }
  else {
    sprintf(tmp_str,"%c%d",up_dp->op_map[op_idx],op_cnt);
  }
}

static void
update_code(char *al_str, int al_str_max, 
	    struct update_code_str *up_dp, int op, 
	    int sim_code,  unsigned char sp0, unsigned char sp1)
{
  char tmp_cnt[MAX_SSTR];

  /* there are two kinds of "op's", one time and accumulating */
  /* op == 2, 4 are one-time: */

  switch (op) {
  case 2:
  case 4:
    sprintf_code(tmp_cnt,up_dp, up_dp->p_op_idx,up_dp->p_op_cnt);
    strncat(al_str,tmp_cnt,al_str_max);
    sprintf_code(tmp_cnt,up_dp, op, 1);
    strncat(al_str,tmp_cnt,al_str_max);
    up_dp->p_op_cnt = 0;
    break;
  case 0:
  case 5:
    if (op == up_dp->p_op_idx) {
      up_dp->p_op_cnt++;
    }
    else {
      sprintf_code(tmp_cnt,up_dp, up_dp->p_op_idx,up_dp->p_op_cnt);
      strncat(al_str,tmp_cnt,al_str_max);
      up_dp->p_op_idx = op;
      up_dp->p_op_cnt = 1;
    }
    break;
  case 1:
  case 3:
    if (sp0 != '*' && sp1 != '*') {	/* default case, not termination */
      if (up_dp->show_ext) {
	if (sim_code != M_IDENT) { op = 1;}
      }
    }
    else {	/* have a termination codon, output for !SHOW_CODE_CIGAR */
      if (!up_dp->cigar_order) {
	if (sp0 == '*' || sp1 == '*') { op = 6;}
      }
      else if (up_dp->show_ext && (sp0 != sp1)) { op = 1;}
    }

    if (up_dp->p_op_cnt == 0) {
      up_dp->p_op_idx = op;
      up_dp->p_op_cnt = 1;
    }
    else if (op != up_dp->p_op_idx) {
      sprintf_code(tmp_cnt,up_dp, up_dp->p_op_idx,up_dp->p_op_cnt);
      strncat(al_str,tmp_cnt,al_str_max);
      up_dp->p_op_idx = op;
      up_dp->p_op_cnt = 1;
    }
    else {
      up_dp->p_op_cnt++;
    }
    break;
  }
  return;
}

int calc_code(const unsigned char *aa0, int n0,
	      const unsigned char *aa1, int n1,
	      struct a_struct *aln,
	      struct a_res_str *a_res, 
	      struct pstruct *ppst,
	      char *al_str, int al_str_n, 
	      const unsigned char *ann_arr,
	      const unsigned char *aa0a,
	      const struct annot_str *annot0_p,
	      const unsigned char *aa1a, 
	      const struct annot_str *annot1_p,
	      struct dyn_string_str *annot_code_dyn,
	      int *score_delta,
	      struct f_struct *f_str,
	      void *pstat_void,
	      int display_code)
{
  int i0, i1, i, j;
  int lenc, not_c, itmp, ngap_p, ngap_d, nfs;
  char op_char[10], ann_ch0, ann_ch1;
  char sp0, sp1;
  struct update_code_str *update_data_p;
  unsigned char *sq;
  const unsigned char *ap0, *ap1, *ap1a;
  int *rp, *rpmax;

  int have_ann = 0;
  char tmp_astr[MAX_STR];
  int sim_code, t_spa;
  int show_code, annot_fmt;
  char *sim_sym= aln_map_sym[MX_ACC];
  int aa1c;
  /* variables for variant changes */
  char tmp_str[MAX_SSTR];

  /* variables for variant changes, regions */
  void *annot_stack;
  struct annot_entry **s_annot1_arr_p;
  int  i1_annot, v_delta, v_tmp;
  long i0_offset, i1_offset;
  int have_push_features, prev_match;

  long i1_left_end;
  int d1_score, d1_ident, d1_alen;
  struct domfeat_link *left_domain_list1;
  
  *score_delta = 0;

  show_code = (display_code & (SHOW_CODE_MASK + SHOW_CODE_EXT));
  annot_fmt = 2;
  if (display_code & SHOW_ANNOT_FULL) {
    annot_fmt = 1;
  }

  if (ppst->ext_sq_set) {sq = ppst->sqx;}
  else {sq = ppst->sq;}

#ifndef TFAST	/* FASTX */
  i0_offset = aln->q_offset;
  i1_offset = aln->l_offset;

  aln->amin1 = a_res->min0;	/* prot, i1 */
  aln->amin0 = a_res->min1;	/* DNA,  i0 */

  ap0 = f_str->aa0y;
  ap1 = aa1;
  have_ann = (ann_arr[0] != '\0' && aa1a != NULL);
  ap1a = aa1a;
#else		/* TFASTX */
  i1_offset = aln->q_offset;
  i0_offset = aln->l_offset;

  aln->amin0 = a_res->min0;	/* DNA,  i1 */
  aln->amin1 = a_res->min1;	/* prot, i0 */

  ap1 = aa0;
  /* with fx_malign(), there is no guarantee that we have a valid f_str->aa1y, so make one */
  pre_cons(aa1,n1,aln->frame, f_str);
  ap0 = f_str->aa1y;

  have_ann = (ann_arr[0] != '\0' && aa0a != NULL);
  ap1a = aa0a;
#endif

  rp = a_res->res;
  rpmax = &a_res->res[a_res->nres];

  lenc = not_c = aln->nident = aln->nmismatch = aln->nsim = aln->npos = ngap_p = ngap_d = nfs = 0;
  
  update_data_p = init_update_data(show_code);

  i0 = a_res->min1;
  i1 = a_res->min0;

  v_delta = 0;
  i1_annot = 0;
  s_annot1_arr_p = NULL;
  have_push_features = prev_match = 0;

  i1_left_end = 0;
  left_domain_list1 = NULL;
  d1_score = d1_ident = d1_alen = 0;

  if (have_ann) {
    
    if (annot0_p || annot1_p) annot_stack = init_stack(64,64);
    if (annot1_p && annot1_p->n_annot > 0) {
      s_annot1_arr_p = annot1_p->s_annot_arr_p;
      while (i1_annot < annot1_p->n_annot) {
	if (s_annot1_arr_p[i1_annot]->pos >= i1+i1_offset) {break;}
	if (s_annot1_arr_p[i1_annot]->end < i1+i1_offset) {i1_annot++; continue;}

	if (s_annot1_arr_p[i1_annot]->label == '-') {
	  process_annot_match(&itmp, NULL, i1_offset+seq_pos(i1,aln->llrev,0), i0_offset + seq_pos(i0,aln->qlrev,0),
			      &sp1, NULL, sq, s_annot1_arr_p[i1_annot],  NULL, 
			      annot_stack, &have_push_features, &v_delta,
			      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end, 0);
	}
	i1_annot++;
      }
    }
  }

  while (rp < rpmax) {
    switch (*rp++) {
    case 0: 	/* aa insertion */
      sim_code = 5; /* indel code */
      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 0, sim_code,'-','-');

      if (s_annot1_arr_p) {
	if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos) {
	  i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				      i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				      i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				      NULL, annot_stack, &have_push_features, &v_delta, 
				      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);
	}

	if (prev_match) d1_score += ppst->gdelval;
	d1_score += ppst->ggapval;
	d1_alen++;
	prev_match = 0;
      }

      /* check for an annotation */
      if (have_ann && !(ann_arr[ap1a[i1]] == ' ' || ann_arr[ap1a[i1]]=='[' || ann_arr[ap1a[i1]]==']')) {
#ifndef TFAST
	sprintf(tmp_astr, "|%ld:%ld:X%c:%c%c%c",
		i0_offset+seq_pos(i0,aln->qlrev,0)+1,i1_offset+seq_pos(i1,aln->llrev,0)+1,ann_arr[ap1a[i1]],sim_sym[sim_code],sp0,sp1);
#else
	sprintf(tmp_astr, "|%ld:%ld:%cX:%c%c%c",
		i0_offset+seq_pos(i1,aln->llrev,0)+1,i1_offset+seq_pos(i0,aln->qlrev,0)+1,ann_arr[ap1a[i1]],sim_sym[sim_code],sp0,sp1);
#endif
	/* SAFE_STRNCAT(annot_code_s, tmp_astr, n_annot_code_s); */
	dyn_strcat(annot_code_dyn, tmp_astr);
      }

      if (s_annot1_arr_p && have_push_features) {
	display_push_features(annot_stack, annot_code_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
			      sim_sym[sim_code],
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, annot_fmt);
	have_push_features = 0;
      }

      i1++;
      lenc++;
      ngap_d++;
      break;
    case 2:	/* -1 frameshift */
      /* close previous run */
      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 2, sim_code,'-','-');

      nfs++;
      i0 -= 1;
      not_c++;

      aa1c = ap1[i1];
      itmp = ppst->pam2[0][ap0[i0]][aa1c];
      sp0 = sq[aa0[i0]];
      sp1 = sq[aa1c];

      /* variant annot_p annotations can cause substitution */
      if (s_annot1_arr_p) {
	if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	  i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				      i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				      i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				      NULL, annot_stack, &have_push_features, &v_delta, 
				      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);
	}

	if (sq[aa1c] != sp1) {
	  t_spa = align_type(itmp, sp0, sp1, 0, NULL, ppst->pam_x_id_sim);

	  comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
		      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
		      sq[aa1c], sim_sym[t_spa], NULL, annot_code_dyn,
		      1,annot_fmt);
	}

	d1_score += ppst->gshift;
	d1_score += itmp;
	prev_match = 1;
      }

      sim_code = align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);

      d1_alen++;
      if (sim_code == M_IDENT) {d1_ident++;}

      /* check for an annotation */
      if (have_ann && !(ann_arr[ap1a[i1]] == ' ' || ann_arr[ap1a[i1]]=='[' || ann_arr[ap1a[i1]]==']')) {
#ifndef TFAST
	sprintf(tmp_astr, "|X%c:%ld%c%c%ld%c",
		ann_arr[ap1a[i1]],i0_offset+seq_pos(i0,aln->qlrev,0)+1,sp0,sim_sym[sim_code],i1_offset+seq_pos(i1,aln->llrev,0)+1,sp1);
#else
	sprintf(tmp_astr, "|%cX:%ld%c%c%ld%c",
		ann_arr[ap1a[i1]],i0_offset+seq_pos(i1,aln->llrev,0)+1,sp0,sim_sym[sim_code],i1_offset+seq_pos(i0,aln->qlrev,0)+1,sp1);

#endif
	/* SAFE_STRNCAT(annot_code_s, tmp_astr, n_annot_code_s); */
	dyn_strcat(annot_code_dyn, tmp_astr);
      }

      if (s_annot1_arr_p && have_push_features) {
	display_push_features(annot_stack, annot_code_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
			      sim_sym[sim_code],
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, annot_fmt);
	have_push_features = 0;
      }

      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 3, sim_code,sp0,sp1);

      if (sim_code == M_IDENT) {
	aln->nident++;
      }
      else {
	aln->nmismatch++;
      }

      i0 += 3;
      i1++;
      lenc++;
      break;
    case 3:	/* codon/aa match */
      aa1c = ap1[i1];
      itmp = ppst->pam2[0][ap0[i0]][aa1c];
      sp0 = sq[ap0[i0]];
      sp1 = sq[aa1c];

      /* variant annot1_p annotations can cause substitution */
      if (s_annot1_arr_p) {
	if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	  i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				      i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				      i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				      NULL, annot_stack, &have_push_features, &v_delta,
				      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);
	}

	if (sq[aa1c] != sp1) {
	  t_spa = align_type(itmp, sp0, sp1, 0, NULL, ppst->pam_x_id_sim);

	  comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
		      i1_offset+seq_pos(i1,aln->llrev,0), sp1, sq[aa1c],
		      sim_sym[t_spa], NULL, annot_code_dyn,1,annot_fmt);
	}

	d1_score += itmp;
	prev_match = 1;
      }

      sim_code = align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);
      d1_alen++;
      if (sim_code == M_IDENT) {d1_ident++;}

      /* check for an annotation */
      if (have_ann && !(ann_arr[ap1a[i1]] == ' ' || ann_arr[ap1a[i1]]=='[' || ann_arr[ap1a[i1]]==']')) {
#ifndef TFAST
	sprintf(tmp_astr, "|X%c:%ld%c%c%ld%c",
		ann_arr[ap1a[i1]],i0_offset+seq_pos(i0,aln->qlrev,0)+1,sp0,sim_sym[sim_code],i1_offset+seq_pos(i1,aln->llrev,0)+1,sp1);
#else
	sprintf(tmp_astr, "|%cX:%ld%c%c%ld%c",
		ann_arr[ap1a[i1]],i0_offset+seq_pos(i1,aln->llrev,0)+1,sp0,sim_sym[sim_code],i1_offset+seq_pos(i0,aln->qlrev,0)+1,sp1);

#endif
	/* SAFE_STRNCAT(annot_code_s, tmp_astr, n_annot_code_s); */
	dyn_strcat(annot_code_dyn, tmp_astr);
      }

      if (s_annot1_arr_p && have_push_features) {
	display_push_features(annot_stack, annot_code_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
			      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
			      sim_sym[sim_code],
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, annot_fmt);
	have_push_features = 0;
      }

      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 3, sim_code,sp0,sp1);

      i0 += 3;
      i1++;
      lenc++;
      break;
    case 4:	/* +1 frameshift */
      /* finish previous run */
      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 4, sim_code,'-','-');
      /* mark frameshift */

      nfs++;
      i0 += 1;
      not_c++;

      aa1c = ap1[i1];
      itmp = ppst->pam2[0][ap0[i0]][aa1c];
      sp0 = sq[ap0[i0]];
      sp1 = sq[aa1c];

      /* variant annot1_p annotations can cause substitution */
      if (s_annot1_arr_p) {
	if (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end) {
	  i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				      i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				      i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				      NULL, annot_stack, &have_push_features, &v_delta,
				      &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);
	}

	if (sq[aa1c] != sp1) {
	  t_spa = align_type(itmp, sp0, sp1, 0, NULL, ppst->pam_x_id_sim);

	  comment_var(i0_offset+seq_pos(i0,aln->qlrev,0), sp0,
		      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
		      sq[aa1c], sim_sym[t_spa], NULL,
		      annot_code_dyn,1,annot_fmt);
	}

	d1_score += itmp;
	prev_match = 1;
      }

      sim_code = align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);
      d1_alen++;
      if (sim_code == M_IDENT) {d1_ident++;}

      /* check for an annotation */
      if (have_ann && !(ann_arr[ap1a[i1]] == ' ' || ann_arr[ap1a[i1]]=='[' || ann_arr[ap1a[i1]]==']')) {
#ifndef TFAST
	sprintf(tmp_astr, "|%ld:%ld:X%c:%c%c%c",
		i0_offset+seq_pos(i0,aln->qlrev,0)+1,i1_offset+seq_pos(i1,aln->llrev,0)+1,
		ann_arr[ap1a[i1]],sim_sym[sim_code],sp0,sp1);
#else
	sprintf(tmp_astr, "|%ld:%ld:%cX:%c%c%c",
		i0_offset+seq_pos(i1,aln->llrev,0)+1,i1_offset+seq_pos(i0,aln->qlrev,0)+1,
		ann_arr[ap1a[i1]],sim_sym[sim_code],sp0,sp1);

#endif
	/* SAFE_STRNCAT(annot_code_s, tmp_astr, n_annot_code_s); */
	dyn_strcat(annot_code_dyn, tmp_astr);
      }
	  
      if (s_annot1_arr_p && have_push_features) {
	display_push_features(annot_stack, annot_code_dyn,
			      i0_offset+seq_pos(i0,aln->qlrev,0), sp0, 
			      i1_offset+seq_pos(i1,aln->llrev,0), sp1,
			      sim_sym[sim_code], 
			      a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, annot_fmt);
	have_push_features = 0;
      }

      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 3, sim_code,sp0,sp1);

      /* start next match/mismatch run */
      if (sim_code == M_IDENT) {
	aln->nident++;
      }
      else {
	aln->nmismatch++;
      }

      i0 += 3;
      i1++;
      lenc++;
      break;
    case 5:	/* codon insertion */
      sim_code = 5;
      update_code(al_str, al_str_n-strlen(al_str), update_data_p, 5, sim_code,'-','-');

      if (prev_match) d1_score += ppst->gdelval;
      d1_score += ppst->ggapval;
      d1_alen++;
      prev_match = 0;

      i0 += 3;
      lenc++;
      ngap_p++;
      break;
    }
  }

  close_update_data(al_str, al_str_n-strlen(al_str), update_data_p);

#ifndef TFAST
  aln->amax0 = i0;
  aln->amax1 = i1;
  aln->ngap_q = ngap_d;
  aln->ngap_l = ngap_p;
#else
  aln->amax1 = i0;
  aln->amax0 = i1;
  aln->ngap_q = ngap_p;
  aln->ngap_l = ngap_d;
#endif
  aln->calc_last_set = 1;

  aln->nfs = nfs;

  if (lenc < 0) lenc = 1;

  if (have_ann) {
    have_push_features = 0;
    if (s_annot1_arr_p) {
      /* also check for regions after alignment */
      while (i1_annot < annot1_p->n_annot && s_annot1_arr_p[i1_annot]->pos < i1_offset+n1) {
	if (s_annot1_arr_p[i1_annot]->label == '[') break;
	if (s_annot1_arr_p[i1_annot]->label == ']') {
	  push_stack(annot_stack, s_annot1_arr_p[i1_annot]);
	  have_push_features = 1;
	}
	i1_annot++;
      }
    }

    if (have_push_features) {
      display_push_features(annot_stack, annot_code_dyn,
			    i0_offset+a_res->max0-1, sp0,
			    i1_offset+a_res->max1-1, sp1,
			    sim_sym[sim_code], 
			    a_res->rst.score[ppst->score_ix], a_res->rst.comp, n0, n1, pstat_void, annot_fmt);
    }
  }

  if (annot0_p || s_annot1_arr_p) free_stack(annot_stack);
  *score_delta = v_delta;

  return lenc;
}

int calc_id(const unsigned char *aa0, int n0,
	    const unsigned char *aa1, int n1,
	    struct a_struct *aln,
	    struct a_res_str *a_res, 
	    struct pstruct *ppst,
	    const struct annot_str *annot0_p,
	    const struct annot_str *annot1_p,
	    int *score_delta,
	    struct dyn_string_str *annot_var_dyn,
	    struct f_struct *f_str)
{
  int i0, i1, i, j;
  int lenc, not_c, ngap_p, ngap_d, nfs;
  char sp0, sp1;
  char tmp_str[MAX_SSTR];
  unsigned char *sq;
  const unsigned char *ap0, *ap1;
  int *rp, *rpmax;

  int aa1c;
  /* variables for variant changes */
  struct annot_entry **s_annot1_arr_p;
  int  itmp, i1_annot, v_delta, v_tmp;
  long i0_offset, i1_offset;

  long i1_left_end;
  int d1_score, d1_ident, d1_alen;
  struct domfeat_link *left_domain_list1;

  *score_delta = 0;
  i1_left_end = -1;
  left_domain_list1 = NULL;

  NULL_dyn_string(annot_var_dyn);

  if (ppst->ext_sq_set) {sq = ppst->sqx;}
  else {sq = ppst->sq;}

#ifndef TFAST	/* FASTX */
  aln->amin1 = a_res->min0;	/* prot */
  aln->amin0 = a_res->min1;	/* DNA */

  i0_offset = aln->q_offset;
  i1_offset = aln->l_offset;

  ap0 = f_str->aa0y;
  ap1 = aa1;
#else	/* TFASTX */
  aln->amin0 = a_res->min0;	/* DNA */
  aln->amin1 = a_res->min1;	/* prot */

  i1_offset = aln->q_offset;
  i0_offset = aln->l_offset;

  ap1 = aa0;
  /* with fx_malign(), there is no guarantee that we have a valid f_str->aa1y, so make one */
  pre_cons(aa1,n1,aln->frame, f_str);
  ap0 = f_str->aa1y;
#endif

  rp = a_res->res;
  rpmax = &a_res->res[a_res->nres];

  lenc = not_c = aln->nident = aln->nmismatch = aln->nsim = aln->npos = ngap_p = ngap_d = nfs = 0;
  i0 = a_res->min1;
  i1 = a_res->min0;

  v_delta = 0;
  i1_annot = 0;

  s_annot1_arr_p = NULL;
  if (annot1_p && annot1_p->n_annot > 0) s_annot1_arr_p = annot1_p->s_annot_arr_p;

  while (rp < rpmax) {
    /*    fprintf(stderr,"%d %d %d (%c) %d (%c)\n"
	  ,(int)(rp-res),*rp,i0,sq[ap0[i0]],i1,sq[ap1[i1]]);
    */
    switch (*rp++) {
    case 0: 	/* aa insertion */
      i1++;
      lenc++;
      ngap_d++;
      break;
    case 2:	/* -1 frameshift */
      nfs++;
      i0 -= 1;
      not_c++;

      /* then check for v_delta after the frameshift */

      itmp = ppst->pam2[0][ap0[i0]][ap1[i1]];

      sp0 = sq[ap0[i0]];
      sp1 = sq[ap1[i1]];

      if (s_annot1_arr_p && (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end)) {
	i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				    i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				    i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				    NULL, NULL, NULL, &v_delta,
				    &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	if (sq[ap1[i1]] != sp1) {
	  sprintf(tmp_str,"%c%d%c;",sq[ap1[i1]],i1+1,sp1);
	  /* SAFE_STRNCAT(annot_var_s,tmp_str,n_annot_var_s); */
	  dyn_strcat(annot_var_dyn, tmp_str);
	}
      }

      align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);

      i0 += 3;
      i1++;

      lenc++;
      break;
    case 3:	/* codon/aa match */

      aa1c = ap1[i1];
      itmp = ppst->pam2[0][ap0[i0]][aa1c];
      sp0 = sq[ap0[i0]];
      sp1 = sq[ap1[i1]];

      if (s_annot1_arr_p && (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end)) {
	i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				    i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				    i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				    NULL, NULL, NULL, &v_delta,
				    &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	if (sq[ap1[i1]] != sp1) {
	  sprintf(tmp_str,"%c%d%c;",sq[ap1[i1]],i1+1,sp1);
	  /* SAFE_STRNCAT(annot_var_s,tmp_str,n_annot_var_s); */
	  dyn_strcat(annot_var_dyn, tmp_str);
	}
      }

      align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);

      i0 += 3;
      i1++;

      lenc++;
      break;
    case 4:	/* +1 frameshift */
      nfs++;
      i0 += 1;
      not_c++;


      itmp = ppst->pam2[0][ap0[i0]][ap1[i1]];

      sp0 = sq[ap0[i0]];
      sp1 = sq[ap1[i1]];

      if (s_annot1_arr_p && (i1+i1_offset == s_annot1_arr_p[i1_annot]->pos || i1+i1_offset == i1_left_end)) {
	i1_annot = next_annot_match(&itmp, ppst->pam2[0][ap0[i0]], i1_offset+seq_pos(i1,aln->llrev,0),
				    i0_offset+seq_pos(i0,aln->qlrev,0), &sp1, NULL, sq,
				    i1_annot, annot1_p->n_annot, s_annot1_arr_p,
				    NULL, NULL, NULL, &v_delta,
				    &d1_score, &d1_ident, &d1_alen, &left_domain_list1, &i1_left_end,0);

	if (sq[ap1[i1]] != sp1) {
	  sprintf(tmp_str,"%c%d%c;",sq[ap1[i1]],i1+1,sp1);
	  /* SAFE_STRNCAT(annot_var_s,tmp_str,n_annot_var_s); */
	  dyn_strcat(annot_var_dyn, tmp_str);
	}
      }

      align_type(itmp, sp0, sp1, 0, aln, ppst->pam_x_id_sim);

      i0 += 3;
      i1++;
      lenc++;

      break;
    case 5:	/* codon insertion */
      i0 += 3;
      lenc++;
      ngap_p++;
      break;
    }
  }

#ifndef TFAST
  aln->amax0 = i0;
  aln->amax1 = i1;
  aln->ngap_q = ngap_d;
  aln->ngap_l = ngap_p;
#else
  aln->amax1 = i0;
  aln->amax0 = i1;
  aln->ngap_q = ngap_p;
  aln->ngap_l = ngap_d;
#endif
  aln->calc_last_set = 1;

  aln->nfs = nfs;

  *score_delta = v_delta;

  if (lenc < 0) lenc = 1;
/*	now we have the middle, get the right end */
  return lenc;
}
