/*	dispn.c	associated subroutines for matching sequences */

/* $Id: c_dispn.c 1124 2013-03-13 20:24:57Z wrp $ */
/* $Revision: 1124 $  */

/* copyright (c) 1988, 1995, 1996, 2008, 2013, 2014 by William R. Pearson and 
   The Rector and Visitors 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. 
*/

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

#include "defs.h"
#include "structs.h"
#include "param.h"

#define XTERNAL

#define YES 1
#define NO 0

#define MAXOUT 201

/* the seqca[] array has the following codes:
   0 - no alignment symbol
   1 - align; pam < 0
   2 - align; pam == 0
   3 - align; pam > 0
   4 - align; ident
   5 - align; del

   the map_sym arrays determine the value to be displayed with each
   type of aligned residue
*/

#include "a_mark.h"

void
discons(FILE *fd, const struct mngmsg *m_msp, 
	char *seqc0, char *seqc0a, 
	char *seqc1, char *seqc1a,
	char *seqca, int *cumm_seq_score, int nc,
	int n0, int n1, char *name0, char *name1, int nml,
	struct a_struct *aln)
{
  char line[3][MAXOUT];	/* alignment lines [0,2], similarity code [1] */
  char cline[2][MAXOUT+10], *clinep[2];	/* coordinate line */
  int il, i, lend, loff, id, tot_score;
  int del0, del1, ic, ll0, ll1, ll01, cl0, cl1, rl0, rl1;
  int ic_save;
  char *map_sym_p;
  int l_llen;
  int ioff0, ioff00, ioff1, ioff10;
  long q_start, q_end, qf_flag, s_start, s_end, sf_flag;
  long qqoff, lloff;
  int llsgn, llfact, qlsgn, qlfact, qfx0, qfxn, lfx0, lfxn;
  long s_digit_max, q_digit_max;
  char digit_tmp[32];
  int digit_len;
  int have_res;
  char *name01;
  char blank[32], afmt[32], afmt0[32];
  int disp_dna_align = ((m_msp->qdnaseq>0) && (m_msp->ldb_info.ldnaseq > 0));

  memset(blank,' ',sizeof(blank)-1);
  blank[sizeof(blank)-1]='\0';

  clinep[0]=cline[0]+1;
  clinep[1]=cline[1]+1;

  if (aln->qlfact == 0) {qlfact = 1;}
  else qlfact = aln->qlfact;
  if (aln->qlrev == 1) {
    qlsgn = -1;
    qfx0 = 0;
    qfxn = 1;
  }
  else {
    qlsgn = 1;
    qfx0 = 1;
    qfxn = 0;
  }

  if (aln->llfact == 0) {llfact = 1;}
  else llfact = aln->llfact;

  if (aln->llrev == 1) {
    llsgn = -1;
    lfx0 = 0;
    lfxn = 1;
  }
  else {
    llsgn = 1;
    lfx0 = 1;
    lfxn = 0;
  }

  l_llen = aln->llen;
  if ((m_msp->markx & MX_M9SUMM) && m_msp->show_code != 1) { l_llen += 40; }

  if ((m_msp->markx & MX_ATYPE)==2) name01=name1;
  else name01 = "\0";

  ioff0=aln->smin0;
  ioff00 = ioff0;
  ioff1=aln->smin1;
  ioff10 = ioff1;
  
  if (m_msp->markx& MX_AMAP && (m_msp->markx & MX_ATYPE)==7) return;

  /* set *map_sym_p to correct match symbol */
  map_sym_p = aln_map_sym[MX_A0];
  if ((m_msp->markx&MX_ATYPE)==1) {map_sym_p = aln_map_sym[MX_A1];}
  else if ((m_msp->markx&MX_ATYPE)==2) {map_sym_p = aln_map_sym[MX_A2];}
  else if (m_msp->markx&MX_M10FORM) { map_sym_p = aln_map_sym[MX_A10]; }
  if (m_msp->markx & MX_MBLAST) { map_sym_p = aln_map_sym[MX_ABLAST];}

  if (m_msp->markx & MX_ASEP) {
    fprintf(fd,">%s ..\n",name0);
    for (i=0; i<nc && seqc0[i]; i++) {
   /* if (seqc0[i]=='-') fputc('.',fd); else */
      fputc(seqc0[i],fd);
      if (i%50 == 49) fputc('\n',fd);
    }
    if ((i-1)%50 != 49) fputc('\n',fd);
    fprintf(fd,">%s ..\n",name1);
    for (i=0; i<nc && seqc1[i]; i++) {
    /* if (seqc1[i]=='-') fputc('.',fd); else */
      fputc(seqc1[i],fd);
      if (i%50 == 49) fputc('\n',fd);
    }
    if ((i-1)%50 != 49) fputc('\n',fd);
    return;
  }

  if (m_msp->markx & MX_M10FORM) {
    fprintf(fd,">%s ..\n",name0);
    fprintf(fd,"; sq_len: %d\n",n0);
    fprintf(fd,"; sq_offset: %ld\n",aln->q_offset+1);
    fprintf(fd,"; sq_type: %c\n",m_msp->sqtype[0]);
    fprintf(fd,"; al_start: %ld\n",aln->d_start0);
    fprintf(fd,"; al_stop: %ld\n",aln->d_stop0);
    /* in the past, this al_display_start does not include sq0off */
    fprintf(fd,"; al_display_start: %ld\n",
	    aln->q_offset+qlsgn*ioff0*aln->llmult+qfx0);

    have_res = 0;
    for (i=0; i<nc && seqc0[i]; i++) {
      if (!have_res && seqc0[i]==' ') fputc('-',fd);
      else if (seqc0[i]==' ') break;
      else {
	have_res = 1;
	fputc(seqc0[i],fd);
      }
      if (i%50 == 49) fputc('\n',fd);
    }
    if ((i-1)%50!=49 || seqc0[i-1]==' ') fputc('\n',fd);
    fprintf(fd,">%s ..\n",name1);
    fprintf(fd,"; sq_len: %d\n",n1);
    fprintf(fd,"; sq_offset: %ld\n",aln->l_offset+1);
    fprintf(fd,"; sq_type: %c\n",m_msp->sqtype[0]);
    fprintf(fd,"; al_start: %ld\n",aln->d_start1);
    fprintf(fd,"; al_stop: %ld\n",aln->d_stop1);
    /* in the past, this al_display_start does not include sq1off */
    fprintf(fd,"; al_display_start: %ld\n",aln->l_offset+llsgn*ioff1+lfx0);

    have_res = 0;
    for (i=0; i<nc && seqc1[i]; i++) {
      if (!have_res && seqc1[i]==' ') fputc('-',fd);
      else if (seqc1[i]==' ') break;
      else {
	have_res = 1;
	fputc(seqc1[i],fd);
      }
      if (i%50 == 49) fputc('\n',fd);
    }
    if ((i-1)%50!=49 || seqc1[i-1]==' ') fputc('\n',fd);
#ifdef M10_CONS
    fprintf(fd,"; al_cons:\n");
    for (i=0,del0=0,id=ioff0; id-del0<aln->amax0 && i < nc; i++,id++) {
      if (seqc0[i] == '\0' || seqc1[i] == '\0') break;
      if (seqc0[i]=='-' || seqc0[i]==' ' || seqc0[i]=='\\') del0++;
      else if (seqc0[i]=='/') del0++;
      if (id-del0<aln->amin0) fputc(' ',fd);
      else if (seqc0[i]=='-'||seqc1[i]=='-') fputc('-',fd);
      else fputc(map_sym_p[seqca[i]],fd);

      if (i%50 == 49) fputc('\n',fd);
    }
    if ((i-1)%50!=49 || seqc1[i-1]==' ') fputc('\n',fd);
#endif
    return;
  }
  else if (m_msp->markx & MX_RES_ALIGN_SCORE) {
    have_res = 0;
    tot_score = 0;
    del0 = del1 = 0;
    fprintf(fd,">%s\t%s\t%s0\t%s1\tscore\ttotal\n",
	    name0,name1,m_msp->sqnam,m_msp->sqnam);
    for (ic=0; ic<nc; ic++, ioff0++, ioff1++) {
      if (seqc0[ic] == ' ' || seqc0[ic] == '-' || seqc0[ic] == '/' || seqc0[ic] == '\\') {
	del0++;
      }
      if (seqc1[ic] == ' ' || seqc1[ic] == '-' || seqc1[ic] == '/' || seqc1[ic] == '\\') {
	del1++;
      }

      tot_score += cumm_seq_score[ic];
      fprintf(fd,"%ld\t%ld\t%c\t%c\t%d\t%d\n",
	      aln->q_offset+qlsgn*(ioff0-del0)*aln->llmult+qfx0,
	      aln->l_offset+llsgn*(ioff1-del1)+lfx0,	      
	      seqc0[ic], seqc1[ic], cumm_seq_score[ic], tot_score);
    }
    return;
  }

  memset(line[0],' ',MAXOUT);
  memset(line[1],' ',MAXOUT);
  memset(line[2],' ',MAXOUT);

  /* cl0 indicates whether a coordinate should be printed over the first
     sequence; cl1 indicates a coordinate for the second;
  */

  ic = 0; del0=del1=0;

  /* we set afmt/afmt0 here, rather than at the start of discons, so
     we can have accurate values for the max and min query/subject
     start/end using qlsgn and qlfact
  */

  if (!(m_msp->markx & MX_MBLAST)) {
    if (nml > 6) {
      blank[nml-6]='\0';
      sprintf(afmt,"%%-%ds %%s\n",nml);
    }
    else {
      blank[0]='\0';
      SAFE_STRNCPY(afmt,"%-6s %s\n",sizeof(afmt));
    }
  }
  else {
    /* for MX_MBLAST format, the size of the numbers is a function of
       the largest numbers in the first or last coordinate - which
       could be either the query or the library sequence.
    */
    if (qlsgn > 0) {q_digit_max = aln->smin0 + (aln->amax0 - aln->amin0); }
    else {q_digit_max = aln->smin0;}
    q_digit_max = aln->q_offset + qlsgn*q_digit_max + 1l;

    if (llsgn > 0) {s_digit_max = aln->smin1 + (aln->amax1 - aln->amin1); }
    else {s_digit_max = aln->smin1;}
    s_digit_max = aln->l_offset + aln->frame + llsgn*aln->llmult*s_digit_max + 1l;

    sprintf(digit_tmp,"%ld",max(q_digit_max, s_digit_max));
    digit_len = strlen(digit_tmp);
    if (digit_len < 4) digit_len = 4;

    sprintf(afmt,"%%-5s  %%-%dld %%s %%-ld\n",digit_len);
    blank[digit_len+6]='\0';
    SAFE_STRNCPY(afmt0,"%-10s  %s\n",sizeof(afmt0));
  }

  if (aln->d_start0 < aln->d_stop0) qf_flag = 1; else qf_flag = 0;
  if (aln->d_start1 < aln->d_stop1) sf_flag = 1; else sf_flag = 0;

  for (il=0; il<(nc+l_llen-1)/l_llen; il++) {
    loff=il*l_llen;
    lend=min(l_llen,nc-loff);

    ll0 = NO; ll1 = NO;

    memset(cline[0],' ',MAXOUT+1);
    memset(cline[1],' ',MAXOUT+1);

    ic_save = ic;

    q_start = aln->q_offset + (long)qlsgn*ioff00 +
      (long)qlsgn*qlfact*(ioff0-del0-ioff00) + qf_flag;
    s_start = aln->l_offset + /* aln->frame + */
      (long)llsgn*aln->llmult*ioff10 +
      (long)llsgn*llfact*(ioff1-del1-ioff10) + sf_flag;

    for (i=0; i<lend; i++, ic++,ioff0++,ioff1++) {
      cl0 =  cl1 = rl0 = rl1 = YES;
      if ((line[0][i]=seqc0[ic])=='-' || seqc0[ic]=='\\') {
	del0++; cl0=rl0=NO;
      }
      else if (seqc0[ic]=='/') {
	del0++; cl0=rl0=NO;
      }
      if ((line[2][i]=seqc1[ic])=='-' || seqc1[ic]=='\\') {
	del1++; cl1=rl1=NO;
      }
      else if (seqc1[ic]=='/') {
	del1++; cl1=rl1=NO;
      }

      if (seqc0[ic]==' ') {del0++; cl0=rl0=NO;}
      else ll0 = YES;
      if (seqc1[ic]==' ') {del1++; cl1=rl1=NO;}
      else ll1 = YES;

      /* the old version used qoffset, this version uses q_offset+q_off */
      qqoff = aln->q_offset + (long)qlsgn*ioff00 +
	(long)qlsgn*qlfact*(ioff0-del0-ioff00);
      if (cl0 && qqoff%10 == 9)  {
	sprintf(&clinep[0][i-qfxn],"%8ld",qqoff+1l);
	clinep[0][i+8-qfxn]=' ';
	rl0 = NO;
      }
      else if (cl0 && qqoff== -1) {
	sprintf(&clinep[0][i-qfxn],"%8ld",0l);
	clinep[0][i+8-qfxn]=' ';
	rl0 = NO;
      }
      else if (rl0 && (qqoff+1)%10 == 0) {
	sprintf(&clinep[0][i-qfxn],"%8ld",qqoff+1);
	clinep[0][i+8-qfxn]=' ';
      }
      
      /* the lloff coordinate of a residue is the sum of:
	 m_msp->sq1off-1	 - the user defined coordinate
	 aln->l_offset	- the offset into the library sequence
	 llsgn*ioff10	- the offset into the beginning of the alignment
	 (given in the "natural" coordinate system,
	 except for tfasta3 which provides context)
	 llsgn*llfact*(ioff1-del1-ioff10)
	 - the position in the consensus aligment, -gaps
      */

      /* it seems like this should be done in calc_coord() */

      lloff = aln->l_offset + /* aln->frame  + */
	(long)llsgn*aln->llmult*ioff10 +
	(long)llsgn*llfact*(ioff1-del1-ioff10);

      if (cl1 && lloff%10 == 9)  {
	sprintf(&clinep[1][i-lfxn],"%8ld",lloff+1l);
	clinep[1][i+8-lfxn]=' ';
	rl1 = NO;
      }
      else if (cl1 && lloff== -1) {
	sprintf(&clinep[1][i],"%8ld",0l);
	clinep[1][i+8-lfxn]=' ';
	rl1 = NO;
      }
      else if (rl1 && (lloff+1)%10 == 0) {
	sprintf(&clinep[1][i-lfxn],"%8ld",lloff+1);
	clinep[1][i+8-lfxn]=' ';
      }

      line[1][i] = ' ';
      if (ioff0-del0 >= aln->amin0 && ioff0-del0 <= aln->amax0) {
	if (m_msp->markx & MX_MBLAST) {
	  if (disp_dna_align) {
	    if (seqca[ic]==4) {line[1][i] = '|';}
	    else {line[1][i] = ' ';}
	  }
	  else {
	    if (seqca[ic]==4) {line[1][i]=line[0][i];}
	    else {line[1][i] = map_sym_p[seqca[ic]];}
	  }
	}
	else {
	  if (seqca[ic]==4) {line[1][i]=map_sym_p[4];}
	  else if ((m_msp->markx&MX_ATYPE)==2) line[1][i]=line[2][i];
	  else line[1][i] = map_sym_p[seqca[ic]];
	}
      }
      else if ((m_msp->markx&MX_ATYPE)==2) line[1][i]=line[2][i];
    }

    q_end = qqoff + qf_flag + (aln->qlfact-1)*(aln->qlrev > 0 ? -1 : 1);
    s_end = lloff + sf_flag + (aln->llfact-1)*(aln->qlrev > 0 ? -1 : 1);

    if (m_msp->ann_flg) {
      for (ic=ic_save,i=0; i<lend; ic++,i++) {
	if (m_msp->markx&MX_ANNOT_MID) {
	  if (seqc0a && seqc0a[ic]!= ' ') {line[1][i] = seqc0a[ic];}
	  if (seqc1a && seqc1a[ic]!= ' ') {line[1][i] = seqc1a[ic];}
	}
	if (m_msp->markx&MX_ANNOT_COORD) {
	  if (seqc0a && seqc0a[ic]!= ' ') clinep[0][i+7-qfxn] = seqc0a[ic];
	  if (seqc1a && seqc1a[ic]!= ' ') clinep[1][i+7-lfxn] = seqc1a[ic];
	}
      }
    }

    line[0][lend]=line[1][lend]=line[2][lend]=0;
    clinep[0][lend+7]=clinep[1][lend+7]=0;
    
    ll01 = ll0&&ll1;
    if ((m_msp->markx&MX_ATYPE)==2 && (!aln->showall || ll0)) ll1=0;
    fprintf(fd,"\n");
    if (!(m_msp->markx & MX_MBLAST)) {
      if (ll0) fprintf(fd,"%s%s\n",blank,clinep[0]);
      if (ll0) fprintf(fd,afmt,name0,line[0]);
      if (ll01) fprintf(fd,afmt,name01,line[1]);
      if (ll1) fprintf(fd,afmt,name1,line[2]);
      if (ll1) fprintf(fd,"%s%s\n",blank,clinep[1]);
    }
    else {
      /* this code emulates BLAST output, but currently only for
	 coordinates < 10000) coordinates > 10000 will require that
	 the offset start and end coordinates across the entire
	 alignment are checked, and then the format is modified to
	 ensure that they will fit.  A simple %-d does not work,
	 because the other sequence (query/library) may have the large
	 coordinate.

	 thus, afmt and afmt0 must be modified for each sequence,
	 based on the boundaries of the alignment
      */

      if (ll0) fprintf(fd,afmt,name0,q_start,line[0],q_end);
      if (ll01) fprintf(fd,afmt0,blank,line[1]);
      if (ll1) fprintf(fd,afmt,name1,s_start,line[2],s_end);
    }
  }
}

static float gscale= -1.0;

void
disgraph(FILE *fd, int n0,int n1, float percent, int score,
	 int min0, int min1, int max0, int max1, long sq0off,
	 char *name0, char *name1, int nml,
	 int mlen, int markx)
{
  int i, gstart, gstop, gend;
  int llen;
  char line[MAXOUT+1];
  char afmt[16], afmtf[64];

  if (nml > 6) {
    sprintf(afmt,"%%-%ds",nml);
  }
  else {
    SAFE_STRNCPY(afmt,"%-6s",sizeof(afmt));
  }
  SAFE_STRNCPY(afmtf,afmt,sizeof(afmtf));
  SAFE_STRNCAT(afmtf," %4ld-%4ld:     %5.1f%%:%s:\n",sizeof(afmtf));

  llen = mlen - 10;
  memset(line,' ',llen);

  line[llen-1]='\0';
  if (gscale < 0.0) {
    gscale = (float)llen/(float)n0;
    if ((markx&MX_ATYPE) == 7 ) 
      fprintf(fd,afmtf,name0,sq0off,sq0off+n0-1,100.0,line);
  }

  gstart = (int)(gscale*(float)min0+0.5);
  gstop = (int)(gscale*(float)max0+0.5);
  gend = gstop+(int)(gscale*(float)(n1-max1));

  if (gstop >= llen) gstop = llen-1;
  if (gend >= llen) gend = llen-1;
  for (i=0; i<gstart; i++) line[i]=' ';
  for (; i<gstop; i++) line[i]='-';
  for (; i<llen; i++) line[i]=' ';

  line[gend]=':';
  line[llen]='\0';

  if (markx & MX_AMAP) {
    if ((markx & MX_ATYPE)==7) {	/* markx==4 - no alignment */
      SAFE_STRNCPY(afmtf,afmt,sizeof(afmtf));
      SAFE_STRNCAT(afmtf," %4ld-%4ld:%4d %5.1f%%:%s\n",sizeof(afmtf));
      fprintf(fd,afmtf,name1,min0+sq0off,max0+sq0off-1,score,percent,line);
    }
    else {
      SAFE_STRNCPY(afmtf,">",sizeof(afmtf));
      SAFE_STRNCAT(afmtf,afmt,sizeof(afmtf));
      SAFE_STRNCAT(afmtf," %4ld-%4ld:%s\n",sizeof(afmtf));
      fprintf(fd,afmtf, name1,min0+sq0off,max0+sq0off-1,line);
    }
  }
}

void
aancpy(char *to, char *from, int count, struct pstruct *ppst)
{
  char *tp;
  unsigned char *sq;
  int nsq;

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

  tp=to;
  while (count-- && *from) {
    if (*from <= nsq) *tp++ = sq[*(from++)];
    else *tp++ = *from++;
  }
  *tp='\0';
}

/* calc_coord transfers alignment boundary coordinates (aln->amin0,
   amin1, amax0, amax1) into display coordinates (aln->d_start0,
   d_start1, etc.)

   this routine now indexes from 1 (rather than 0) because sq starts
   with a 0
*/

void
calc_coord(int n0, int n1,
	  long q_offset,
	  long l_offset,
	  struct a_struct *aln)
{
  int l_lsgn, q_lsgn, q_fx0, q_fxn, l_fx0, l_fxn;

  if (aln->qlrev == 1) {
    aln->q_start_off = q_offset+n0;
    aln->q_end_off = q_offset+1;
    q_offset += n0;
    q_lsgn = -1;
    q_fx0 = 0;
    q_fxn = 1;
  }
  else {
    aln->q_start_off = q_offset + 1;
    aln->q_end_off = q_offset+n0;
    q_lsgn = 1;
    q_fx0 = 1;
    q_fxn = 0;
  }

  if (aln->llrev == 1) {
    aln->l_start_off = l_offset + n1;
    aln->l_end_off = l_offset+1;
    l_offset += n1;
    l_lsgn = -1;
    l_fx0 = 0;
    l_fxn = 1;
  }
  else {
    aln->l_start_off = l_offset + 1;
    aln->l_end_off = l_offset+n1;
    l_lsgn = 1;
    l_fx0 = 1;
    l_fxn = 0;
  }
  aln->q_offset = q_offset;
  aln->l_offset = l_offset;
  aln->d_start0 = q_offset+q_lsgn*aln->amin0+q_fx0;
  aln->d_stop0  = q_offset+q_lsgn*aln->amax0+q_fxn;
  aln->d_start1 = l_offset+l_lsgn*aln->amin1*aln->llmult+l_fx0;
  aln->d_stop1  = l_offset+l_lsgn*aln->amax1*aln->llmult+l_fxn;
}