%{
#include "dyna.h"


%}


%{
#include "seqaligndisplay.h"


%func
This gives an interface into the alignment
display using sequences and files. A more
generic function is write_pretty_str_align
%% 
boolean write_pretty_seq_align(AlnBlock * alb,Sequence * q,Sequence * t,int name,int main,FILE * ofp)
{
  char qname[64];
  char tname[64];
  btCanvas * btc;
  char * temp;

  if( name > 64 ) {
    warn("Sorry - hard coded limited, can't have names longer than 64");
    return FALSE;
  }

  
  if(  strlen(q->name) > name ) {
    warn("Name %s is longer than allowed name block (%d). Truncating\n",q->name,name);
    strncpy(qname,q->name,name);
    qname[name] = '\0';
  } else {
    strcpy(qname,q->name);
  }

  if(  strlen(t->name) > name ) {
    warn("Name %s is longer than allowed name block (%d). Truncating\n",t->name,name);
    strncpy(tname,t->name,name);
    tname[name] = '\0';
  } else {
    strcpy(tname,t->name);
  }
  
  btc = new_Ascii_btCanvas(ofp,name+6,main,0,3); /*+6 in case we want to put in numbers */

  write_pretty_str_align(alb,qname,q->seq,tname,t->seq,btc);

  /** destroy btc canvas **/

  free_btCanvas(btc);

  return TRUE;
}



%func
This function writes precisely
what you expect for a a simple alignment.

We can reuse this routine all over the place because 
we dont use any hard coded structure for the
query or the target sequence letters.

Also we use a generic btCanvas that could have
any implementation underneath (eg, ASCII, postscript etc).
%%
boolean write_pretty_str_align(AlnBlock * alb,char * qname,char * query,char * tname,char * target,btCanvas * btc)
{
  AlnColumn * alc;
  AlnUnit * q;
  AlnUnit * t;

  btPasteArea * btp;

  for(alc=alb->start;alc != NULL;) {

    /** put names in **/

    btp = get_reserved_left_btCanvas(btc);
    paste_string_btPasteArea(btp,0,0,qname,BC_RIGHT,0);
    paste_string_btPasteArea(btp,0,2,tname,BC_RIGHT,0);

    free_btPasteArea(btp);
    /** now loop over this block **/

    for(;alc != NULL &&  can_get_paste_area_btCanvas(btc,1) == TRUE;alc=alc->next) {
      
      q = alc->alu[0];
      t = alc->alu[1];

      /*
       * at the end, break
       */
      if( strcmp(q->text_label,"END") == 0 ) {
	alc = NULL;
	break;
      }

      /*
       * Get the paste area, length 1, depth will be 3
       */

      btp = get_paste_area_btCanvas(btc,1);

      /*
       * Write in the query sequence
       *
       */

      if( strcmp(q->text_label,"SEQUENCE") == 0 ) {
	paste_char_btPasteArea(btp,0,0,query[q->start+1],0);
      } else {
	/** is insert- we could check **/
	if( strcmp(q->text_label,"INSERT") != 0 ) {
	  warn("Got an uninterpretable label, %s",q->text_label);
	  paste_char_btPasteArea(btp,0,0,'?',0);
	} else {
	  paste_char_btPasteArea(btp,0,0,'-',0);
	}
      }

      /*
       * Write in the target sequence
       *
       */

      if( strcmp(t->text_label,"SEQUENCE") == 0 ) {
	paste_char_btPasteArea(btp,0,2,target[t->start+1],0);
      } else {
	/** is insert- we could check **/
	if( strcmp(t->text_label,"INSERT") != 0 ) {
	  warn("Got an uninterpretable label, %s",t->text_label);
	  paste_char_btPasteArea(btp,0,2,'?',0);
	} else {
	  paste_char_btPasteArea(btp,0,2,'-',0);
	}
      }

      /*
       * Match line
       */



      if( strcmp(q->text_label,"SEQUENCE") == 0 && strcmp(t->text_label,"SEQUENCE") == 0 ) {
	if( q->score[0] > 0 ) {
	  if( query[q->start+1] == target[t->start+1] ) {
	    paste_char_btPasteArea(btp,0,1,target[t->start+1],0);
	  } else {	   
	    paste_char_btPasteArea(btp,0,1,'+',0);
	  }
	}
      } else 
	paste_char_btPasteArea(btp,0,1,' ',0);
      
      free_btPasteArea(btp);

    } /* end of for this block */

    advance_line_btCanvas(btc);
  } /* end of for the alignment */

  return TRUE; /* we never returned false. Ooops! */
}



%}