%{
#include "dyna.h"


%}

api
func write_pretty_str_align
func write_pretty_seq_align
func write_pretty_Protein_align
endapi


%{
#include "seqaligndisplay.h"

%func
This gives an interface into the
alignment display using Protein
objects
%arg
alb alignment structure
q   first sequence
t   second sequence 
name length of the name block
main length of the main block
ofp  output file
%%
boolean write_pretty_Protein_align(AlnBlock * alb,Protein * q,Protein * t,int name,int main,FILE * ofp)
{
  if( alb == NULL || q == NULL || t == NULL ) {
    warn("NULL objects being passed into write_pretty_Protein_align");
    return FALSE;
  }
  return write_pretty_seq_align(alb,q->baseseq,t->baseseq,name,main,ofp);
}



%func
This gives an interface into the alignment
display using sequences and files. A more
generic function is write_pretty_str_align
%arg
alb alignment structure
q   first sequence
t   second sequence 
name length of the name block
main length of the main block
ofp  output file
%% 
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;

  if( alb == NULL || q == NULL || t == NULL ) {
    warn("NULL objects being passed into write_pretty_seq_align");
    return FALSE;
  }

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

  /** destroy btc canvas **/

  free_btCanvas(btc);

  return TRUE;
}


%func
This gives an interface into the alignment
display using strings and files.
%arg
alb alignment structure
qname name of first sequence
tname name of second sequence
query  first sequence
target second sequence
name length of the name block
main length of the main block
ofp  output file
%% 
boolean write_pretty_str_align(AlnBlock * alb,char * qname,char * query,char * tname,char * target,int name,int main,FILE * ofp)
{
  boolean out;
  btCanvas * btc;
  
  btc = new_Ascii_btCanvas(ofp,name+6,main,0,3); /*+6 in case we want to put in numbers */

  out = write_pretty_str_align_btc(alb,qname,query,tname,target,btc);

  /** destroy btc canvas **/

  free_btCanvas(btc);

  return out;
}

%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. ... but crap
type checking it has to be said!

Also we use a generic btCanvas that could have
any implementation underneath (eg, ASCII, postscript etc).
%%
boolean write_pretty_str_align_btc(AlnBlock * alb,char * qname,char * query,char * tname,char * target,btCanvas * btc)
{
  AlnColumn * alc;
  AlnUnit * q;
  AlnUnit * t;
  char buffer[14];

  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);
    
    sprintf(buffer,"%d",alc->alu[0]->start+1+1);

    paste_string_btPasteArea(btp,12,0,buffer,BC_RIGHT,0);

    sprintf(buffer,"%d",alc->alu[1]->start+1+1);

    paste_string_btPasteArea(btp,12,2,buffer,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,toupper((int)query[q->start+1]),0);
      } else if( strcmp(q->text_label,"UNMATCHED_SEQUENCE") == 0 ) {
	paste_char_btPasteArea(btp,0,0,tolower((int)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,toupper((int)target[t->start+1]),0);
      } else if( strcmp(t->text_label,"UNMATCHED_SEQUENCE") == 0 ) {
	paste_char_btPasteArea(btp,0,2,tolower((int)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! */
}



%}