%{
#include "dyna.h"


%}


%{
#include "geneutil.h"


%func
Makes a new GenomicRegion with the genes
predicted from this AlnBlock

Really a wrapper around the add_Genes_to_GenomicRegion_GeneWise
and other functionality
%arg
gen genomic sequence to use
pseudo If true, predicts frameshifted genes as pseudogenes
alb genewise alignment to predict genes from
return a newly allocated structure
%%
GenomicRegion * new_GenomicRegion_from_GeneWise(Genomic * gen,boolean pseudo,AlnBlock * alb)
{
  GenomicRegion * out;

  out = new_GenomicRegion(gen);
  
  add_Genes_to_GenomicRegion_GeneWise(out,gen->baseseq->offset,gen->baseseq->end,alb,NULL,pseudo,NULL);

  return out;
}

%func
Potential an Alnblock may have more
than one gene due to looping models

This adds all the genes to gr

%arg
gr genomic region to add genes to
org_start    start point of the dna to which the alb was made from
org_end      end point of the dna to which the alb was made from
alb          logical label alignment
pseudo       If true, frameshifted genes are predicted as pseudo genes
root         the second argument to make_name
make_name fN a pointer to a function to actually make the name of the gene
%%
int add_Genes_to_GenomicRegion_GeneWise(GenomicRegion * gr,int org_start,int org_end,AlnBlock * alb,char * root,boolean pseudo,char * (*make_name)(Wise2_Genomic *,char *,int ,Wise2_Gene * ))
{
  int count = 0;
  Gene * gene;
  AlnColumn * alc;

  alc = alb->start;

  while( (gene = Gene_from_AlnColumn_GeneWise(alc,org_start,org_end,pseudo,&alc)) != NULL ) {
    if( make_name != NULL ) {
      gene->name = (*make_name)(gr->genomic,root,gr->len,gene);
    } 
    if( root != NULL ) {
      gene->seqname = stringalloc(root);
    }

    add_Gene_to_GenomicRegion(gr,gene);
    count++;
    if( alc == NULL ) 
      break;
  }

  return count;
}
 

%func
A wrap for making a gene structure from
an AlnBlock derived from one of the genewise
methods
%arg
alc Alignment column in an AlnBlock produced by genewise
org_start offset that the genewise alignment was to the coordinate system
org_end emd that the genewise alignment was to the coordinate system
end w pointer to a AlnColumn * to say when it has finished with this gene
%%
Gene * Gene_from_AlnColumn_GeneWise(AlnColumn * alc,int org_start,int org_end,boolean predict_pseudo_for_frameshift,AlnColumn ** end)
{
  Gene * out;
  Transcript * tr;
  Translation * ts;
  Exon * ex;
  AlnColumn * prev;
  SupportingFeature * sf;
  int score = 0; 
  int dosf = 0;
  int phase = 0;
  int frame_break = 0;

  while(alc != NULL && is_random_AlnColumn_genewise(alc) == TRUE )
    alc = alc->next;

  while (alc != NULL && strcmp(alc->alu[1]->text_label,"CODON") != 0 ) 
    alc = alc->next;

  if( alc == NULL)
    return NULL;

  out = Gene_alloc_len(1);
  tr = Transcript_alloc_std();
  add_Gene(out,tr);

  out->start = alc->alu[1]->start +1; 

  score += alc->alu[0]->score[0];

  for(;;) {

    /*    fprintf(stderr,"Top loop - alc at %s %s\n",alc->alu[1]->text_label,alc->alu[0]->text_label); */

    /*    fprintf(stderr,"2 Score is %.2f %s %d %.2f\n",Score2Bits(score),alc->alu[1]->text_label,alc->alu[0]->score[0],Score2Bits(alc->alu[0]->score[0]));*/
    ex = Exon_alloc_std();
    add_ex_Transcript(tr,ex);

    /*
     * this is always the start of an exon 
     */

    dosf = 0;
 
    if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {      
      ex->start = alc->alu[1]->start+1 - out->start; /* coordinated in alignment coords */
      dosf = 1;
      phase = 0;
    } else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_0") == 0  ) {
      ex->start = alc->alu[1]->start +4 - out->start; 
      dosf = 1;
      phase = 0;
    } else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_1") == 0  ) {
      ex->start = alc->alu[1]->start +4 - out->start; 
      phase = 1;
    } else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_2") == 0  ) {
      ex->start = alc->alu[1]->start +4 - out->start; 
      phase = 2;
    } else {
      ex->start = alc->alu[1]->start +1 - out->start; /* coordinated in alignment coords */
      phase = -1;
    }

    ex->phase = phase;

    /* 
     * Exons can start in INSERTs (yuk). In which case we don't 
     * make a supporting feature
     */


    if( dosf == 1 && strstartcmp(alc->alu[0]->text_label,"INSERT") != 0 ) {
      sf = SupportingFeature_alloc();
      /* we fill in start and end from the exon at the moment. Not pretty */
      sf->hstart  = alc->alu[0]->start+1;
      sf->hstrand = 1; /* currently only got proteins. Thank the lord! */
      sf->start = ex->start;
    } else {
      sf = NULL; /* make sure we don't generate a sf here */
    }
  


    for(prev=alc,alc=alc->next;alc != NULL; ) {
      /*      fprintf(stderr,"Exon loop - alc at %s %s %d\n",alc->alu[1]->text_label,alc->alu[0]->text_label,sf); */

      score += alc->alu[0]->score[0];
      /*      fprintf(stderr,"1 Score is %.2f %s\n",Score2Bits(score),alc->alu[1]->text_label); */
      if( is_frameshift_AlnColumn_genewise(alc) == TRUE && predict_pseudo_for_frameshift == TRUE ) {
	score += alc->alu[0]->score[0];
	fprintf(stderr,"Score is %.2f\n",Score2Bits(score));
	out->ispseudo = TRUE;
	alc = alc->next;
	continue;
      }

      if( is_random_AlnColumn_genewise(alc) == TRUE)
	break;
      if( strcmp(alc->alu[1]->text_label,"CODON") != 0 ) {
	if( strstartcmp(alc->alu[0]->text_label,"DELETE") == 0 ) {
	  /* must add sf and start a new one */
	  /*fprintf(stderr,"Looking at alc at %s %s %d %d %d\n",alc->alu[1]->text_label,alc->alu[0]->text_label,prev,out,sf);*/

	  if( sf != NULL ) {
	    sf->end  = prev->alu[1]->end+1 - out->start;
	    sf->hend = prev->alu[0]->end+1;
	    add_Exon(ex,sf);
	    sf = NULL;
	  }
	
	  /* 
	   * go the end of this delete run, which are residues in the query with no
	   * target info
	   */
	  while( alc->next != NULL && strstartcmp(alc->next->alu[0]->text_label,"DELETE") == 0 ) {
	    alc = alc->next;
	  }
	  if( alc->next != NULL && strcmp(alc->next->alu[1]->text_label,"CODON") == 0 ) {
	    /* the next position is the start of the new alignment */
	    sf = SupportingFeature_alloc();
	    sf->hstart = alc->next->alu[0]->start+1;
	    sf->start  = alc->next->alu[1]->start+1 - out->start;
	  } else {
	    sf = NULL;
	  }
	} else {
	  break;
	}
      
      } else {
	/* it is a codon match, but it could be an insert */
	if( strstartcmp(alc->alu[0]->text_label,"INSERT") == 0) {
	  /* break at this point, add this supporting feature */
	  if( sf != NULL ) {
	    sf->end  = prev->alu[1]->end+1 - out->start;
	    sf->hend = prev->alu[0]->end+1;
	    add_Exon(ex,sf);
	    sf = NULL;
	  }
	  
	  frame_break = 0;

	  /* go to the end of this insert run, watching for frameshifts */
	  while( alc->next != NULL && strstartcmp(alc->next->alu[0]->text_label,"INSERT") == 0 ) {

	    if( is_frameshift_AlnColumn_genewise(alc->next) == TRUE || is_random_AlnColumn_genewise(alc->next) == TRUE) {

	      if( is_frameshift_AlnColumn_genewise(alc->next) == TRUE && predict_pseudo_for_frameshift == TRUE ) {
		out->ispseudo = TRUE;
		alc = alc->next;
		continue;
	      } else {
		alc = alc->next;
		frame_break = 1;
		break;
	      }
	    }
	    alc = alc->next;
	  }
	  if( frame_break == 1 ) {
	    break; /* out of this gene */
	  }

	  if( alc->next != NULL && strcmp(alc->next->alu[1]->text_label,"CODON") == 0 ) {
	    /* the next position is the start of the new alignment */
	    sf = SupportingFeature_alloc();
	    /* do not understand why not having a +1 here is correct. Hmph */
	    sf->hstart = alc->next->alu[0]->start+1;
	    sf->start  = alc->next->alu[1]->start+1 - out->start;
	  } else {
	    sf = NULL;
	  }
	
	} else {
	  /* could be the start of a run from INSERT into match */
	  if( sf == NULL ) {
	    sf = SupportingFeature_alloc();
	    /* we fill in start and end from the exon at the moment. Not pretty */
	    sf->hstart  = alc->alu[0]->start+1;
	    sf->hstrand = 1; /* currently only got proteins. Thank the lord! */
	    sf->start = alc->alu[1]->start+1 - out->start;
	  }
	}
      } /* end of else it is a codon match */
      prev  = alc;
      alc = alc->next;
      
    }

    /*
     * The exon has ended. But why?
     */

    if( sf != NULL ) {
      sf->hend = prev->alu[0]->end+1;
      add_Exon(ex,sf);
    }

    if( alc == NULL ) {
      out->end = prev->alu[1]->end +1;
      ex->end = out->end - out->start;
      if( sf != NULL ) {
	sf->end = ex->end;
      }
      break;
    } 

    if( is_random_AlnColumn_genewise(alc) == TRUE) {
      out->end = prev->alu[1]->end +1;
      ex->end = out->end - out->start;
      if( sf != NULL ) {
	sf->end = ex->end;
      }
      break;
    }

   
   


    if( strcmp(alc->alu[1]->text_label,"5SS_PHASE_0") == 0 ) {
      out->end = alc->alu[1]->start+1;
      phase = 0;
    } else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_1") == 0 ) {
      out->end = alc->alu[1]->start+2;
      phase = 1;
    } else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_2") == 0 ) {
      out->end = alc->alu[1]->start+3;
      phase = 2;
    } else {
      phase = 0;
      out->end = prev->alu[1]->end +1;
      ex->end = out->end - out->start;
      if( sf != NULL ) {
	sf->end = ex->end;
      }
      break;
      
    }


    /** set end of exon to the correct size from here **/
    ex->end = out->end - out->start;


    /** sf is to the codon, not to the exon */
    if( sf != NULL ) {
      if( phase == 0 ) {
	sf->end = ex->end;
      } else if ( phase == 1 ) {
	sf->end = ex->end-1;
      } else {
	sf->end = ex->end-2;
      }
    }
      

    while( alc != NULL && strstartcmp(alc->alu[1]->text_label,"3SS") != 0 ) {
      alc = alc->next;
      score += alc->alu[0]->score[0];
    }

    if( alc == NULL ) {
      warn("Got to the end of an alignment inside an intron. Oooops!");
      break;
    }

  }/* back to for(;;) */

  
  if( end != NULL ) 
    *end = alc;

  if( org_start < org_end) {
    out->start += org_start-1;
    out->end   += org_start-1;
  } else {
    /*    fprintf(stderr,"was %d to %d\n",out->start,out->end); */
    out->start = org_start-1 - out->start;
    out->end   = org_start-1 - out->end;
    /*    fprintf(stderr,"now %d to %d (%d)\n",out->start,out->end,org_start); */
  }

  if( out->ispseudo == FALSE ) {
    ts = Translation_alloc();
    ts->start = 0;
    ts->end = length_Transcript(tr);
    ts->parent = tr;  
    add_Transcript(tr,ts);
  }

  tr->parent = out;
  
  out->bits = Score2Bits(score);
  return out;
}


%func
This function is to say what is a frameshift label
%type internal
%%
boolean is_frameshift_AlnColumn_genewise(const AlnColumn * alc)
{
  if( strcmp(alc->alu[1]->text_label,"SEQUENCE_INSERTION") == 0 ) {
    return TRUE;
  }
  if( strcmp(alc->alu[1]->text_label,"SEQUENCE_DELETION") == 0 ) {
    return TRUE;
  }
  return FALSE;
}

%func
This function is to say where this should
be skipped in alignment/gene prediction problems
%type internal
%%
boolean is_random_AlnColumn_genewise(const AlnColumn * alc)
{
  char * la;

  la  = alc->alu[1]->text_label;

  if( strcmp(la,"RANDOM_SEQUENCE") == 0 )
    return TRUE;
  if( strcmp(la,"END") == 0 )
    return TRUE;

  la  = alc->alu[0]->text_label;
  
  if( strstr(la,"_RND_") != NULL )
    return TRUE;

  return FALSE;
}


%func
This function is to say where things are introns
%type internal
%%
boolean is_intron_AlnColumn_genewise(const AlnColumn * alc)
{
  char * la;

  la  = alc->alu[1]->text_label;

  if( strcmp(la,"CENTRAL_INTRON") == 0 )
    return TRUE;
  if( strcmp(la,"PYRIMIDINE_TRACT") == 0 )
    return TRUE;
  if( strcmp(la,"SPACER") == 0 )
    return TRUE;

  return FALSE;
}


%}