%{
#include "gwrap.h"

#define MatchSummarySetLISTLENGTH 128

%}


struct MatchSummary
double bits
char * qname
char * tname
int qstart
int qend
int tstart
int tend
int qintron     !def="0"
int qframeshift !def="0"
int tintron     !def="0"
int tframeshift !def="0"
%info
A Match Summary has summary statistics
for a single alignment, with the
two start/end ranges and the number of
introns and frameshifts for each
sequence (obviously, if one is a protein
then neither are valid!)
%%

struct MatchSummarySet
MatchSummary ** ms !list
%info
This holds a set of MatchSummaries,
%%

api
object MatchSummarySet
des free_MatchSummarySet
func MatchSummarySet_from_AlnBlock_estwise
func MatchSummarySet_from_AlnBlock_genewise
endobject
object MatchSummary
des    free_MatchSummary
endobject
endapi

%{
#include "matchsum.h"

%func
Builds a MatchSummarySet from a
EstWise alignment. this makes
alot of assumptions about the labels
setc in alb, so make sure it was a 
estwise alignment  - however as you
can notice this is exactly the same 
labels as found in genewise set
%%
MatchSummarySet * MatchSummarySet_from_AlnBlock_estwise(AlnBlock * alb,char * qname,int offset,Sequence * target)
{
  return MatchSummarySet_from_AlnBlock_genewise(alb,qname,offset,target);
}

%func
Builds a MatchSummarySet from a
GeneWise alignment. this makes
alot of assumptions about the labels
setc in alb, so make sure it was a 
genewise alignment 
%%
MatchSummarySet * MatchSummarySet_from_AlnBlock_genewise(AlnBlock * alb,char * qname,int protoff,Sequence * target)
{
  MatchSummarySet * out;
  MatchSummary * ms;
  AlnColumn * alc;
  int len;

  out = MatchSummarySet_alloc_std();

  alc = alb->start;

  while( (ms = MatchSummary_from_AlnColumn_genewise(alc,&alc)) != NULL ) {
    ms->qstart+= protoff-1; /*** offset in old-style offset mode ***/
    ms->qend += protoff-1;
    if( target->offset > target->end ) {
      len = ms->tend - ms->tstart;
      /*    fprintf(stderr,"Look - length %d\n",len); */
      ms->tstart = target->offset-1 - ms->tstart;
      ms->tend   = ms->tstart - len;
    } else {
      ms->tstart += target->offset-1;
      ms->tend += target->offset-1;
    }

    ms->qname = stringalloc(qname);
    ms->tname = stringalloc(target->name);
    add_MatchSummarySet(out,ms);
  }

  return out;
}
  
%func
For making each alignment
%type internal
%%
MatchSummary * MatchSummary_from_AlnColumn_genewise(AlnColumn * alc,AlnColumn ** end)
{
  MatchSummary * out;
  int score;
  

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

  if( alc == NULL ) {
    *end = NULL;
    return NULL;
  }

  out = MatchSummary_alloc();

  /* NB alignment start is one before the C ordinate start system */

  out->qstart = alc->alu[0]->start+1; /* in C coords */
  out->tstart = alc->alu[1]->start+1; /* in C coords */
  score  = alc->alu[0]->score[0]; 

  for(;alc->next != NULL && is_random_AlnColumn_genewise(alc->next) == FALSE;alc = alc->next) {
    score += alc->next->alu[0]->score[0];
    if( strcmp(alc->alu[1]->text_label,"SEQUENCE_DELETION") == 0 || strcmp(alc->alu[1]->text_label,"SEQUENCE_INSERTION") == 0) 
      out->tframeshift++;
    else if ( strcmp(alc->alu[1]->text_label,"CENTRAL_INTRON") == 0 ) 
      out->tintron++; /* NB, assuming we have collapsed central intron labels! */
  }

  out->qend = alc->alu[0]->end+1; /* in C coords */
  out->tend = alc->alu[1]->end+1;
  /*score += alc->alu[0]->score[0];*/
  out->bits = Score2Bits(score); /*** hmm... this could be bad news ***/

  *end = alc->next;

  return out;
}

%func
Shows a header (bits Query start etc) which matches
the order of the show_MatchSummarySet_genewise
%%
void show_MatchSummary_genewise_header(FILE * ofp)
{
  fprintf(ofp,"Bits   Query         start end Target      start end   idels introns\n");
}

%func
shows Matchsummary for genewise
results, ie with target indels and introns
%%
void show_MatchSummarySet_genewise(MatchSummarySet * mss,FILE * ofp)
{
  int i;

  for(i=0;i<mss->len;i++)
    show_MatchSummary_genewise(mss->ms[i],ofp);
}

%func
shows a single match summary
%type internal
%% 
void show_MatchSummary_genewise(MatchSummary * ms,FILE * ofp)
{
  if( ms->tstart < ms->tend ) 
    fprintf(ofp,"%4.2f %-12s %4d %4d %-12s %4d %4d %4d %4d\n",
	    ms->bits,
	    ms->qname,
	    ms->qstart+1, /* map to bio coords */
	    ms->qend,
	    ms->tname,
	    ms->tstart+1, /* map to 'bio coords */
	    ms->tend,
	    ms->tframeshift,
	    ms->tintron);
  else 
    fprintf(ofp,"%4.2f %-12s %4d %4d %-12s %4d %4d %4d %4d\n",
	    ms->bits,
	    ms->qname,
	    ms->qstart+1, /* map to bio coords */
	    ms->qend,
	    ms->tname,
	    ms->tstart+1, /* map to 'bio coords */
	    ms->tend+2, /* map to bio coords */
	    ms->tframeshift,
	    ms->tintron);
}


%func
Shows a header (bits Query start etc) which matches
the order of the show_MatchSummarySet_estwise
%%
void show_MatchSummary_estwise_header(FILE * ofp)
{
  fprintf(ofp,"Bits Query         start end Target      start end   idels\n");
}

%func
Shows an estwise match, ie with only the target with indels
%%
void show_MatchSummarySet_estwise(MatchSummarySet * mss,FILE * ofp)
{
  int i;

  for(i=0;i<mss->len;i++)
    show_MatchSummary_estwise(mss->ms[i],ofp);
}

 
%func
shows a single estwise match
%type internal
%%
void show_MatchSummary_estwise(MatchSummary * ms,FILE * ofp)
{
  fprintf(ofp,"%4.2f %-12s %4d %4d %-12s %4d %4d %4d\n",
	  ms->bits,
	  ms->qname,
	  ms->qstart+1, /* map to bio coords */
	  ms->qend,
	  ms->tname,
	  ms->tstart+1, /* map to 'bio coords */
	  ms->tend,
	  ms->tframeshift);
}