%{
#include "dyna.h"

#define SegmentHitListLISTLENGTH 128
%}

friend SegmentHit
  
struct SegmentHit
char * name
int qstart
int qend
int tstart
int tend
double score
SegmentHit * next_hit // for collecting hits together ;)


struct SequenceHit
char * name
SegmentHit * start 

struct SegmentHitList
SegmentHit ** seghit !list  

struct DnaSequenceHitList
SegmentHitList * forward;
SegmentHitList * backward;


api
object DnaSequenceHitList
des free_DnaSequenceHitList
func show_DnaSequenceHitList
func read_MSPcrunch_DnaSequenceHitList
endobject
object SegmentHitList
des    free_SegmentHitList
endobject
object SegmentHit
des    free_SegmentHit
endobject
endapi



%{
#include "seqhit.h"



DnaSequenceHitList * new_DnaSequenceHitList(void)
{
  DnaSequenceHitList * out;

  out = DnaSequenceHitList_alloc();
  out->forward = SegmentHitList_alloc_std();
  out->backward = SegmentHitList_alloc_std();

  return out;
}

%func
shows a DnaSequenceHitsList -

only really useful for debugging
%%
void show_DnaSequenceHitList(DnaSequenceHitList * dsl,FILE * ofp)
{
  show_SegmentHitList(dsl->forward,ofp);
  show_SegmentHitList(dsl->backward,ofp);
}

void show_SegmentHitList(SegmentHitList * shl,FILE * ofp)
{
  int i;
  for(i=0;i<shl->len;i++)
    show_SegmentHit(shl->seghit[i],ofp);
  
}

void show_SegmentHit(SegmentHit * sh,FILE * ofp)
{
  fprintf(ofp,"%4d %4d %4d %4d %4.2f %s\n",sh->qstart,sh->qend,sh->tstart,sh->tend,sh->score,sh->name);
}

void sort_SegmentHitList_by_qstart(SegmentHitList * sgl)
{
  sort_SegmentHitList(sgl,compare_SegmentHit_by_qstart);
}

int compare_SegmentHit_by_qstart(SegmentHit * one,SegmentHit * two)
{
  return one->qstart - two->qstart;
}

DnaSequenceHitList * read_msptmp_DnaSequenceHitList(FILE * ifp)
{
  DnaSequenceHitList * out;
  SegmentHit * sh;
  char buffer[MAXLINE];
  char copy[MAXLINE];
  int strand;

  out = new_DnaSequenceHitList();

  while( fgets(buffer,MAXLINE,ifp) != NULL ) {
    strcpy(copy,buffer);
    if( (sh = SegmentHit_from_msptmp_line(buffer,&strand)) == NULL ) {
      warn("Cannot parse [%s] as a MSP crunch line",copy);
      continue;
    }

    if( strand < 0 ) {
      add_SegmentHitList(out->backward,sh);
    } else {
      add_SegmentHitList(out->forward,sh);
    }
  }

  sort_SegmentHitList_by_qstart(out->forward);
  sort_SegmentHitList_by_qstart(out->backward);

  return out;
}

boolean verify_SegmentHit(SegmentHit * sh)
{
  boolean ret = TRUE;

  if ( sh->qstart <= 0 ) {
    ret = FALSE;
    warn("Got a less than zero index in query start %d",sh->qstart);
  }
  if ( sh->qend <= 0 ) {
    ret = FALSE;
    warn("Got a less than zero index in query end %d",sh->qend);
  }
  if ( sh->tstart <= 0 ) {
    ret = FALSE;
    warn("Got a less than zero index in target start %d",sh->tstart);
  }
  if ( sh->tend <= 0 ) {
    ret = FALSE;
    warn("Got a less than zero index in target end %d",sh->tend);
  }

  return ret;
}

%func
Reads a MSPcrunch -x output file 
%arg
ifp input file to read
return newly allocated structure
%%
DnaSequenceHitList * read_MSPcrunch_DnaSequenceHitList(FILE * ifp)
{
  DnaSequenceHitList * out;
  SegmentHit * sh;
  char buffer[MAXLINE];
  char copy[MAXLINE];
  int strand;

  out = new_DnaSequenceHitList();

  while( fgets(buffer,MAXLINE,ifp) != NULL ) {
    strcpy(copy,buffer);
    if( (sh = SegmentHit_from_MSPcrunch_line(buffer,&strand)) == NULL ) {
      warn("Cannot parse [%s] as a MSP crunch line",copy);
      continue;
    }
    if( verify_SegmentHit(sh) == FALSE ) {
      warn("Segment hit read in from [%s] was considered bad. Discarding",copy);
      sh = free_SegmentHit(sh);
      continue;
    }

    if( strand < 0 ) {
      add_SegmentHitList(out->backward,sh);
    } else {
      add_SegmentHitList(out->forward,sh);
    }
  }

  sort_SegmentHitList_by_qstart(out->forward);
  sort_SegmentHitList_by_qstart(out->backward);

  /*  fprintf(stderr,"We have %d forward and %d backward guys\n",out->forward->len,out->backward->len); */
  return out;
}



SegmentHit * SegmentHit_from_msptmp_line(char * line,int * strand)
{
  SegmentHit * out;
  char * runner;

  out = SegmentHit_alloc();

  runner = strtok(line,spacestr);

  if( runner == NULL || is_double_string(runner,&out->score) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL ) 
    goto error;

  if( *runner != '(' || runner[strlen(runner)-1] != ')' ) 
    goto error;

  runner[strlen(runner)-1] = '\0';
  runner++;
  if( is_integer_string(runner,strand) == FALSE)
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->qstart) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->qend) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->tstart) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->tend) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL ) 
    goto error;

  out->name = stringalloc(runner);

  return out;

  error :

    free_SegmentHit(out);
  return NULL;

}


SegmentHit * SegmentHit_from_MSPcrunch_line(char * line,int * strand)
{
  SegmentHit * out;
  char * runner;

  out = SegmentHit_alloc();

  runner = strtok(line,spacestr);

  if( runner == NULL || is_double_string(runner,&out->score) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL ) 
    goto error;

  if( *runner != '(' || runner[strlen(runner)-1] != ')' ) 
    goto error;

  runner[strlen(runner)-1] = '\0';
  runner++;
  if( is_integer_string(runner,strand) == FALSE)
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->qstart) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->qend) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->tstart) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL || is_integer_string(runner,&out->tend) == FALSE ) 
    goto error;

  if( (runner=strtok(NULL,spacestr)) == NULL ) 
    goto error;

  out->name = stringalloc(runner);

  return out;

  error :

    free_SegmentHit(out);
  return NULL;

}

  

  


%}