%{
#include "dyna.h"
#include "genewisemodel.h"
#include "threestatedb.h"
#include "gwlitemodel.h"


%}


struct GeneWiseDB
ThreeStateDB * tdb
double cds_factor;
CodonMapper * cm     // NB, hard linked.
RandomModelDNA * rmd // NB hard linked
GeneWiseScore * gws  // hardlinked, only if single.
GeneParameter21 * gpara // if a genomic model - est models wont use this!
boolean is_single !def="FALSE"
boolean is_syn       !def="TRUE"
Probability allN     !def="1.0"
boolean flat_insert  !def=FALSE
GwLiteScore * gwls   // only if single
%info
This is a database of genewisemodels
for database searching versions of
genewise and estwise type algorithms.

The actual HMM database streaming
happens via the ThreeStateDB (tdb).
This object holds the necessary conversion
system for the HMM database as it
is mapped into the genewisemodel
%%

%{
#include "genewisemodeldb.h"



%func
inits a genewise database. Remember this is used
for both genomic and cdna searches

%%
GeneWiseScore * init_GeneWiseDB(GeneWiseDB * gdb,int * return_status)
{
  ThreeStateModel * tsm;
  GeneWise * gw;
  GeneWiseScore * gws;
 

  *return_status = DB_RETURN_ERROR;

  if( gdb->is_single == TRUE ) {
    *return_status = DB_RETURN_OK;
    return gdb->gws;
  }

  if( open_ThreeStateDB(gdb->tdb) == FALSE ) {
    warn("Could not open three state db, so no genewisemodel possible!");
    return NULL;
  }

  tsm = read_TSM_ThreeStateDB(gdb->tdb,return_status);

  if( *return_status == DB_RETURN_ERROR) {
    warn("Cannot read a ThreeStateModelDB for the GeneWiseDB. Problem!");
    return NULL;
  }

  gw  =  GeneWise_from_ThreeStateModel_GDB(tsm,gdb);
  gws =  GeneWiseScore_from_GeneWise(gw);

  free_ThreeStateModel(tsm);
  free_GeneWise(gw);


  return gws;
}

%func
Reloads a genewise database

%%
GeneWiseScore * reload_GeneWiseDB(GeneWiseScore * prev,GeneWiseDB * gdb,int * return_status)
{
  ThreeStateModel * tsm;
  GeneWise * gw;
  GeneWiseScore * gws;
 


  if( gdb->is_single == TRUE ) {
    *return_status = DB_RETURN_END;
    return NULL;
  }

  if( prev != NULL)
    free_GeneWiseScore(prev);


  *return_status = DB_RETURN_ERROR;

  tsm = read_TSM_ThreeStateDB(gdb->tdb,return_status);

  if( *return_status != DB_RETURN_OK) {
    if( *return_status == DB_RETURN_END) {
      return NULL;
    }

    warn("Cannot read a ThreeStateModelDB for the GeneWiseDB. Problem!");
    return NULL;
  }

  gw  =  GeneWise_from_ThreeStateModel_GDB(tsm,gdb);
  gws =  GeneWiseScore_from_GeneWise(gw);

  /*  fprintf(stderr,"And %f %f %d %d is start %d %d %d\n",gw->seg[gw->len-1]->transition[GW_MATCH2END],tsm->unit[tsm->len-1]->transition[TSM_MATCH2END],gws->seg[0]->transition[GW_START2MATCH],gws->seg[1]->transition[GW_START2MATCH],gws->seg[1]->match[12],gws->seg[1]->match[113],gws->seg[gws->len-1]->transition[GW_MATCH2END]);
   */

  free_ThreeStateModel(tsm);
  free_GeneWise(gw);

  *return_status = DB_RETURN_OK;

  return gws;
}

%func
closes a GeneWiseDB
%%
boolean close_GeneWiseDB(GeneWiseScore * gws,GeneWiseDB * gdb)
{
  if( gdb->is_single == TRUE ) {
    return TRUE;
  }

  if( gws != NULL)
    free_GeneWiseScore(gws);

  return close_ThreeStateDB(NULL,gdb->tdb);
}

%func
adds dataentry stuff to a query. Relies completely
on threestatedb
%%
boolean dataentry_add_GeneWiseDB(DataEntry * de,GeneWiseScore * gws,GeneWiseDB * gdb)
{
  if( gdb->is_single == TRUE) {
    if ( gdb->gws->name == NULL ) {
      warn("No name for a single GeneWiseDB unit.");
      de->name = stringalloc("NoName");
    } else {
      de->name = stringalloc(gdb->gws->name);
    }

    return TRUE;
  }

  
  /*de->name = stringalloc(gws->name);*/

  /* otherwise, pass it on to tdb */
  dataentry_add_ThreeStateDB(de,NULL,gdb->tdb);
  if( de->name == NULL ) {
    if( gws->name != NULL ) {
      de->name = stringalloc(gws->name);
    }
  }
  return TRUE;
}

%func
Makes a genewise models from the threestatemodel
and parameters held in the GeneWiseDB
%type internal
%%
GeneWise * GeneWise_from_ThreeStateModel_GDB(ThreeStateModel * tsm,GeneWiseDB * gdb)
{
  int i;
  GeneWise * out;


  if( gdb->gpara != NULL ) {
    out=GeneWise_from_ThreeStateModel(tsm,gdb->gpara->gp,gdb->gpara->cm,gdb->allN,gdb->gpara->gwcm);
    if( out == NULL ) {
      return NULL;
    }

    if( gdb->gpara->modelled_splice == FALSE)
      flatten_balance_scores_GeneWise(out);
  } else {
    out = GeneWise_alloc_len(tsm->len);
    out->name = stringalloc(tsm->name);

    for(i=0;i<tsm->len;i++) {
      add_GeneWise(out,GeneWiseSegment_from_ThreeStateUnit(tsm->unit[i],gdb->cds_factor,gdb->cm,NULL,gdb->allN));
    }
  }


  if( gdb->is_syn == TRUE ) {
    if( tsm->rm == NULL ) {
      warn("Bad error. ThreeStateModel does not have a random model!");
      return free_GeneWise(out);
    }
    GeneWise_fold_in_synchronised_RandomModel(out,tsm->rm,gdb->cm,gdb->cm->ct,0.5);
  } else {
    GeneWise_fold_in_RandomModelDNA(out,gdb->rmd);
  }
  
  if( gdb->flat_insert == TRUE ) {
    check_flat_insert(out,1,0,gdb->cm->ct);
  }

  return out;
}

%func
makes a new GeneWiseDB from its component parts,
assumming a cDNA db.

All the objects are hard-linked internally, so you can, if you
wish, free them once passing them into this function
%arg
tdb three state model db to use
cp codon parser function to remove from match state
rmd random model (dna)
syn if ture, use a synchronous coding model vs internally stored tdb rm's
%%
GeneWiseDB * new_GeneWiseDB_cdna(ThreeStateDB * tdb,cDNAParser * cp,CodonMapper * cm,RandomModelDNA * rmd,boolean use_syn,boolean flat_insert,Probability allN) 
{
  GeneWiseDB * out;

  out = GeneWiseDB_alloc();

  out->tdb = hard_link_ThreeStateDB(tdb);
  out->is_single = FALSE;
  
  out->rmd = hard_link_RandomModelDNA(rmd);
  out->cm = hard_link_CodonMapper(cm);
  out->cds_factor = (1.0 - removed_probability_from_cds_cdna(cp));
  out->is_syn = use_syn;
  out->allN = allN;
  out->flat_insert = flat_insert;
  return out;
}

%func
makes a new GeneWiseDB from its component parts.
All the objects are hard-linked internally, so you can, if you
wish, free them once passing them into this function
%%
GeneWiseDB * new_GeneWiseDB(ThreeStateDB * tdb,GeneParameter21 * gp,RandomModelDNA * rmd,boolean use_syn,Probability allN)
{
  GeneWiseDB * out;

  out = GeneWiseDB_alloc();

  out->tdb = hard_link_ThreeStateDB(tdb);
  out->is_single = FALSE;
  
  out->rmd = hard_link_RandomModelDNA(rmd);
  out->gpara = hard_link_GeneParameter21(gp);
  out->cm = hard_link_CodonMapper(gp->cm);
  out->is_syn = use_syn;
  out->allN   = allN;
  return out;
}

%func
makes a new GeneWiseDB from a single GeneWiseScore.
It hard links it, so you should free it afterwards
in its own scope.
%%
GeneWiseDB * new_single_GeneWiseDB(GeneWiseScore * gws)
{
  GeneWiseDB * out;

  out = GeneWiseDB_alloc();
  out->gws = hard_link_GeneWiseScore(gws);
  out->is_single = TRUE;

  return out;
}


%func
inits a genewise database for gwlite models


%%
GwLiteScore * init_GwLite_GeneWiseDB(GeneWiseDB * gdb,int * return_status)
{
  ThreeStateModel * tsm;
  GeneWise * gw;
  GwLite * gl;
  GwLiteScore * gws;
 

  *return_status = DB_RETURN_ERROR;

  if( gdb->is_single == TRUE ) {
    *return_status = DB_RETURN_OK;
    /* at the moment, die horribly */
    fatal("Apologies. We don't handle single genewise model databases for gwlite yet");
    return gdb->gwls;
  }

  if( open_ThreeStateDB(gdb->tdb) == FALSE ) {
    warn("Could not open three state db, so no genewisemodel possible!");
    return NULL;
  }

  tsm = read_TSM_ThreeStateDB(gdb->tdb,return_status);

  if( *return_status == DB_RETURN_ERROR) {
    warn("Cannot read a ThreeStateModelDB for the GeneWiseDB. Problem!");
    return NULL;
  }

  gw  =  GeneWise_from_ThreeStateModel_GDB(tsm,gdb);
  gl  =  GwLite_from_GeneWise(gw);
  gws =  GwLiteScore_from_GwLite(gl);

  free_ThreeStateModel(tsm);
  free_GeneWise(gw);
  free_GwLite(gl);

  return gws;
}

%func
Reloads a genewise database for a GwLite database

%%
GwLiteScore * reload_GwLite_GeneWiseDB(GwLiteScore * prev,GeneWiseDB * gdb,int * return_status)
{
  ThreeStateModel * tsm;
  GeneWise * gw;
  GwLite * gl;
  GwLiteScore * gws;
 


  if( gdb->is_single == TRUE ) {
    *return_status = DB_RETURN_END;
    return NULL;
  }

  if( prev != NULL)
    free_GwLiteScore(prev);


  *return_status = DB_RETURN_ERROR;

  tsm = read_TSM_ThreeStateDB(gdb->tdb,return_status);

  if( *return_status != DB_RETURN_OK) {
    if( *return_status == DB_RETURN_END) {
      return NULL;
    }

    warn("Cannot read a ThreeStateModelDB for the GeneWiseDB. Problem!");
    return NULL;
  }

  gw  =  GeneWise_from_ThreeStateModel_GDB(tsm,gdb);
  gl  =  GwLite_from_GeneWise(gw);
  gws =  GwLiteScore_from_GwLite(gl);

  free_ThreeStateModel(tsm);
  free_GeneWise(gw);
  free_GwLite(gl);

  *return_status = DB_RETURN_OK;

  return gws;
}

%func
closes a GeneWiseDB
%%
boolean close_GwLite_GeneWiseDB(GwLiteScore * gws,GeneWiseDB * gdb)
{
  if( gdb->is_single == TRUE ) {
    return TRUE;
  }

  if( gws != NULL)
    free_GwLiteScore(gws);

  return close_ThreeStateDB(NULL,gdb->tdb);
}

%func
adds dataentry stuff to a query. Relies completely
on threestatedb
%%
boolean dataentry_add_GwLite_GeneWiseDB(DataEntry * de,GwLiteScore * gws,GeneWiseDB * gdb)
{
  if( gdb->is_single == TRUE) {
    if ( gdb->gws->name == NULL ) {
      warn("No name for a single GeneWiseDB unit.");
      de->name = stringalloc("NoName");
    } else {
      de->name = stringalloc(gdb->gws->name);
    }

    return TRUE;
  }

  
  /*de->name = stringalloc(gws->name);*/

  /* otherwise, pass it on to tdb */
  dataentry_add_ThreeStateDB(de,NULL,gdb->tdb);
  if( de->name == NULL ) {
    if( gws->name != NULL ) {
      de->name = stringalloc(gws->name);
    }
  }
  return TRUE;
}

%}