%{
#include "threestatemodel.h"
#define NO_HMMER_INCLUDES
#include "wise2xhmmer2.h"

#define PfamHmmer1DBLISTLENGTH 512

%}

struct PfamHmmer1Entry
char * entryname
boolean is_random
boolean is_hmmls
double bits_cutoff


struct PfamHmmer1DB
PfamHmmer1Entry ** en !list
char * dirname // directory name with the models
int cur !def="0"
RandomModel * def; // default random model
%info

Pfam Hmmer1db is a wrapper around a Pfam Hmmer database.  This is file
called HMM.s in a directory which has appropiate .HMM and .random
files

Although this DB will be phased out, it is still around for a while.

This wont be used directly, but rather in a threestatedb model. 
It does not implement a full dynamite style db stream. rather it expects
threestatedb to prod it in the correct manner.

%%

api
object PfamHmmer1DB
des free_PfamHmmer1DB
endobject
object PfamHmmer1Entry
des free_PfamHmmer1Entry
endobject
endapi

%{
#include "pfamhmmer1db.h"


%func
reads a named model - akin to indexing
%%
ThreeStateModel * ThreeStateModel_from_name_PfamHmmer1DB(PfamHmmer1DB * phd,char * name)
{
  char buffer[512];
  ThreeStateModel * tsm;

  sprintf(buffer,"%s/%s.hmm",phd->dirname,name);

  /*  tsm = Wise2_read_ThreeStateModel_from_hmmer1_file(buffer); */
  tsm = HMMer2_read_ThreeStateModel(buffer);

  if( tsm == NULL ) {
    warn("Could not open Hmmer1 style hmm from Pfam db on file [%s]",buffer);
    return NULL;
  }

  if( tsm->name != NULL ) {
    ckfree(tsm->name);
  }
  tsm->name = stringalloc(name);

  /* ignore random stuff for the moment */

  return tsm;
}

%func
reads the next threestatemodel
for PfamHmmer1DB, placing the correct
status into return_status( DB_RETURN_OK, etc).
%%
ThreeStateModel * read_next_TSM_PfamHmmer1DB(PfamHmmer1DB * phd,int * return_status)
{
  ThreeStateModel * out;

  if( phd->cur >= phd->len ) {
    *return_status = DB_RETURN_END;
    return NULL;
  }
  out = read_TSM_from_PfamHmmer1Entry(phd->en[phd->cur++],phd->dirname);

  if( out == NULL ) {
    *return_status = DB_RETURN_ERROR;
    return NULL;
  } else {
    *return_status = DB_RETURN_OK;
    out->rm = hard_link_RandomModel(phd->def);
    return out;
  }
  return out;
}

%func
reads an individual HMMer model from the entry
specification
%%
ThreeStateModel * read_TSM_from_PfamHmmer1Entry(PfamHmmer1Entry * en,char * dir)
{
  char buffer[512];
  ThreeStateModel * tsm;

  sprintf(buffer,"%s/%s.hmm",dir,en->entryname);

  /*  tsm = Wise2_read_ThreeStateModel_from_hmmer1_file(buffer); */
  tsm = HMMer2_read_ThreeStateModel(buffer);

  if( tsm == NULL ) {
    warn("Could not open Hmmer1 style hmm from Pfam db on file [%s]",buffer);
    return NULL;
  }

  if( tsm->name != NULL ) {
    ckfree(tsm->name);
  }
  tsm->name = stringalloc(en->entryname);
  display_char_in_ThreeStateModel(tsm);

  /* ignore random stuff for the moment */

  if( en->is_hmmls == FALSE ) {
    force_weighted_local_model(tsm,1.0,1.0,1.0);
  } else {
    force_weighted_local_model(tsm,1.0,0.5,0.5);
  }

  return tsm;
}

%func
Makes a new PfamHmmer1DB from the dir name.

The directory should have a file HMMs which has
entries like

rrm hmmls 12

with -r indicating a specialised random model.
%%
PfamHmmer1DB * PfamHmmer1DB_from_dirname(char * dirname)
{
  char buffer[512];
  PfamHmmer1DB * out;
  FILE * ifp;
  char * runner;
  PfamHmmer1Entry * en;

  if( dirname == NULL ) {
    warn("passed through a NULL dirname into PfamHmmer1DB!");
    return NULL;
  }
  
  sprintf(buffer,"%s/HMMs",dirname);
  if( (ifp= openfile(buffer,"r")) == NULL ) {
    warn("Could not open %s as PfamHmmer1DB file list",buffer);
    return NULL;
  }

  out = PfamHmmer1DB_alloc_std();
  out->def = default_RandomModel();
  out->dirname = stringalloc(dirname);

  while( fgets(buffer,512,ifp) != NULL ) {
    if( (runner=strtok(buffer,spacestr)) == NULL) {
      continue; /* silently */
    }
    en  = PfamHmmer1Entry_alloc();
    en->entryname = stringalloc(runner);
    if( (runner=strtok(NULL,spacestr)) == NULL) {
      warn("Got a bad HMM.s line for a Pfam db. Skipping");
      free_PfamHmmer1Entry(en);
      continue;
    }
    if( strstr(runner,"hmmls") != NULL ) {
      en->is_hmmls = TRUE;
    } else {
      en->is_hmmls = FALSE;
    }


    if( strstr(runner,"-r") != NULL ) {
      en->is_random = TRUE;
    } else {
      en->is_random = FALSE;
    }

    if( (runner=strtok(NULL,spacestr)) == NULL) {
      warn("Got a bad HMM.s line for a Pfam db. Skipping");
      free_PfamHmmer1Entry(en);
      continue;
    }

    if( is_double_string(runner,&en->bits_cutoff) == FALSE ) {
      warn("%s does not look like a bits cutoff to me. Calling it 25",en->entryname,runner);
      en->bits_cutoff = 25;
    }
    add_PfamHmmer1DB(out,en);
  }

  fclose(ifp);
  return out;
}


%}