#define _GNU_SOURCE
#include "load_asn.h"
#include <string.h>
#include <asn.h>
#include <objgbseq.h>
#include <objsset.h>
#include <sqnutils.h>

void
print_asn (ObjectIdPtr oid, SeqIdPtr id, ValNodePtr descr, SeqAnnotPtr annot)
{
  /*
   * Print the record identifiers.
   */
  printf ("  IDENTIFIERS\n");
  printf ("  -----------\n");
  while (oid != NULL)
    {
      printf("%i, %s\n", oid->id, oid->str);
    }
  while (id != NULL)
    {
      //      printf ("ID: %i\n", id->choice);

      char idval[256];
      SeqIdPrint (id, idval, PRINTID_FASTA_SHORT);
      printf ("  %s\n", idval);

      //     if (id->choice == SEQID_GI)
      //	printf ("GI: %i\n", id->data.intvalue);
 
      id = id->next;
    }

  /*
   * Print descriptions.
   * [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/BIOSEQ.HTML#_Seq-descr:_Describing_the]
   */
  printf ("\n  DESCRIPTIONS\n");
  printf ("  ------------\n");
  while (descr != NULL)
    {
      switch (descr->choice)
	{
	case Seq_descr_title:
	  printf ("  TITLE: %s\n", (char*)descr->data.ptrvalue);
	  break;
	case Seq_descr_genbank:
	  printf ("  GENBANK\n");
	  break;
	case Seq_descr_pub:
	  printf ("  PUB\n");
	  break;
	case Seq_descr_create_date:
	  printf ("  CREATE DATE\n");
	  break;
	case Seq_descr_update_date:
	  printf ("  UPDATE DATE\n");
	  break;
	case Seq_descr_source:
	  printf ("  BIOSOURCE\n");
	  break;
	case Seq_descr_molinfo:
	  printf ("  MOLINFO\n");
	  break;
	default:
	  printf ("  DESCRIPTION CHOICE=%i\n", descr->choice);
	  break;
	}

      descr = descr->next;
    }

  /*
   * Print annotations.
   */
  printf ("\n  ANNOTATIONS\n");
  printf ("  -----------\n");
  while (annot != NULL)
    {
      printf ("  ANNOTATION: %s, ", annot->name);
      if (annot->desc != NULL) {
	switch (annot->desc->choice)
	  {
	  case Annot_descr_name:
	    printf ("  NAME: %s\n", (char*)annot->desc->data.ptrvalue);
	    break;
	  default:
	    printf ("  CHOICE=%i\n", annot->desc->choice);
	    break;
	  }
      }
      else
	printf ("  NONE\n");

      annot = annot->next;
    }

}

/*
 * Based on example at
 * [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQUTIL.HTML].
 */
void
load_asn (hid_t file_id, const char* file_name)
{
  char* asn_file = strdup(file_name);
  AsnIoPtr aip = AsnIoOpen (asn_file, "r"); 
  SeqEntryPtr sep = SeqEntryAsnRead (aip, NULL);
  BioseqSetPtr bsetp = 0;
  ValNodePtr descr = 0;
  SeqAnnotPtr annot = 0;
  SeqIdPtr id = 0;
  ObjectIdPtr oid = 0;

  /*
   * Data file statistics.
   */
  printf ("NODES: %i\tBIOSEQS: %i\n", ValNodeLen (sep), BioseqCount (sep));
  printf ("\n");

  /*
   * This loop needs to be corrected to handle nesting of sets.
   */

  while (sep != NULL)
    {
      bsetp = (BioseqSetPtr) sep->data.ptrvalue;  
      if (bsetp != NULL)
	{
	  oid = bsetp->id;
	  id = NULL;
	  descr = bsetp->descr;
	  annot = bsetp->annot;
	}

      printf ("BIOSEQSET\n");
      printf ("\n");
      print_asn (oid, id, descr, annot);
      printf ("\n");
      
      /*
       * Process Bioseqs in the set.
       */
      SeqEntryPtr sep2 = bsetp->seq_set;
      while (sep2 != NULL)
	{
	  BioseqPtr bsp = sep2->data.ptrvalue;
	  if (bsp != NULL)
	    {
	      oid = NULL;
	      id = bsp->id;
	      descr = bsp->descr;
	      annot = bsp->annot;
	      
	      printf ("BIOSEQ\n");
	      printf ("\n");	      
	      print_asn (oid, id, descr, annot);
	      printf ("\n");
	    }

	  sep2 = sep2->next;
	}
      
      sep = sep->next;
    } 

  AsnIoClose (aip);
  free (asn_file);

  return;
}