#include "load_influenza_aa_dat.h"
#include "hdf5_hl.h"

#define NFIELDS (hsize_t) 11
//#define NRECORDS (hsize_t) 138052
#define NRECORDS (hsize_t) 1
#define TABLE_NAME "influenza_aa.dat"

void
load_influenza_aa_dat (hid_t file_id)
{
  /*
   * Model the data using native types.
   */
  typedef struct supplementary_data
  {
    char genbank_accession_number[9];
    char host[15];
    int genome_segment_number;
    char subtype[7];
    char country[25];
    int year;
    int sequence_length;
    char virus_name[196];
    char age[17];
    char gender[6];
    char full_length_indicator[4];
  } supplementary_data;

  /*
   * Use an HDF5 Table for storage.
   * http://www.hdfgroup.org/HDF5/Tutor/h5table.html
   */

  /*
   * "Calculate the size and the offsets of our struct members in
   * memory."
   */
  size_t dst_size = sizeof (supplementary_data);
  size_t dst_offset[NFIELDS] = { HOFFSET ( supplementary_data, genbank_accession_number ),
				 HOFFSET ( supplementary_data, host ),
				 HOFFSET ( supplementary_data, genome_segment_number ),
				 HOFFSET ( supplementary_data, subtype ),
				 HOFFSET ( supplementary_data, country ),
				 HOFFSET ( supplementary_data, year ),
				 HOFFSET ( supplementary_data, sequence_length ),
				 HOFFSET ( supplementary_data, virus_name ),
				 HOFFSET ( supplementary_data, age ),
				 HOFFSET ( supplementary_data, gender ),
				 HOFFSET ( supplementary_data, full_length_indicator )};

  /*

    Only needed for reading?

  supplementary_data dst_buf[NRECORDS];

  size_t dst_sizes[NFIELDS] = { sizeof ( dst_buf[0].genbank_accession_number ),
				sizeof ( dst_buf[0].host ),
				sizeof ( dst_buf[0].genome_segment_number ),
				sizeof ( dst_buf[0].subtype ),
				sizeof ( dst_buf[0].country ),
				sizeof ( dst_buf[0].year ),
				sizeof ( dst_buf[0].sequence_length ),
				sizeof ( dst_buf[0].virus_name ),
				sizeof ( dst_buf[0].age ),
				sizeof ( dst_buf[0].gender ),
				sizeof ( dst_buf[0].full_length_indicator)};
  */

  /*
   * "Define field information."
   */
  const char *field_names[NFIELDS] =
    { "GenBank accession number",
      "Host",
      "Genome segment number",
      "Subtype",
      "Country",
      "Year",
      "Sequence length",
      "Virus name",
      "Age",
      "Gender",
      "Full-length Indicator" };
  hsize_t chunk_size = 10;
  int *fill_data = NULL;
  int compress = 0;
  
  /*
   * "Initialize field type."
   */
  hid_t field_type[NFIELDS];

  hid_t genbank_accession_number_type = H5Tcopy ( H5T_C_S1 );
  H5Tset_size ( genbank_accession_number_type, 9 );
  field_type[0] = genbank_accession_number_type;

  hid_t host_type = H5Tcopy ( H5T_C_S1 );
  H5Tset_size ( host_type, 15 );
  field_type[1] = host_type;
  
  field_type[2] = H5T_NATIVE_INT;

  hid_t subtype_type = H5Tcopy ( H5T_C_S1 );
  H5Tset_size (subtype_type, 7 );
  field_type[3] = subtype_type;

  hid_t country_type = H5Tcopy ( H5T_C_S1 );
  H5Tset_size (country_type, 25 );
  field_type[4] = country_type;

  field_type[5] = H5T_NATIVE_INT; 

  field_type[6] = H5T_NATIVE_INT;

  hid_t virus_name_type = H5Tcopy ( H5T_C_S1 );
  H5Tset_size (virus_name_type, 196);
  field_type[7] = virus_name_type;

  hid_t age_type = H5Tcopy (H5T_C_S1);
  H5Tset_size (age_type, 17);
  field_type[8] = age_type;

  hid_t gender_type = H5Tcopy (H5T_C_S1);
  H5Tset_size (gender_type, 6);
  field_type[9] = gender_type;

  hid_t full_length_indicator_type = H5Tcopy (H5T_C_S1);
  H5Tset_size (full_length_indicator_type, 4);
  field_type[10] = full_length_indicator_type;

  supplementary_data p_data[NRECORDS] = {
    {"BAC53999", "Human", 7, "", "Zambia", 1999, 109, "Influenza B virus (B/Lusaka/270/99)",
     "", "", "yes"}
  };

  herr_t status = H5TBmake_table ("influenza_aa.dat", file_id, TABLE_NAME,NFIELDS,NRECORDS,
				  dst_size,field_names, dst_offset, field_type,
				  chunk_size, fill_data, compress, p_data);

  H5Tclose (genbank_accession_number_type);
  H5Tclose (host_type);
  H5Tclose (subtype_type);
  H5Tclose (country_type);
  H5Tclose (virus_name_type);
  H5Tclose (age_type);
  H5Tclose (gender_type);
  H5Tclose (full_length_indicator_type);

  return;
}