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#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;
}
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