22 files changed, 181 insertions, 71 deletions

diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c
new file mode 100644
index 0000000..a217989
--- a/dev/null
+++ b/src/load/load_influenza_faa.c
@@ -0,0 +1,97 @@
+#include "error/check_error.h"
+#include "error/check_h5_error.h"
+#include "load_influenza_faa.h"
+#include "model/sequence_data.h"
+#include "model/sequence_data_init.h"
+#include <hdf5_hl.h>
+#include <string.h>
+#include <stdlib.h>
+
+void
+load_influenza_faa (hid_t file_id)
+{
+  size_t dst_size;
+  size_t dst_offset[SEQUENCE_DATA_FIELD_NUM];
+  size_t dst_sizes[SEQUENCE_DATA_FIELD_NUM];
+  hid_t field_type[SEQUENCE_DATA_FIELD_NUM];
+
+  sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type);
+  
+  hsize_t chunk_size = 10;
+  int *fill_data = NULL;
+  int compress = 0;
+
+  sequence_data p_data;
+  FILE *dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza.faa",
+		     "r");
+  if (dat == NULL)
+    check_error (__FILE__, __LINE__);
+  char *line = NULL;
+  size_t len = 0;
+  int current_line = 0;
+
+  while (getline (&line, &len, dat) != -1)
+    {
+      current_line++;      
+
+      // Header line.
+      if (line[0] == '>')
+	{
+	  char *running = strdup (line);
+	  char *token = NULL;
+	  
+	  // Eat the ">gi".
+	  strsep (&running, "|");
+	  
+	  // GI value.
+	  token = strsep (&running, "|");
+	  p_data.gi = atoi (token);
+
+	  // Eat the "gb"
+	  strsep (&running, "|");
+
+	  // GB value.
+	  strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb));
+
+	  // Description value.
+	  strncpy (p_data.description, strsep (&running, "|"),
+		   sizeof (p_data.description));
+
+	  const char* sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] =
+	    SEQUENCE_DATA_FIELD_NAMES;
+
+	  if (current_line == 1)
+	    {
+	      herr_t status = H5TBmake_table ("influenza.faa", file_id,
+					      "influenza.faa",
+					      SEQUENCE_DATA_FIELD_NUM, 1,
+					      dst_size, sequence_data_field_names,
+					      dst_offset, field_type,
+					      chunk_size, fill_data, compress,
+					      &p_data);
+	      if (status < 0)
+		check_h5_error (status, __FILE__, __LINE__);
+	    }
+	  else
+	    {
+	      herr_t status =
+		H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
+				    dst_offset, dst_sizes, &p_data);
+	      if (status < 0)
+		check_h5_error (status, __FILE__, __LINE__);
+	    }
+
+	  if (running)
+	    free (running);
+
+	}
+      
+    }
+
+  if (line)
+    free (line);
+
+  fclose (dat);
+
+  return;
+}