Moved updating the HDF5 file to a separate driver.

3 files changed, 43 insertions, 8 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index fcbcdd5..a7e6852 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,15 +1,18 @@
-bin_PROGRAMS = aggregator
+bin_PROGRAMS = aggregator updator
 
 aggregator_SOURCES = \
         aggregator.c \
-        assign_protein_type.c \
         check_error.c \
         check_h5_error.c \
-        check_ncbi_error.c \
         load_influenza_aa_dat.c \
         load_influenza_faa.c
 
-aggregator_LDADD = -lhdf5
+updator_SOURCES = \
+        updator.c \
+        check_error.c \
+        check_h5_error.c \
+        check_ncbi_error.c \
+        assign_protein_type.c
 
 noinst_HEADERS = \
         assign_protein_type.h \
diff --git a/src/aggregator.c b/src/aggregator.c
index 36ea18c..07aba39 100644
--- a/src/aggregator.c
+++ b/src/aggregator.c
@@ -3,7 +3,6 @@
  * container.
  */
 
-#include "assign_protein_type.h"
 #include "check_h5_error.h"
 #include "load_influenza_aa_dat.h"
 #include "load_influenza_faa.h"
@@ -17,6 +16,8 @@ main ()
    * Create the HDF5 file.
    */
   hid_t file_id = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+  if (file_id < 0)
+    check_h5_error (file_id, __FILE__, __LINE__);
 
   /*
    * Load the supplementary protein data file.
@@ -29,13 +30,11 @@ main ()
   load_influenza_faa (file_id);
 
   /*
-   * Close the HD5 file.
+   * Close the HDF5 file.
    */
   herr_t status = H5Fclose (file_id);
   if (status < 0)
     check_h5_error (status, __FILE__, __LINE__);
 
-  // assign_protein_type (0);
-
   return 0;
 }
diff --git a/src/updator.c b/src/updator.c
new file mode 100644
index 0000000..8d556da
--- a/dev/null
+++ b/src/updator.c
@@ -0,0 +1,33 @@
+/*
+ * Update derived fields.
+ */
+
+#include "assign_protein_type.h"
+#include "check_h5_error.h"
+
+#define FILE "influenza.h5"
+
+int
+main ()
+{
+  /*
+   * Open the HDF5 file.
+   */
+  hid_t file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);
+  if (file_id < 0)
+    check_h5_error (file_id, __FILE__, __LINE__);
+
+  /*
+   * Assign protein type values to the sequence records.
+   */
+  assign_protein_type (file_id);
+
+  /*
+   * Close the HDF5 file.
+   */
+  herr_t status = H5Fclose (file_id);
+  if (status < 0)
+    check_h5_error (status, __FILE__, __LINE__);
+
+  return 0;
+}