22 files changed, 181 insertions, 71 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index 6dd8e16..06a6f5c 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -2,28 +2,31 @@ bin_PROGRAMS = aggregator updator
 
 aggregator_SOURCES = \
         aggregator.c \
-        check_error.c \
-        check_h5_error.c \
-        load_influenza_aa_dat.c \
-        load_influenza_faa.c \
-        sequence_data_init.c
+        error/check_error.c \
+        error/check_h5_error.c \
+        load/load_influenza_aa_dat.c \
+        load/load_influenza_faa.c \
+        model/sequence_data_init.c
 
 updator_SOURCES = \
         updator.c \
-        check_error.c \
-        check_h5_error.c \
-        check_ncbi_error.c \
-        assign_protein_type.c \
-        sequence_data_init.c
+        assign/assign_protein_type.c \
+        error/check_error.c \
+        error/check_h5_error.c \
+        error/check_ncbi_error.c \
+        model/gi_type_data_init.c \
+        model/sequence_data_init.c
 
 noinst_HEADERS = \
-        assign_protein_type.h \
-        check_error.h \
-        check_h5_error.h \
-        check_ncbi_error.h \
-        load_influenza_aa_dat.h \
-        load_influenza_faa.h \
-        sequence_data.h \
-        sequence_data_init.h
+        assign/assign_protein_type.h \
+        error/check_error.h \
+        error/check_h5_error.h \
+        error/check_ncbi_error.h \
+        load/load_influenza_aa_dat.h \
+        load/load_influenza_faa.h \
+        model/gi_type_data.h \
+        model/gi_type_data_init.h \
+        model/sequence_data.h \
+        model/sequence_data_init.h
 
 AM_CFLAGS = -Wall -std=gnu99 -ggdb