Reorganization of include files. Added missing license.

include/bayes/factor.h → attic/factor.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_FACTOR_H_
+#ifdef _SPEL_BAYES_FACTOR_H_
+#error "_SPEL_BAYES_FACTOR_H_ already defined!"
+#else
 #define _SPEL_BAYES_FACTOR_H_
 
 #include "message.h"

include/bayes/factor_var.h → attic/factor_var.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_FACTOR_VAR_H_
+#ifdef _SPEL_BAYES_FACTOR_VAR_H_
+#error "_SPEL_BAYES_FACTOR_VAR_H_ already defined!"
+#else
 #define _SPEL_BAYES_FACTOR_VAR_H_
 
 

include/bayes/factor_var2.h → attic/factor_var2.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_FACTOR_VAR_H_
+#ifdef _SPEL_BAYES_FACTOR_VAR_H_
+#error "_SPEL_BAYES_FACTOR_VAR_H_ already defined!"
+#else
 #define _SPEL_BAYES_FACTOR_VAR_H_
 
 

include/bayes/factor_var3.h → attic/factor_var3.h

@@ -15,11 +15,13 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_FACTOR_VAR_H_
+#ifdef _SPEL_BAYES_FACTOR_VAR_H_
+#error "_SPEL_BAYES_FACTOR_VAR_H_ already defined!"
+#else
 #define _SPEL_BAYES_FACTOR_VAR_H_
 
 
-#include "../pedigree.h"
+#include "pedigree.h"
 #include <forward_list>
 
 inline double huge_double()

include/bayes/factor_var4.h → attic/factor_var4.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_FACTOR_VAR_H_
+#ifdef _SPEL_BAYES_FACTOR_VAR_H_
+#error "_SPEL_BAYES_FACTOR_VAR_H_ already defined!"
+#else
 #define _SPEL_BAYES_FACTOR_VAR_H_
 
 

include/cache/factory.h → attic/factory.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_CACHE_FACTORY_H_
+#ifdef _SPEL_CACHE_FACTORY_H_
+#error "_SPEL_CACHE_FACTORY_H_ already defined!"
+#else
 #define _SPEL_CACHE_FACTORY_H_
 
 #include <vector>
@@ -24,14 +26,14 @@
 #include <future>
 #include <typeinfo>
 
-#include "md5.h"
+#include "cache/md5.h"
 #include "input.h"
 
 /*#include "call_tuple.h"*/
-#include "tuple_utils.h"
-#include "value.h"
-#include "cartesian_product.h"
-#include "file.h"
+#include "cache/tuple_utils.h"
+#include "cache/value.h"
+#include "cache/cartesian_product.h"
+#include "cache/file.h"
 
 template <typename T>
 using only_if_derives_from_wof = typename std::enable_if<std::is_base_of<cache::with_output_func, T>::value, T>::type;

include/fmin.h → attic/fmin.h

@@ -22,7 +22,9 @@
  * Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., http://www.netlib.org/f2c/libf2c.zip
  */
 
-#ifndef _SPEL_FMIN_H_
+#ifdef _SPEL_FMIN_H_
+#error "_SPEL_FMIN_H_ already defined!"
+#else
 #define _SPEL_FMIN_H_
 
 #include <utility>

include/computations/from_settings.h → attic/from_settings.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_COMPUTATIONS_FROM_SETTINGS_H_
+#ifdef _SPEL_COMPUTATIONS_FROM_SETTINGS_H_
+#error "_SPEL_COMPUTATIONS_FROM_SETTINGS_H_ already defined!"
+#else
 #define _SPEL_COMPUTATIONS_FROM_SETTINGS_H_
 
 typedef cache::value<const ::generation_rs*> generation_value;

include/computations/genetic.h → attic/genetic.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_COMPUTATIONS_GENETIC_H_
+#ifdef _SPEL_COMPUTATIONS_GENETIC_H_
+#error "_SPEL_COMPUTATIONS_GENETIC_H_ already defined!"
+#else
 #define _SPEL_COMPUTATIONS_GENETIC_H_
 
 namespace computations {

include/geno_matrix0.h → attic/geno_matrix0.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_GENO_MATRIX_H_
+#ifdef _SPEL_GENO_MATRIX_H_
+#error "_SPEL_GENO_MATRIX_H_ already defined!"
+#else
 #define _SPEL_GENO_MATRIX_H_
 
 #include "eigen.h"

include/geno_matrix1.h → attic/geno_matrix1.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_GENO_MATRIX_H_
+#ifdef _SPEL_GENO_MATRIX_H_
+#error "_SPEL_GENO_MATRIX_H_ already defined!"
+#else
 #define _SPEL_GENO_MATRIX_H_
 
 #include "eigen.h"

include/bayes/graph.h → attic/graph.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_GRAPH_H_
+#ifdef _SPEL_BAYES_GRAPH_H_
+#error "_SPEL_BAYES_GRAPH_H_ already defined!"
+#else
 #define _SPEL_BAYES_GRAPH_H_
 
 #include <list>

include/bayes/graph2.h → attic/graph2.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_GRAPH_H_
+#ifdef _SPEL_BAYES_GRAPH_H_
+#error "_SPEL_BAYES_GRAPH_H_ already defined!"
+#else
 #define _SPEL_BAYES_GRAPH_H_
 
 #include <list>

include/bayes/graphnode.h → attic/graphnode.h

@@ -15,12 +15,14 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BAYES_GRAPH_NODE_H_
+#ifdef _SPEL_BAYES_GRAPH_NODE_H_
+#error "_SPEL_BAYES_GRAPH_NODE_H_ already defined!"
+#else
 #define _SPEL_BAYES_GRAPH_NODE_H_
 
 #include "graphnode_base.h"
 
-#include "../pedigree.h"
+#include "pedigree.h"
 
 struct graph_type {
     node_vec rank;