stop including our own std_vector.i, instead just extend the one provided with swig; duplicate the std_list file into the csharp wrapper in case it ends up needing to be different

Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i

@@ -46,8 +46,8 @@
 /* Include the base types before anything that will utilize them */
 %include "stdint.i"
 %include "std_string.i"
-%include "../gmwrapper/std_list.i"
-%include "../gmwrapper/std_vector.i"
+%include "std_list.i"
+%include "extend_std_vector.i"
 %include "std_map.i"
 %include "std_pair.i"
 %include "carrays.i"

Code/JavaWrappers/csharp_wrapper/std_list.i

@@ -0,0 +1,65 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * std_list.i
+ * ----------------------------------------------------------------------------- */
+
+%include <std_common.i>
+
+%{
+#include <list>
+#include <stdexcept>
+%}
+
+namespace std {
+    
+    template<class T> class list {
+      public:
+        typedef size_t size_type;
+        typedef T value_type;
+        typedef const value_type& const_reference;
+        list();
+        size_type size() const;
+        %rename(isEmpty) empty;
+        bool empty() const;
+        void clear();
+        %rename(add) push_back;
+        void push_back(const value_type& x);
+        %extend {
+            const_reference get(int i) throw (std::out_of_range) {
+                int size = int(self->size());
+                int j;
+                if (i>=0 && i<size) {
+                  std::list< T >::const_iterator p;  
+                  p=self->begin(); 
+                  for (j=0; j<i; j++) {p++;}
+                  return (*p);   
+                }
+                else
+                    throw std::out_of_range("list index out of range");
+            }
+
+            bool equals(const list<T> &o){
+              if(self->size()==o.size()){
+                std::list< T >::const_iterator sIt=self->begin();
+                std::list< T >::const_iterator oIt=o.begin();
+                while(sIt != self->end()){
+                  if(*sIt != *oIt) return false;
+                  ++sIt;
+                  ++oIt;
+                }
+                return true;
+              } else {
+                return false;
+              }
+            }
+
+        }
+   };
+}
+
+%define specialize_std_list(T)
+#warning "specialize_std_list - specialization for type T no longer needed"
+%enddef
+

Code/JavaWrappers/extend_std_vector.i

@@ -0,0 +1,27 @@
+/* -----------------------------------------------------------------------------
+ * extend_std_vector.i
+ * ----------------------------------------------------------------------------- */
+
+
+%extend std::vector {
+  bool equals(const vector<T> &o){
+    if(self->size()==o.size()){
+      std::vector< T >::const_iterator sIt=self->begin();
+      std::vector< T >::const_iterator oIt=o.begin();
+      while(sIt != self->end()){
+        if(*sIt != *oIt) return false;
+        ++sIt;
+        ++oIt;
+      }
+      return true;
+    } else {
+      return false;
+    }
+  }
+ };
+
+%include <std_vector.i>
+
+
+
+

Code/JavaWrappers/gmwrapper/GraphMolJava.i

@@ -47,7 +47,7 @@
 %include "stdint.i"
 %include "std_string.i"
 %include "std_list.i"
-%include "std_vector.i"
+%include "extend_std_vector.i"
 %include "std_map.i"
 %include "std_pair.i"
 %include "carrays.i"
@@ -262,4 +262,4 @@ typedef unsigned long long int	uintmax_t;
 %{
 #include <RDGeneral/versions.h>
 %}
-%include <RDGeneral/versions.h>
+%include <RDGeneral/versions.h>

Code/JavaWrappers/gmwrapper/std_vector.i

@@ -1,99 +0,0 @@
-/* -----------------------------------------------------------------------------
- * std_vector.i
- * ----------------------------------------------------------------------------- */
-
-%include <std_common.i>
-
-%{
-#include <vector>
-#include <stdexcept>
-%}
-
-namespace std {
-    
-    template<class T> class vector {
-      public:
-        typedef size_t size_type;
-        typedef T value_type;
-        typedef const value_type& const_reference;
-        vector();
-        vector(size_type n);
-        size_type size() const;
-        size_type capacity() const;
-        void reserve(size_type n);
-        %rename(isEmpty) empty;
-        bool empty() const;
-        void clear();
-        %rename(add) push_back;
-        void push_back(const value_type& x);
-        %extend {
-            const_reference get(int i) throw (std::out_of_range) {
-                int size = int(self->size());
-                if (i>=0 && i<size)
-                    return (*self)[i];
-                else
-                    throw std::out_of_range("vector index out of range");
-            }
-            void set(int i, const value_type& val) throw (std::out_of_range) {
-                int size = int(self->size());
-                if (i>=0 && i<size)
-                    (*self)[i] = val;
-                else
-                    throw std::out_of_range("vector index out of range");
-            }
-            bool equals(const vector<T> &o){
-              if(self->size()==o.size()){
-                std::vector< T >::const_iterator sIt=self->begin();
-                std::vector< T >::const_iterator oIt=o.begin();
-                while(sIt != self->end()){
-                  if(*sIt != *oIt) return false;
-                  ++sIt;
-                  ++oIt;
-                }
-                return true;
-              } else {
-                return false;
-              }
-            }
-        }
-    };
-
-    // bool specialization
-    template<> class vector<bool> {
-      public:
-        typedef size_t size_type;
-        typedef bool value_type;
-        typedef bool const_reference;
-        vector();
-        vector(size_type n);
-        size_type size() const;
-        size_type capacity() const;
-        void reserve(size_type n);
-        %rename(isEmpty) empty;
-        bool empty() const;
-        void clear();
-        %rename(add) push_back;
-        void push_back(const value_type& x);
-        %extend {
-            const_reference get(int i) throw (std::out_of_range) {
-                int size = int(self->size());
-                if (i>=0 && i<size)
-                    return (*self)[i];
-                else
-                    throw std::out_of_range("vector index out of range");
-            }
-            void set(int i, const value_type& val) throw (std::out_of_range) {
-                int size = int(self->size());
-                if (i>=0 && i<size)
-                    (*self)[i] = val;
-                else
-                    throw std::out_of_range("vector index out of range");
-            }
-        }
-    };
-}
-
-%define specialize_std_vector(T)
-#warning "specialize_std_vector - specialization for type T no longer needed"
-%enddef
-