Patch for Lilly MedChem Rules to compile on OS X Mavericks with clang.

lilly.diff

diff --git a/include/iwaray.h b/include/iwaray.h
index 1b58e95..213f25a 100644
--- a/include/iwaray.h
+++ b/include/iwaray.h
@@ -341,7 +341,7 @@ resizable_array_p<T>::resizable_array_p (int n)
 template <typename T>
 resizable_array_p<T>::resizable_array_p (T * item)
 {
-  add (item);
+  this->add (item);
 
   return;
 }
@@ -1068,9 +1068,9 @@ resizable_array_base<T>::insert_at_beginning (const T item_to_insert)
   assert (ok ());
 
   if (0 == _number_elements )
-    return add (item_to_insert);
+    return this->add (item_to_insert);
   else
-    return insert_before (0, item_to_insert);
+    return this->insert_before (0, item_to_insert);
 }
 
 template <typename T>
@@ -1081,7 +1081,7 @@ resizable_array_base<T>::insert_in_order (T item_to_insert,
   assert (ok ());
 
   if (0 == _number_elements)
-    return add (item_to_insert);
+    return this->add (item_to_insert);
 
   int i;
   for (i = 0; i < _number_elements; i++)
@@ -1091,9 +1091,9 @@ resizable_array_base<T>::insert_in_order (T item_to_insert,
   }
 
   if (i == _number_elements)
-    return add (item_to_insert);
+    return this->add (item_to_insert);
 
-  return insert_before (i, item_to_insert);
+  return this->insert_before (i, item_to_insert);
 }
 
 template <typename T>
@@ -1101,39 +1101,39 @@ int
 resizable_array<T>::insert_in_order (const T item_to_insert, int increasing_order)
 {
   if (0 == _number_elements)
-    return add (item_to_insert);
+    return this->add (item_to_insert);
 
   if (increasing_order)
   {
     if (item_to_insert < _things[0])
-      return insert_at_beginning (item_to_insert);
+      return this->insert_at_beginning (item_to_insert);
 
     if (item_to_insert >= _things[_number_elements - 1])
-      return add (item_to_insert);
+      return this->add (item_to_insert);
 
     for (int i = 0; i < _number_elements; i++)
     {
       if (item_to_insert < _things[i])
-        return insert_before (i, item_to_insert);
+        return this->insert_before (i, item_to_insert);
     }
 
-    return add (item_to_insert);
+    return this->add (item_to_insert);
   }
   else     // decreasing order, largest first.
   {
     if (item_to_insert > _things[0])
-      return insert_at_beginning (item_to_insert);
+      return this->insert_at_beginning (item_to_insert);
 
     if (item_to_insert <= _things[_number_elements - 1])
-      return add (item_to_insert);
+      return this->add (item_to_insert);
 
     for (int i = 0; i < _number_elements; i++)
     {
       if (item_to_insert > _things[i])
-        return insert_before (i, item_to_insert);
+        return this->insert_before (i, item_to_insert);
     }
 
-    return add (item_to_insert);
+    return this->add (item_to_insert);
   }
 }
 
@@ -1142,33 +1142,33 @@ int
 resizable_array<T>::insert_in_order_if_not_already_present (const T item_to_insert, int increasing_order)
 {
   if (0 == _number_elements)
-    return add (item_to_insert);
+    return this->add (item_to_insert);
 
   if (increasing_order)
   {
     for (int i = 0; i < _number_elements; i++)
     {
       if (item_to_insert < _things[i])
-        return insert_before (i, item_to_insert);
+        return this->insert_before (i, item_to_insert);
 
       if (item_to_insert == _things[i])
         return 0;
     }
 
-    return add (item_to_insert);
+    return this->add (item_to_insert);
   }
   else     // decreasing order, largest first.
   {
     for (int i = 0; i < _number_elements; i++)
     {
       if (item_to_insert > _things[i])
-        return insert_before (i, item_to_insert);
+        return this->insert_before (i, item_to_insert);
 
       if (item_to_insert == _things[i])
         return 0;
     }
 
-    return add (item_to_insert);
+    return this->add (item_to_insert);
   }
 
   return 0;     // no path to here
@@ -1205,7 +1205,7 @@ resizable_array_base<T>::operator += (const resizable_array_base<T> & oo)
 
   for (int i = 0; i < noo; i++)
   {
-    add (oo.item (i));
+    this->add (oo.item (i));
   }
 
   return;
@@ -1215,7 +1215,7 @@ template <typename T>
 void
 resizable_array_base<T>::operator += (T extra)
 {
-  (void) add (extra);
+  (void) this->add (extra);
 
   return;
 }
@@ -1260,7 +1260,7 @@ resizable_array_p<T>::transfer_in (resizable_array_p<T> & oo,
   assert (oo.ok_index (item_to_transfer));
 
   T * tmp = oo._things[item_to_transfer];
-  add (tmp);
+  this->add (tmp);
   oo.remove_no_delete (item_to_transfer);
 
   return 1;
@@ -1462,7 +1462,7 @@ resizable_array<T>::add_non_duplicated_elements (const resizable_array<T> & qq)
     }
     if (0 == foundqi)
     {
-      add (qi);
+      this->add (qi);
       rc++;
     }
   }
@@ -1482,7 +1482,7 @@ resizable_array<T>::add_if_not_already_present (const T qq)
 
 // No match found, add qq
 
-  return add (qq);
+  return this->add (qq);
 }
 
 /*template <typename T>
diff --git a/include/iwarchive.h b/include/iwarchive.h
index b59e8e1..bdaa730 100644
--- a/include/iwarchive.h
+++ b/include/iwarchive.h
@@ -104,7 +104,7 @@ iwarchive<T>::debug_print (ostream & os) const
 
   if (_match_any)
     os << "This archive will match any value\n";
-  
+
   for (int i = 0; i < _number_elements; i++)
   {
     os << "Item " << i << " will match " << _things[i] << endl;
@@ -177,7 +177,7 @@ iwarchive<T>::operator = (const iwarchive<T> & other)
 {
   _match_any = other._match_any;
 
-  resize (other._elements_allocated);
+  this->resize (other._elements_allocated);
   for (int i = 0; i < other._number_elements; i++)
   {
     _things[i] = other._things[i];
diff --git a/include/minmaxspc.h b/include/minmaxspc.h
index f9daa46..6fa3a68 100644
--- a/include/minmaxspc.h
+++ b/include/minmaxspc.h
@@ -168,7 +168,7 @@ Min_Max_Specifier<T>::ok () const
 }
 
 template <typename T>
-int 
+int
 Min_Max_Specifier<T>::debug_print (ostream & os) const
 {
   os << "Details on Min_Max_Specifier<T>::";
@@ -191,7 +191,7 @@ Min_Max_Specifier<T>::debug_print (ostream & os) const
 
   for (int i = 0; i < _number_elements; i++)
     os << "Value " << i << " set " << _things[i] << endl;
-  
+
   return 1;
 }
 
@@ -272,7 +272,7 @@ template <typename T>
 int
 Min_Max_Specifier<T>::set_max (T v)
 {
-  if (_number_elements) 
+  if (_number_elements)
     this->resize(0);
 
   _max_val.set (v);
@@ -406,7 +406,7 @@ Min_Max_Specifier<T>::adjust_to_accommodate (const T v)
   if (! check_archive)
     return 1;
 
-  if (! contains (v))
+  if (! this->contains (v))
     add (v);
 
   _match_any = 0;
@@ -581,7 +581,7 @@ Min_Max_Specifier<T>::write_compact_representation (ostream & os) const
 
 template <class T>
 ostream &
-operator << (ostream & os, const Min_Max_Specifier<T> & qq) 
+operator << (ostream & os, const Min_Max_Specifier<T> & qq)
 {
   os << "minmax: ";
 
@@ -590,7 +590,7 @@ operator << (ostream & os, const Min_Max_Specifier<T> & qq)
     os << "min " << tmp;
   if (qq.max (tmp))
     os << " max " << tmp;
-  
+
 // This next line commented out because of template instantiation problems.
 // The way things work now, this forces instantiation of the iwarchive<T>
 // class, which then conflicts with the iwarchive<T> instantiation in its