From 17f44d57164b123be802b3474f674d2e0df4d216 Mon Sep 17 00:00:00 2001
From: Tuowen Zhao <ztuowen@gmail.com>
Date: Mon, 19 Sep 2016 11:30:09 -0600
Subject: Template definition back in header files

---
 .gitignore                                  |   3 +
 chill/src/ir_rose.cc                        |   1 +
 omegalib/omega/include/basic/Bag.h          | 328 +++++++++++++++++++++++++++-
 omegalib/omega/include/basic/DynamicArray.h | 223 ++++++++++++++++++-
 omegalib/omega/include/basic/List.h         | 151 ++++++++++++-
 omegalib/omega/include/basic/Map.h          |  67 +++++-
 omegalib/omega/include/basic/Section.h      |  83 ++++++-
 omegalib/omega/include/basic/SimpleList.h   | 109 ++++++++-
 omegalib/omega/include/basic/Tuple.c        |   2 +-
 omegalib/omega/include/basic/Tuple.h        | 256 +++++++++++++++++++++-
 10 files changed, 1193 insertions(+), 30 deletions(-)

diff --git a/.gitignore b/.gitignore
index ba18327..f0d8fa3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,8 @@
 # Cmake build directory
 /build
 
+# CLion config directory
+/.idea
+
 # Vim swap file
 *.swap
diff --git a/chill/src/ir_rose.cc b/chill/src/ir_rose.cc
index 36e2db9..27930e6 100644
--- a/chill/src/ir_rose.cc
+++ b/chill/src/ir_rose.cc
@@ -844,6 +844,7 @@ IR_roseCode::IR_roseCode(const char *filename, const char* proc_name) :
   symtab2_ = func->get_definition()->get_symbol_table();
   symtab3_ = func->get_definition()->get_body()->get_symbol_table();
   // Manu:: added is_fortran_ parameter
+  // TODO Substitute it with a better builder
   ocg_ = new omega::CG_roseBuilder(is_fortran_, root, firstScope,
                                    func->get_definition()->get_symbol_table(),
                                    func->get_definition()->get_body()->get_symbol_table(),
diff --git a/omegalib/omega/include/basic/Bag.h b/omegalib/omega/include/basic/Bag.h
index 3bd7143..a3d07a0 100644
--- a/omegalib/omega/include/basic/Bag.h
+++ b/omegalib/omega/include/basic/Bag.h
@@ -5,6 +5,7 @@
 #include <basic/Iterator.h>
 #include <basic/Collection.h>
 #include <basic/Link.h>
+#include <assert.h>
 
 namespace omega {
 
@@ -71,10 +72,6 @@ public:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/Bag.c>
-#endif
-
 #define instantiate_Bag(T)		template class Bag<T>; \
 					instantiate_List_Element(T);
 #define instantiate_Ordered_Bag(T)	template class Ordered_Bag<T>; \
@@ -82,4 +79,327 @@ public:
 #define instantiate_Set(T)		template class Set<T>; \
 					instantiate_Ordered_Bag(T)
 
+
+namespace omega {
+
+template<class T> Bag<T>::Bag() {
+	 contents = new List_Element <T>;
+	 contents->tail = 0;
+	}
+template<class T> Bag<T>::~Bag() {
+	 delete contents;
+	}
+
+template<class T> Ordered_Bag<T>::Ordered_Bag() {}
+
+template<class T> Set<T>::Set() {}
+
+template<class T> Bag<T>::Bag(const Bag<T> &L) {
+		contents = new List_Element<T>(*L.contents);
+		}
+
+template<class T> Bag<T> & Bag<T>::operator=(const Bag<T> &L) {
+                if (this != &L) {
+		  delete contents;
+                  contents = new List_Element<T>(*L.contents);
+                }
+                return *this;
+                }
+
+
+
+template<class T> Set<T>::Set(T e) {
+	 assert(this->contents);
+	 this->contents->tail = new List_Element<T>(e, 0);
+	}
+	
+
+/****************************************************************
+ *								*
+ *  Misc. simple Collection operations 				*
+ *								*
+ ****************************************************************/
+
+template<class T> bool Bag<T>::empty() const {
+	 return contents->tail == 0;
+	}
+
+template<class T> Iterator<T> *Bag<T>::new_iterator()
+		{
+		return new List_Element_Iterator<T>(contents->tail);
+		}
+
+
+template<class T> void Bag<T>::clear() {
+		if (contents->tail) delete contents->tail;
+		contents->tail = 0;
+		}
+
+template<class T> int Bag<T>::size() const {
+		int i = 0;
+		List_Element<T> * p = contents->tail;
+		while (p) {
+			p = p->tail;
+			i++;
+			};
+		return i;
+		}
+
+
+/****************************************************************
+ *								*
+ *  Collection/Element operations (e.g. insert, contains)	*
+ *								*
+ ****************************************************************/
+
+template<class T> void Bag<T>::remove(T e) {
+		List_Element<T> * p = contents;
+		while (p->tail && p->tail->head != e) p = p->tail;
+		if (p->tail && p->tail->head == e) {
+			List_Element<T> * q = p->tail;
+			p->tail = q->tail;
+			q->tail = 0;
+			delete q;
+			}
+		}
+
+template<class T> T Bag<T>::extract() {
+		List_Element<T> * p = contents->tail;
+		T e = p->head;
+		contents->tail = p->tail;
+		p->tail = 0;
+		delete p;
+		return e;
+		}
+
+
+template<class T> void Bag<T>::insert(T e) {
+		List_Element<T> * q = new List_Element<T>(e,contents->tail);
+		contents->tail = q;
+		}
+
+template<class T> void Ordered_Bag<T>::insert(T e) {
+		List_Element<T> * p = this->contents;
+		while (p->tail && p->tail->head < e) p = p->tail;
+		if (!p->tail || p->tail->head != e) {
+			List_Element<T> * q = new List_Element<T>(e,p->tail);
+			p->tail = q;
+			}
+		}
+
+
+template<class T> bool Bag<T>::contains(T e) const {
+		List_Element<T> * p = contents;
+		while (p->tail && p->tail->head != e) p = p->tail;
+		return (p->tail && p->tail->head == e);
+		}
+
+template<class T> bool Ordered_Bag<T>::contains(T e) const {
+		List_Element<T> * p = this->contents;
+		while (p->tail && p->tail->head < e) p = p->tail;
+		return (p->tail && p->tail->head == e);
+		}
+
+
+template<class T> bool Set<T>::contains (const Set<T>& b) const {
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents;
+		do {
+		  /* consume matched elements in p and q */
+		  p = p->tail;
+		  q = q->tail;
+		  if (!q) return 1; /* no more elements to match */
+		  if (!p) return 0; /* nothing left in p to match with */
+ 		  if (q->head < p->head) {
+				/* nothing smaller than
+				p->head left in p, so q->head
+				can't be matched */
+				return 0;
+				};
+		  while (p && p->head < q->head) {
+			/* toss away some elements from p */
+			p = p->tail;
+			}
+		  if (!p || q->head < p->head) return 0;
+		  } while (q);
+		    
+		  return 1;
+		}
+		
+
+
+/****************************************************************
+ *								*
+ *  Collection/Collection operations (e.g. |=)			*
+ *								*
+ ****************************************************************/
+
+template<class T> void Bag<T>::operator |= (const Bag<T> & b) {
+		assert(this != &b);
+		List_Element<T> * q = b.contents->tail;
+
+		while (q) {
+		  List_Element<T> * r = new List_Element<T>(q->head,contents->tail);
+		  contents->tail = r;
+		  q = q->tail;
+		  }
+		}
+
+template<class T> void Ordered_Bag<T>::operator |= (const Ordered_Bag<T> & b) {
+		if (this == &b) return;
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents->tail;
+
+		while (q) {
+		  while (p->tail && p->tail->head < q->head) p = p->tail;
+		  List_Element<T> * r = new List_Element<T>(q->head,p->tail);
+		  p->tail = r;
+		  q = q->tail;
+		  }
+		}
+
+template<class T> void Ordered_Bag<T>::operator |= (const Bag<T> & b) {
+		Ordered_Bag<T> tmp;
+		for (List_Element<T> *p = b.contents; p; p=p->tail) {
+		  tmp.insert(p->head);
+		}
+		*this |= tmp;
+}
+
+template<class T> void Set<T>::operator |= (const Set<T> & b) {
+		if (this == &b) return;
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents->tail;
+
+		while (q) {
+		  while (p->tail && p->tail->head < q->head) p = p->tail;
+		  if (!p->tail || p->tail->head != q->head) {
+			List_Element<T> * r = new List_Element<T>(q->head,p->tail);
+			p->tail = r;
+			}
+		  q = q->tail;
+		  }
+		}
+
+template<class T> void Set<T>::operator |= (const Ordered_Bag<T> & b) {
+		Set<T> tmp;
+		for (List_Element<T> *p = b.contents; p; p=p->tail) {
+		  tmp.insert(p->head);
+		}
+		*this |= tmp;
+}
+
+template<class T> void Set<T>::operator |= (const Bag<T> & b) {
+		Set<T> tmp;
+		for (List_Element<T> *p = b.contents; p; p=p->tail) {
+		  tmp.insert(p->head);
+		}
+		*this |= tmp;
+}
+
+
+
+// delete items also in b
+template<class T> void Set<T>::operator -= (const Set<T> & b) {
+		if (this == &b) {
+			this->clear();
+			return;
+			}
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents->tail;
+
+		while (q) {
+		  while (p->tail && p->tail->head < q->head) p = p->tail;
+		  if (p->tail && p->tail->head == q->head) {
+			List_Element<T> * r = p->tail;
+			p->tail = r->tail;
+			r->tail = 0;
+			delete r;
+			}
+		  q = q->tail;
+		  }
+		}
+
+
+// delete items not in b
+template<class T> void Set<T>::operator &= (const Set<T> & b)
+       {
+		if (this == &b) return;
+                List_Element<T> * p = this->contents;
+                List_Element<T> * q = b.contents->tail;
+
+                while (q) {
+                  while (p->tail && p->tail->head < q->head) {
+                        List_Element<T> * r = p->tail;
+                        p->tail = r->tail;
+                        r->tail = 0;
+                        delete r;
+                        };
+                  if (p->tail && p->tail->head == q->head) {
+                        /* allow p->tail->head into the result */
+                        p  = p->tail;
+                        }
+                  /* q->head has matched anything it is going to match */
+                  q = q->tail;
+                  }
+		if (p->tail) {
+			delete p->tail;
+			p->tail = 0;
+			};
+
+        }
+
+
+template<class T> bool Set<T>::operator & (const Set<T>& b) const {
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents;
+		do {
+		  p = p->tail;
+		  q = q->tail;
+		  while (p && q && p->head != q->head) {
+		     while (p && p->head < q->head) p = p->tail;
+		     while (p && q && q->head < p->head) q = q->tail;
+		     };
+		  if (p && q && p->head == q->head) return 1;
+		  } while (p && q);
+		    
+		  return 0;
+		}
+
+
+template<class T> bool Ordered_Bag<T>::operator == (const Ordered_Bag<T>& b) const {
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents;
+		while (1) {
+		  p = p->tail;
+		  q = q->tail;
+		  if (!p && !q) return 1;
+		  if (!p || !q) return 0;
+		  if (p->head != q->head) return 0;
+		  };
+		    
+		}
+
+template<class T> bool Ordered_Bag<T>::operator != (const Ordered_Bag<T>& b) const {
+              return !(*this == b);
+              }
+
+template<class T> bool Ordered_Bag<T>::operator < (const Ordered_Bag<T>& b) const {
+		List_Element<T> * p = this->contents;
+		List_Element<T> * q = b.contents;
+		while (1) {
+		  p = p->tail;
+		  q = q->tail;
+		  if (!p && !q) return 0;
+		  if (!p) return 1;
+		  if (!q) return 0;
+		  if (p->head < q->head) return 1;
+		  if (q->head < p->head) return 0;
+		  };
+		    
+		  return 1;
+		  }
+
+} // namespace
+
 #endif
diff --git a/omegalib/omega/include/basic/DynamicArray.h b/omegalib/omega/include/basic/DynamicArray.h
index ac9bae4..08f8b91 100644
--- a/omegalib/omega/include/basic/DynamicArray.h
+++ b/omegalib/omega/include/basic/DynamicArray.h
@@ -1,6 +1,8 @@
 #ifndef Already_Included_DynamicArray
 #define Already_Included_DynamicArray
 
+#include <assert.h>
+
 namespace omega {
 
 template <class T> class DynamicArray2;
@@ -82,10 +84,6 @@ template <class T> class DynamicArray4 : public DynamicArray<T,4>
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/DynamicArray.c>
-#endif
-
 #define instantiate_DynamicArray1(T)	template class DynamicArray1<T>; \
 					template class DynamicArray<T,1>;
 
@@ -100,4 +98,221 @@ template <class T> class DynamicArray4 : public DynamicArray<T,4>
 #define instantiate_DynamicArray4(T)	template class DynamicArray4<T>;  \
 					template class DynamicArray<T,4>; \
 					instantiate_DynamicArray3(T);
+
+namespace omega {
+  
+template<class T, int d> void DynamicArray<T,d>::do_constr()
+    {
+// #if ! defined SHUT_UP_ABOUT_STATEMENT_WITH_NO_EFFECT_IN_DYNAMIC_ARRAY_CREATION
+//     assert(d > 0);
+// #endif
+    bounds = 0;
+    elements = 0;
+    partial = false;
+    }
+
+
+template<class T> void DynamicArray1<T>::do_construct(int d0)
+    {
+    this->bounds = new int[1];
+    this->bounds[0] = d0;
+    this->elements = new T [d0];
+    this->partial = false;
+    }
+
+template<class T> void DynamicArray2<T>::do_construct(int d0, int d1)
+    {
+    this->bounds = new int[2];
+    this->bounds[0] = d0;
+    this->bounds[1] = d1;
+    this->elements = new T [d0 * d1];
+    this->partial = false;
+    }
+
+template<class T> void DynamicArray3<T>::do_construct(int d0,int d1,int d2)
+    {
+    this->bounds = new int[3];
+    this->bounds[0] = d0;
+    this->bounds[1] = d1;
+    this->bounds[2] = d2;
+    this->elements = new T [d0 * d1 * d2];
+    this->partial = false;
+    }
+
+template<class T> void DynamicArray4<T>::do_construct(int d0,int d1,int d2,int d3)
+    {
+    this->bounds = new int[4];
+    this->bounds[0] = d0;
+    this->bounds[1] = d1;
+    this->bounds[2] = d2;
+    this->bounds[3] = d3;
+    this->elements = new T [d0 * d1 * d2 * d3];
+    this->partial = false;
+    }
+
+template<class T, int d> DynamicArray<T,d>::DynamicArray()
+    {
+    do_constr();
+    }
+
+template<class T> DynamicArray1<T>::DynamicArray1(const char *)
+    {
+    this->do_constr();
+    }
+
+template<class T> DynamicArray2<T>::DynamicArray2(const char *,const char *)
+    {
+    this->do_constr();
+    }
+
+template<class T> DynamicArray3<T>::DynamicArray3(const char *,const char *,const char *)
+    {
+    this->do_constr();
+    }
+
+template<class T> DynamicArray4<T>::DynamicArray4(const char *,const char *,const char *,const char *)
+    {
+    this->do_constr();
+    }
+
+template<class T> DynamicArray1<T>::DynamicArray1(int d0)
+    {
+    do_construct(d0);
+    } 
+
+template<class T> DynamicArray2<T>::DynamicArray2(int d0, int d1)
+    {
+    do_construct(d0, d1);
+    }
+
+template<class T> DynamicArray3<T>::DynamicArray3(int d0,int d1,int d2)
+    {
+    do_construct(d0, d1, d2);
+    }
+
+template<class T> DynamicArray4<T>::DynamicArray4(int d0,int d1,int d2,int d3)
+    {
+    do_construct(d0, d1, d2, d3);
+    }
+
+
+template<class T, int d> void DynamicArray<T,d>::do_destruct()
+    {
+    if (! partial)
+	{
+        delete [] bounds;
+        delete [] elements;
+	}
+    }
+
+
+template<class T, int d> DynamicArray<T,d>::~DynamicArray()
+    {
+    do_destruct();
+    }
+
+
+template<class T> void DynamicArray1<T>::resize(int d0)
+    {
+    assert(!this->partial);
+    this->do_destruct();
+    if (d0 == 0)
+        this->do_constr();
+    else
+        do_construct(d0);
+    } 
+
+template<class T> void DynamicArray2<T>::resize(int d0, int d1)
+    {
+    assert(!this->partial);
+    this->do_destruct();
+    if (d0 == 0 && d1 == 0)
+        this->do_constr();
+    else
+        do_construct(d0, d1);
+    }
+
+template<class T> void DynamicArray3<T>::resize(int d0, int d1, int d2)
+    {
+    assert(!this->partial);
+    this->do_destruct();
+    if (d0 == 0 && d1 == 0 && d2 == 0)
+        this->do_constr();
+    else
+        do_construct(d0, d1, d2);
+    }
+
+template<class T> void DynamicArray4<T>::resize(int d0, int d1, int d2, int d3)
+    {
+    assert(!this->partial);
+    this->do_destruct();
+    if (d0 == 0 && d1 == 0 && d2 == 0 && d3 == 0)
+        this->do_constr();
+    else
+        do_construct(d0, d1, d2, d3);
+    }
+
+
+template<class T> T& DynamicArray1<T>::operator[](int d0)
+    { 
+#if !defined (NDEBUG)
+    assert(this->elements != 0 && "Trying to dereference undefined array");
+    assert(0 <= d0 && d0 < this->bounds[0] && "Array subscript out of bounds");
+#endif
+
+    return this->elements[d0];
+    }
+
+template<class T>  DynamicArray1<T> DynamicArray2<T>::operator[](int d0)
+    { 
+#if !defined (NDEBUG)
+    assert(this->elements != 0 && "Trying to dereference undefined array");
+    assert(0 <= d0 && d0 < this->bounds[0] && "Array subscript out of bounds");
+#endif
+
+    DynamicArray1<T> result;
+    result.bounds = this->bounds+1;
+    result.elements = this->elements + this->bounds[1] * d0;
+    result.partial = true;
+    return result;
+    }
+
+template<class T>  DynamicArray2<T> DynamicArray3<T>::operator[](int d0)
+    { 
+#if !defined (NDEBUG)
+    assert(this->elements != 0 && "Trying to dereference undefined array");
+    assert(0 <= d0 && d0 < this->bounds[0] && "Array subscript out of bounds");
+#endif
+    DynamicArray2<T> result;
+    result.bounds = this->bounds+1;
+    result.elements = this->elements + this->bounds[1] * this->bounds[2] * d0;
+    result.partial = true;
+    return result;
+    } 
+
+template<class T>  DynamicArray3<T> DynamicArray4<T>::operator[](int d0)
+    { 
+#if !defined (NDEBUG)
+    assert(this->elements != 0 && "Trying to dereference undefined array");
+    assert(0 <= d0 && d0 < this->bounds[0] && "Array subscript out of bounds");
+#endif
+
+    DynamicArray3<T> result;
+    result.bounds = this->bounds+1;
+    result.elements = this->elements + this->bounds[1] * this->bounds[2] * this->bounds[3] * d0;
+    result.partial = true;
+    return result;
+    } 
+
+
+template<class T, int d> 
+    DynamicArray<T,d>::DynamicArray(DynamicArray<T,d> &D)
+    {
+    assert(D.elements != 0 && "Trying to copy an undefined array");
+    partial = true;
+    bounds = D.bounds;
+    elements = D.elements;
+    }
+
+} // namespace
 #endif
diff --git a/omegalib/omega/include/basic/List.h b/omegalib/omega/include/basic/List.h
index ee394d9..28ab1d5 100644
--- a/omegalib/omega/include/basic/List.h
+++ b/omegalib/omega/include/basic/List.h
@@ -8,6 +8,7 @@
 #include <basic/Iterator.h>
 #include <basic/Collection.h>
 #include <basic/Link.h>
+#include <assert.h>
 
 namespace omega {
   
@@ -77,14 +78,156 @@ private:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/List.c>
-#endif
-
 #define instantiate_List(T)	template class List<T>; \
 				template class List_Iterator<T>; \
 				instantiate_Only_List_Element(T) \
 				instantiate_Sequence(T)
 
+namespace omega {
+  
+template<class T> List_Iterator<T>::List_Iterator(List<T> &l) 
+: List_Element_Iterator<T>(l.contents) {}
+
+template<class T> List_Iterator<T>::List_Iterator(const List<T> &l) 
+: List_Element_Iterator<T>(l.contents) {}
+
+template<class T> List_Iterator<T>::List_Iterator()
+: List_Element_Iterator<T>(0) {}
+
+template<class T> Iterator<T> *List<T>::new_iterator()
+{
+    return new List_Iterator<T>(*this);
+}
+
+template<class T> const T &List<T>::operator[](int i) const
+{
+    assert(i > 0 && "Subscript out of bounds");
+    List_Iterator<T> p(*this);
+
+    while(--i > 0 && p)
+	p++;
+
+    if (p)
+	return *p;
+    else
+	return *((T *)0);
+}
+
+template<class T>       T &List<T>::operator[](int i)
+{
+    assert(i > 0 && "Subscript out of bounds");
+    List_Iterator<T> p(*this);
+
+    while(--i > 0 && p)
+	p++;
+
+    if (p)
+	return *p;
+    else
+	return *((T *)0);
+}
+
+template<class T>      int List<T>::index(const T &item) const
+{
+    List_Iterator<T> p(*this);
+    int i = 1;
+
+    while(p && *p != item)
+    {
+	p++;
+	i++;
+    }
 
+    if (p)
+	return i;
+    else
+	return 0;
+}
+
+template<class T> int List<T>::size() const
+    {
+    int i = 0;
+    List_Element<T> * p = contents;
+    while (p)
+	{
+	p = p->tail;
+	i++;
+	}
+    return i;
+    }
+
+template<class T> T &List<T>::front() const
+    {
+    return contents->head;
+    }
+
+template<class T> T List<T>::remove_front()
+    {
+    List_Element<T> *frunt = contents;
+    contents = contents->tail;
+    T fruntT = frunt->head;
+    frunt->tail = 0;
+    delete frunt;
+    return fruntT;
+    }
+
+template<class T> void List<T>::prepend(const T &item)
+    {
+    contents = new List_Element<T>(item, contents);
+    }
+
+
+template<class T> void List<T>::append(const T &item)
+    {
+    *(end()) = new List_Element<T>(item, 0);
+    }
+
+template<class T> void List<T>::ins_after(List_Iterator<T> i,
+					     const T &item)
+    {
+#if ! defined NDEBUG
+    for (List_Element<T> *e = contents; e != &(i.element()); e=e->tail)
+	{
+	assert(e);
+	}
+#endif
+    i.element().tail = new List_Element<T>(item, i.element().tail);
+    }
+
+template<class T> void List<T>::del_front()
+    {
+    List_Element<T> *e = contents;
+    contents = contents->tail;
+    e->tail = 0;
+    delete e;
+    }
+
+template<class T> void List<T>::del_after(List_Iterator<T> i)
+    {
+#if ! defined NDEBUG
+    for (List_Element<T> *e0 = contents; e0 != &(i.element()); e0=e0->tail)
+	{
+	assert(e0);
+	}
+#endif
+    List_Element<T> *e = i.element().tail;
+    i.element().tail = e->tail;
+    e->tail = 0;
+    delete e;
+    }
+
+template<class T> void List<T>::clear()
+    {
+    delete contents;
+    contents = 0;
+    }
+
+template<class T> void List<T>::join(List<T> &consumed)
+    {
+    List_Element<T> *e = consumed.contents;
+    consumed.contents = 0;
+    *(end()) = e;
+    }
+
+} // namespace
 #endif
diff --git a/omegalib/omega/include/basic/Map.h b/omegalib/omega/include/basic/Map.h
index f94a10c..25a116d 100644
--- a/omegalib/omega/include/basic/Map.h
+++ b/omegalib/omega/include/basic/Map.h
@@ -55,14 +55,73 @@ private:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/Map.c>
-#endif
-
 #define instantiate_Map(T1,T2)	template class Map<T1,T2>; \
 				template class MapElement<T1,T2>; \
 				template class MapElementIterator<T1,T2>;
 #define instantiate_MapElement(T1,T2)		instantiate_Map(T1,T2)
 #define instantiate_MapElementIterator(T1,T2)	instantiate_Map(T1,T2)
 
+namespace omega {
+
+template<class K, class V> MapElement<K,V>:: MapElement(const MapElement<K,V>& M) {
+		if (M.tail) tail = new MapElement<K,V>(*M.tail);
+		else tail = 0;
+		k = M.k;
+		v = M.v;
+		}
+
+template<class K, class V> MapElement<K,V> & 
+	MapElement<K,V>:: operator=(const MapElement<K,V>& M) {
+                if (this != &M) {
+		  if (tail) delete tail;
+                  if (M.tail) tail = new MapElement<K,V>(*M.tail);
+		  else tail = 0;
+		k = M.k;
+		v = M.v;
+                }
+	return *this;
+	}
+
+
+
+
+#if ! defined linux
+template <class K, class V> Map <K,V>::Map(const V &default_value)
+#else
+template <class K, class V> Map <K,V>::Map(V default_value)
+#endif
+                : _default_value(default_value)
+                {
+		    contents = 0;
+		}
+
+template <class K, class V> Map <K,V>::~Map()
+    {
+    delete contents;
+    }
+
+template <class K, class V> V Map<K,V>::operator()(K k) const {
+		MapElement <K,V> * P = contents;
+		while (P) {
+			if (P->k == k) return P->v;
+			P = P->tail;
+			};
+		return _default_value;
+		}
+
+template <class K, class V> V & Map<K,V>::operator[](K k) {
+		MapElement <K,V> * P = contents;
+		while (P) {
+			if (P->k == k) return P->v;
+			P = P->tail;
+			};
+		P = new MapElement <K,V>;
+		P->k = k;
+		P->v = _default_value;
+		P->tail = contents;
+		contents = P;
+		return P->v;
+		}
+
+} // namespace
 #endif
diff --git a/omegalib/omega/include/basic/Section.h b/omegalib/omega/include/basic/Section.h
index 60821d1..7a4d241 100644
--- a/omegalib/omega/include/basic/Section.h
+++ b/omegalib/omega/include/basic/Section.h
@@ -5,6 +5,7 @@
   */
 
 #include <basic/Collection.h>
+#include <assert.h>
 
 namespace omega {
 
@@ -51,13 +52,87 @@ private:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/Section.c>
-#endif
-
 #define instantiate_Section(T)	template class Section<T>; \
 				template class Section_Iterator<T>; \
 				instantiate_Sequence(T)
 #define instantiate_Section_Iterator(T)	  instantiate_Section(T)
 
+
+namespace omega {
+
+template <class T> Section<T>::Section(Sequence<T> *s, int start, int length)
+    {
+    assert(s->size() >= start-1 + length);
+    it = s;
+    _start = start;
+    _length = length;
+    }
+
+template <class T> Iterator<T> *Section<T>::new_iterator()
+    {
+    return new Section_Iterator<T>(*this);
+    }
+
+template <class T> const T &Section<T>::operator[](int i) const
+    {
+    assert(1 <= i && i <= size());
+    return (*it)[i+(_start-1)];
+    }
+
+template <class T> T &Section<T>::operator[](int i)
+    {
+    assert(1 <= i && i <= size());
+    return (*it)[i+(_start-1)];
+    }
+
+template <class T> int Section<T>::index(const T &var) const
+    {
+    int i;
+    for (i=1; i<=size(); i++)
+	if ((*this)[i] == var)
+	    return i;
+    return 0;
+    }
+
+template <class T> int Section<T>::size() const
+    {
+    return _length;
+    }
+
+
+template <class T> Section_Iterator<T>::Section_Iterator(Section<T> &sec)
+    {
+    it = sec.it->new_iterator();
+    for (int i = 1; i < sec._start; i++)
+	(*it)++;
+    remaining = sec.size();
+    }
+
+
+template <class T> Section_Iterator<T>::Section_Iterator(const Section_Iterator<T> &si) : it(si.it), remaining(si.remaining) {}
+
+
+template <class T> void Section_Iterator<T>::operator++()
+    {  this->operator++(0);  }
+
+template <class T> void Section_Iterator<T>::operator++(int)
+    {
+    if (remaining > 0)
+	{
+	(*it)++;
+	remaining--;
+	}
+    }
+
+template <class T> bool Section_Iterator<T>::live() const
+    {
+    return (remaining > 0);
+    }
+
+template <class T> Iterator<T> *Section_Iterator<T>::new_copy() const
+    {
+    return new Section_Iterator<T>(*this);
+    }
+
+} // namespace
 #endif
diff --git a/omegalib/omega/include/basic/SimpleList.h b/omegalib/omega/include/basic/SimpleList.h
index a08b307..104390d 100644
--- a/omegalib/omega/include/basic/SimpleList.h
+++ b/omegalib/omega/include/basic/SimpleList.h
@@ -81,13 +81,114 @@ private:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/SimpleList.c>
-#endif
-
 #define instantiate_Simple_List(T)	template class Simple_List<T>;  \
   template class Simple_List_Iterator<T>;                           \
   instantiate_Only_List_Element(T)                                  \
   instantiate_Sequence(T)
 
+namespace omega {
+  
+template<class T> Simple_List_Iterator<T>::Simple_List_Iterator(Simple_List<T> &l) 
+: List_Element_Iterator<T>(l.contents) {}
+
+template<class T> Simple_List_Iterator<T>::Simple_List_Iterator(const Simple_List<T> &l) 
+: List_Element_Iterator<T>(l.contents) {}
+
+template<class T> Simple_List_Iterator<T>::Simple_List_Iterator()
+: List_Element_Iterator<T>(0) {}
+
+template<class T> Iterator<T> *Simple_List<T>::new_iterator()
+{
+    return new Simple_List_Iterator<T>(*this);
+}
+
+template<class T> const T &Simple_List<T>::operator[](int i) const
+{
+    Simple_List_Iterator<T> p(*this);
+
+    while(--i > 0 && p)
+	p++;
+
+    if (p)
+	return *p;
+    else
+	return *((T *)0);
+}
+
+template<class T>       T &Simple_List<T>::operator[](int i)
+{
+    Simple_List_Iterator<T> p(*this);
+
+    while(--i > 0 && p)
+	p++;
+
+    if (p)
+	return *p;
+    else
+	return *((T *)0);
+}
+
+
+template<class T> int Simple_List<T>::size() const
+    {
+    int i = 0;
+    List_Element<T> * p = contents;
+    while (p)
+	{
+	p = p->tail;
+	i++;
+	}
+    return i;
+    }
+
+template<class T> T &Simple_List<T>::front() const
+    {
+    return contents->head;
+    }
+
+template<class T> T Simple_List<T>::remove_front()
+    {
+    List_Element<T> *frunt = contents;
+    contents = contents->tail;
+    T fruntT = frunt->head;
+    frunt->tail = 0;
+    delete frunt;
+    return fruntT;
+    }
+
+template<class T> void Simple_List<T>::prepend(const T &item)
+    {
+    contents = new List_Element<T>(item, contents);
+    }
+
+
+template<class T> void Simple_List<T>::append(const T &item)
+    {
+    *(end()) = new List_Element<T>(item, 0);
+    }
+
+
+template<class T> void Simple_List<T>::del_front()
+    {
+    List_Element<T> *e = contents;
+    contents = contents->tail;
+    e->tail = 0;
+    delete e;
+    }
+
+
+template<class T> void Simple_List<T>::clear()
+    {
+    delete contents;
+    contents = 0;
+    }
+
+template<class T> void Simple_List<T>::join(Simple_List<T> &consumed)
+    {
+    List_Element<T> *e = consumed.contents;
+    consumed.contents = 0;
+    *(end()) = e;
+    }
+
+} // namespace
 #endif
diff --git a/omegalib/omega/include/basic/Tuple.c b/omegalib/omega/include/basic/Tuple.c
index ce99e82..ee6648f 100644
--- a/omegalib/omega/include/basic/Tuple.c
+++ b/omegalib/omega/include/basic/Tuple.c
@@ -149,7 +149,7 @@ template<class T> void Tuple<T>::join(Tuple<T>& t) {
     assert(alloc_sz >= sz);
     for(int i=0; i<t.sz; i++)
 	data[i+old_sz] = t.data[i];
-    t.clear();
+    t.clear();ation will not fail, it would generate the object file but it won't generate any code for the template class in the object file.
 }
 
 template<class T> void Tuple<T>::clear() { if (sz) delete [] data; data = 0; alloc_sz = 0; sz = 0; }
diff --git a/omegalib/omega/include/basic/Tuple.h b/omegalib/omega/include/basic/Tuple.h
index 28e83bd..7bb3c24 100644
--- a/omegalib/omega/include/basic/Tuple.h
+++ b/omegalib/omega/include/basic/Tuple.h
@@ -79,12 +79,258 @@ private:
 
 } // namespace
 
-#if ! defined DONT_INCLUDE_TEMPLATE_CODE
-#include <basic/Tuple.c>
-#endif
-
 #define instantiate_Tuple(T)	template class Tuple<T>; \
 				template class Tuple_Iterator<T>; \
 				instantiate_Sequence(T)
-     
+
+namespace omega {
+  
+template<class T>  T &Tuple<T>::operator[](int index)
+    {
+    assert(1 <= index && index <= sz); return data[index-1];
+    }
+
+template<class T>  const T &Tuple<T>::operator[](int index) const
+    {
+    assert(1 <= index && index <= sz); return data[index-1];
+    }
+
+
+template<class T> Tuple<T>::~Tuple()
+    {
+    if (data)
+	delete [] data;
+    }
+
+template<class T> Tuple<T>::Tuple()  : sz(0), alloc_sz(0),
+ prealloc_min(20),prealloc_pad(5), data(0)
+{
+	// nothing needs be done
+	}
+
+template<class T> Tuple<T>::Tuple(int size)  : sz(size),
+ prealloc_min(20),prealloc_pad(5)
+{
+    if (sz > 0)
+	{
+	    alloc_sz = prealloc_size(sz);
+	    data = new T[alloc_sz];
+	    assert(alloc_sz >= sz);
+	    //Need some handling for out of memory.
+	    assert (data!=0);
+      } 
+    else {
+      alloc_sz = 0;
+      data = 0;
+    }
+}
+
+
+template<class T> Tuple<T>::Tuple(const Tuple<T>& t) 
+    : sz(t.sz), alloc_sz(t.alloc_sz),  prealloc_min(20),prealloc_pad(5)
+{
+    if (sz > 0) {
+	data = new T[alloc_sz];
+	assert (data!=0);
+	assert (alloc_sz >= sz);
+	for (int i=0; i<sz; i++)
+	    data[i] = t.data[i];
+    } else {
+	data = 0;   
+	alloc_sz = 0;  // THis might not be 0 if it was a "clear"ed Tuple
+//        assert(alloc_sz == 0);
+    }
+}
+
+
+template<class T> Tuple<T>& Tuple<T>::operator=(const Tuple<T>& t)
+{
+    if (this != &t) {                 // Delete this
+	if (data)
+	    delete [] data;
+	sz = t.sz;
+	alloc_sz = t.alloc_sz;
+	assert(alloc_sz >= sz);
+	if (sz > 0) {                 // Copy old
+	    data = new T[alloc_sz];
+	    assert (data!=0);
+	    for (int i=0; i<sz; i++)
+		data[i] = t.data[i];
+	} else {
+	    data=0;
+	    alloc_sz = 0;   // THis might not be 0 if it was a "clear"ed Tuple
+//	    assert(alloc_sz == 0);
+	}
+    }   
+    return *this;
+}
+
+
+template<class T> void Tuple<T>::reallocate(const int req_size) 
+{
+    if (alloc_sz >= req_size) { // if (sz >= req_size), does this.
+	sz = req_size;
+	return;
+    }
+    alloc_sz = prealloc_size(req_size);
+    T* tmp_data = new T[alloc_sz];
+    for(int i=0;i<sz;i++)
+	tmp_data[i] = data[i];
+    delete [] data;
+    data = tmp_data;
+    sz = req_size;
+    assert(alloc_sz >= req_size);
+}
+
+template<class T> void Tuple<T>::delete_last()
+{
+assert(sz > 0);
+sz --;
+}
+
+template<class T> void Tuple<T>::append(const T &v)
+{ 
+    // Check if reallocation is necessary.
+    if (sz == 0)  {                 // Empty Tuple
+	assert(alloc_sz >= 0);      // May be nonzero for cleared tuple
+
+	if(alloc_sz == 0) {         // If it's > 1 no allocation is necessary
+	    alloc_sz = prealloc_size(1);
+	    data = new T[alloc_sz];
+	}
+	assert (alloc_sz > 0 && data != 0);
+    } else {
+	if(sz == alloc_sz)  {       // Requires new allocation
+	    alloc_sz = realloc_size(alloc_sz);
+	    T * data_tmp = new T[alloc_sz];
+	    assert (data_tmp!=0);
+	    assert (alloc_sz > sz);
+	    for (int i=0; i<sz; i++)
+		data_tmp[i] = data[i];
+	    delete [] data;
+	    data=data_tmp; 
+	}              // Otherwise big enough, no reallocation necessary
+    }
+    // Make assignment
+    assert(alloc_sz >= sz);
+    data[sz++] = v; 
+}
+
+template<class T> void Tuple<T>::append(const Tuple<T>& t) {
+    int old_sz = sz;
+    reallocate(t.size()+size());
+    assert(alloc_sz >= sz);
+    for(int i=0; i<t.sz; i++)
+	data[i+old_sz] = t.data[i];
+}
+
+template<class T> void Tuple<T>::join(Tuple<T>& t) {
+    int old_sz = sz;
+    reallocate(t.size()+size());
+    assert(alloc_sz >= sz);
+    for(int i=0; i<t.sz; i++)
+	data[i+old_sz] = t.data[i];
+    t.clear();ation will not fail, it would generate the object file but it won't generate any code for the template class in the object file.
+}
+
+template<class T> void Tuple<T>::clear() { if (sz) delete [] data; data = 0; alloc_sz = 0; sz = 0; }
+
+template<class T> int  Tuple<T>::empty() const { return (sz == 0); }
+
+template<class T> Iterator<T> *Tuple<T>::new_iterator() 
+{
+    return new Tuple_Iterator<T>(*this);
+}
+
+template<class T> int Tuple<T>::index(const T & var) const
+/* returns index or 0 if var isn't in the tuple */
+{
+ int i;
+ for (i=0; i<sz; i++)
+   if (data[i]== var)
+    return i+1;
+ return 0;  
+}
+
+template<class T> bool Tuple<T>::operator == (const Tuple<T>& b) const 
+{
+ int i;
+ if (sz != b.size()) return false;
+ for (i=0; i<sz; i++)
+   if (!(data[i] == b[i+1])) return false;
+ return true;  
+}
+
+/* class Tuple_Iterator */
+
+template<class T> Tuple_Iterator<T>::Tuple_Iterator(const Tuple<T> &tpl) : 
+current(tpl.data), lastptr(tpl.data+tpl.sz-1), firstptr(tpl.data), sz(tpl.sz)
+{
+}					     
+
+template<class T> Tuple_Iterator<T>::Tuple_Iterator(T * cr, T *frst, T * lst,
+						  int insz) 
+    : current(cr), lastptr(lst), firstptr(frst), sz(insz)
+{
+}
+
+template<class T> const T & Tuple_Iterator<T>::operator*() const
+{
+    assert (current<=lastptr && current>=firstptr);
+    return *current;
+}
+
+template<class T> T & Tuple_Iterator<T>::operator*()
+{
+    assert (current<=lastptr && current >=firstptr);
+    return *current;
+}
+
+template<class T> void Tuple_Iterator<T>::operator++(int)
+{
+    current++;
+}
+
+template<class T> void Tuple_Iterator<T>::operator++()
+{
+    current++;
+}
+
+template<class T> void Tuple_Iterator<T>::operator--(int)
+{
+    current--;
+}
+
+template<class T> void Tuple_Iterator<T>::operator--()
+{
+    current--;
+}
+
+template<class T> void Tuple_Iterator<T>::set_to_last()
+{
+    current = lastptr;
+}
+
+template<class T> void Tuple_Iterator<T>::set_to_first()
+{
+    current = firstptr;
+}
+
+template<class T> void Tuple_Iterator<T>::set_position(const int req_pos)
+{
+    assert(req_pos <= sz && 1 <= req_pos);
+    current = firstptr + (req_pos - 1);
+}
+
+
+template<class T> bool Tuple_Iterator<T>::live() const
+{
+    return (current !=0 &&  current<=lastptr && current >= firstptr);
+}
+
+template<class T> Iterator<T> *Tuple_Iterator<T>::new_copy() const {
+    return new Tuple_Iterator<T>(current, firstptr, lastptr, sz); 
+}
+
+} // namespace
 #endif
-- 
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