X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgeneorder.h;h=4659e0efee62ca5194a3505b75d868bfe865c416;hb=HEAD;hp=e411a37253f932ec9788a3f5533bff19c695f2fe;hpb=47b1f5c0294e079bc120dc8366977951aa0778bf;p=germs.git

diff --git a/src/geneorder.h b/src/geneorder.h
index e411a37..4659e0e 100644
--- a/src/geneorder.h
+++ b/src/geneorder.h
@@ -23,12 +23,17 @@
 
 #include <vector>
 #include <stdexcept>
-#include <cstdlib>
 
 #include "misc.h"
 
 /**
- * Stores a gene order permutation and ensures that all genes are present and not duplicated.
+ * Stores a gene order permutation and ensures that all genes are present 
+ * and not duplicated.
+ *
+ * It has limited support for acting as an STL container, but still maintaining
+ * the invariant of a permutation starting with 0 and ending with n, with all
+ * genes present.
+ *
  * \author Michael Andreen
 */
 class GeneOrder{
@@ -36,6 +41,7 @@ class GeneOrder{
 
 		typedef std::vector<Gene> GeneList;
 		typedef GeneList::size_type size_type;
+		typedef GeneList::const_iterator iterator;
 
 		/**
 		 * Creates a copy of the given gene order
@@ -43,9 +49,20 @@ class GeneOrder{
 		GeneOrder(const GeneOrder& go);
 
 		/**
-		 * Creates a gene order from a given list.
+		 * Creates a gene order from a given list, using STL-type iterators.
 		 *
-		 * \throws invalid_argument if the list is not a valid permutation.
+		 * The given permutation needs to contain all genes 1 to n, if 0 is
+		 * included it has to be the first item, if it is not present it will
+		 * be added automatically. Similarily, if n is not the last item, then
+		 * n+1 will be added to the end.
+		 *
+		 * \param begin iterator to the first element in the list, from begin()
+		 * on stl collections and pointer to first item on plain arrays.
+		 *
+		 * \param end iterator to the element behind the last, from end() in
+		 * stl collections or pointer to first element+size on plain arrays.
+		 *
+		 * \throws std::invalid_argument if the list is not a valid permutation.
 		 */
 		template<class T>
 		GeneOrder(T begin, T end);
@@ -63,14 +80,14 @@ class GeneOrder{
 		/**
 		 * Returns the gene at the given index.
 		 *
-		 * \throws out_of_range if i is smaller than 0 or too big.
+		 * \throws std::out_of_range if i is smaller than 0 or bigger than n.
 		 */
 		const Gene& operator[](size_type i) const;
 
 		/**
 		 * Returns the size of the permutation.
 		 */
-		int size() const;
+		size_type size() const;
 
 		/**
 		 * Returns the vector containing the gene order permutation.
@@ -78,17 +95,42 @@ class GeneOrder{
 		const GeneList& list() const;
 
 		/**
-		 * Reverses an interval and returns the new permutation
+		 * Returns the start iterator for the permutation.
+		 * To be used with STL style functions.
+		 *
+		 * \see end
+		 */
+		iterator begin() const;
+
+		/**
+		 * Returns the end iterator for the permutation.
+		 * To be used with STL style functions.
+		 *
+		 * \see begin
 		 */
-		GeneOrder reverse(size_type i, size_type j) const;
+		iterator end() const;
 
 		/**
-		 * Moves the gene on position i to position j, returning a new permutation
+		 * Reverserses the interval [i,j], changing the sign on all elements
+		 * affected.
+		 *
+		 * \throws std::out_of_range if i is smaller than 0 or bigger than n.
 		 */
-		GeneOrder transpos(size_type i, size_type j) const;
+		void reverse(size_type i, size_type j);
+
 
 	private:
 		GeneList _geneorder;
+		/**
+		 * pads the permutation with 0 in front and n+1 at the end if needed
+		 */
+		void pad();
+
+		/**
+		 * Verifies that the permutation starts with 0, ends with n+1 and that all genes i, 0 < i < n+1
+		 * are present, without duplication.
+		 */
+		void verify();
 };
 
 
@@ -98,22 +140,8 @@ class GeneOrder{
  */
 template<typename T>
 GeneOrder::GeneOrder(T begin, T end): _geneorder(begin,end){
-
-	/*TODO: Pad code, just not sure if I need it all the time.
-	if (_geneorder[0] != 0)
-		_geneorder.insert(_geneorder.begin(),0);
-	if(_geneorder[_geneorder.size()-1] != _geneorder.size() - 1)
-		_geneorder.push_back(_geneorder.size());
-	*/
-
-	GeneList genes(_geneorder.size());
-	for (GeneList::iterator gene = _geneorder.begin(); gene != _geneorder.end(); ++gene){
-		++genes[std::abs(*gene)];
-	}
-	for (GeneList::iterator gene = genes.begin(); gene != genes.end(); ++gene){
-		if (*gene != 1)
-			throw std::invalid_argument("Not all genes are present only 1 time");
-	}
+	pad();
+	verify();
 }
 
 #endif