X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgeneorder.h;h=ebc427a9c4c0f49bb770de0af27a3c8c795c80de;hb=3610a7961eaea08a41bf1c0354c68cdee3884278;hp=e411a37253f932ec9788a3f5533bff19c695f2fe;hpb=47b1f5c0294e079bc120dc8366977951aa0778bf;p=germs.git

diff --git a/src/geneorder.h b/src/geneorder.h
index e411a37..ebc427a 100644
--- a/src/geneorder.h
+++ b/src/geneorder.h
@@ -23,7 +23,6 @@
 
 #include <vector>
 #include <stdexcept>
-#include <cstdlib>
 
 #include "misc.h"
 
@@ -34,7 +33,7 @@
 class GeneOrder{
 	public:
 
-		typedef std::vector<Gene> GeneList;
+		typedef std::vector<long> GeneList;
 		typedef GeneList::size_type size_type;
 
 		/**
@@ -77,18 +76,19 @@ class GeneOrder{
 		 */
 		const GeneList& list() const;
 
+
+	private:
+		GeneList _geneorder;
 		/**
-		 * Reverses an interval and returns the new permutation
+		 * pads the permutation with 0 in front and n+1 at the end if needed
 		 */
-		GeneOrder reverse(size_type i, size_type j) const;
+		void pad();
 
 		/**
-		 * Moves the gene on position i to position j, returning a new permutation
+		 * Verifies that the permutation starts with 0, ends with n+1 and that all genes i, 0 < i < n+1
+		 * are present, without duplication.
 		 */
-		GeneOrder transpos(size_type i, size_type j) const;
-
-	private:
-		GeneList _geneorder;
+		void verify();
 };
 
 
@@ -98,22 +98,8 @@ 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