GeneOrder::reverse implemented

[germs.git] / src / geneorder.h

diff --git a/src/geneorder.h b/src/geneorder.h
index e411a37253f932ec9788a3f5533bff19c695f2fe..a4b7aaa0ae51a7567c450a7f87655627c0639ab4 100644 (file)
--- a/src/geneorder.h
+++ b/src/geneorder.h
@@ -23,7 +23,6 @@
 
 #include <vector>
 #include <stdexcept>
-#include <cstdlib>
 
 #include "misc.h"
 
@@ -36,6 +35,7 @@ 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 +43,20 @@ 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 +74,14 @@ 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 +89,42 @@ 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 +134,8 @@ 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