class SortAction;
class GeneOrder;
+class Model;
/**
* Sorts genes
* Takes a GeneOrder, finds the actions to transform it into a sorted
* permutation and returns the list with required actions.
*/
- ActionList sort(const GeneOrder& go1);
+ ActionList sort(const GeneOrder& go1, const Model& m);
/**
* Find the safe actions for this GeneOrder.
*/
ActionList safeActions(const GeneOrder& go1);
- size_t scoreActions(const GeneOrder& go, SortAction& sa);
+ /**
+ * Calculates the score for an action given a gene order
+ */
+ size_t scoreAction(const GeneOrder& go, SortAction& sa);
~GeneSorter(){};
};