X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fmodels.h;h=f037071b0843684ce16ccb2e29e94aaac38aeb9a;hb=ca651f2fd25147f88dbb27a27bc79bedcd9e4c81;hp=8d7f9e8a7a7980ffe10634dcc7eb732de43ae2de;hpb=d7c119fefaf9cce07974afbefb4b6a017689a961;p=germs.git

diff --git a/src/models.h b/src/models.h
index 8d7f9e8..f037071 100644
--- a/src/models.h
+++ b/src/models.h
@@ -26,41 +26,97 @@ class GeneOrder;
 
 namespace Models {
 
+/**
+ * Basic implementation of a model. All sort actions are considered equal.
+ */
 class ModelImpl {
 	public:
 		virtual ~ModelImpl();
 
+		/**
+		 * All actions return 1 in this model.
+		 *
+		 * \see Model::score
+		 */
 		virtual double score(const SortAction& sa, const GeneOrder& go);
 
+		/**
+		 * \see Model::name
+		 */
 		virtual const char* name();
 };
 
 
+/**
+ * A model that favors symmetric reversal, resulting in an X-like
+ * picture in a dot plot.
+ */
 class X : public ModelImpl {
 	public:
+		/**
+		 * Returns a higher score for reversals around the center
+		 *
+		 * \see Model::score
+		 */
 		double score(const SortAction& sa, const GeneOrder& go);
 
+		/**
+		 * \see Model::name
+		 */
 		const char* name();
 };
 
+/**
+ * A model that favors short reversals, resulting in a zipper-like
+ * picture in a dot plot
+ */
 class Zipper : public ModelImpl {
 	public:
+		/**
+		 * Returns higher score for shorter reversals.
+		 *
+		 * \see Model::score
+		 */
 		double score(const SortAction& sa, const GeneOrder& go);
 
+		/**
+		 * \see Model::name
+		 */
 		const char* name();
 };
 
+/**
+ * A model that favors single gene transpositions, resulting in a
+ * very scattered dot plot.
+ */
 class Cloud : public ModelImpl {
 	public:
+		/**
+		 * \todo has to be implemented
+		 * \see Model::score
+		 */
 		double score(const SortAction& sa, const GeneOrder& go);
 
+		/**
+		 * \see Model::name
+		 */
 		const char* name();
 };
 
+/**
+ * A model similar to X, but a wider X in the dot plot.
+ */
 class FatX : public ModelImpl {
 	public:
+		/**
+		 * \todo has to be implemented
+		 * \see Model::score
+		 */
 		double score(const SortAction& sa, const GeneOrder& go);
 
+		/**
+		 * \see Model::name
+		 */
 		const char* name();
 };