X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fmodels.h;h=c1c96d1cb52addfdade3d847df8929b1536d8fd7;hb=40d817fd1c0ec184927450858ca95b722ae8acba;hp=6a61506ffe38efb0ea87778fc392b47826130220;hpb=f8575ea6c0982bba5ccf42771b2994d19500c0a3;p=germs.git

diff --git a/src/models.h b/src/models.h
index 6a61506..c1c96d1 100644
--- a/src/models.h
+++ b/src/models.h
@@ -21,48 +21,121 @@
 #ifndef __MODELS_H__
 #define __MODELS_H__
 
-#include <string>
-
 class SortAction;
+class GeneOrder;
 
 namespace Models {
 
+/**
+ * Basic implementation of a model. All sort actions are considered equal.
+ */
 class ModelImpl {
 	public:
 		virtual ~ModelImpl();
 
-		virtual double score(const SortAction& sa);
-
-		virtual std::string name();
+		/**
+		 * 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 reversals.
+ */
+class Whirl : public ModelImpl {
+	public:
+		/**
+		 * Returns a higher score for reversals and a lower score
+		 * for all other actions.
+		 *
+		 * \see Model::score
+		 */
+		double score(const SortAction& sa, const GeneOrder& go);
+
+		/**
+		 * \see Model::name
+		 */
+		const char* name();
+};
 
+/**
+ * A model that favors symmetric reversal, resulting in an X-like
+ * picture in a dot plot.
+ */
 class X : public ModelImpl {
 	public:
-		double score(const SortAction& sa);
-
-		std::string name();
+		/**
+		 * 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:
-		double score(const SortAction& sa);
-
-		std::string name();
+		/**
+		 * 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:
-		double score(const SortAction& sa);
-
-		std::string name();
+		/**
+		 * \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:
-		double score(const SortAction& sa);
-
-		std::string name();
+		/**
+		 * \todo has to be implemented
+		 * \see Model::score
+		 */
+		double score(const SortAction& sa, const GeneOrder& go);
+
+		/**
+		 * \see Model::name
+		 */
+		const char* name();
 };
 
 }