document win_append, thres_append

and remove some unused parameters win_override and thres_override.

diff --git a/alg/mussa.hpp b/alg/mussa.hpp
index 20b1069fd2a9c0134d51f78841e7ff8e41b2d273..c5a5ba00fe27af295202bd9bb3b50eb6ae019a11 100644 (file)
--- a/alg/mussa.hpp
+++ b/alg/mussa.hpp
@@ -113,12 +113,20 @@ class Mussa
   private:
     // Private variables
     // parameters needed for a mussa analysis
+    //! name of this analysis. (will also be used when saving an analysis)
     std::string analysis_name;
-    int window, threshold, soft_thres;
+    //! how many base pairs to include in a sliding window
+    int window;
+    //! how many base pairs need to match order to record a window as conserved
+    int threshold;
+    int soft_thres;
+    //! which nway comparison algorithm to use.
     enum analysis_modes ana_mode;
     double ent_thres;
-    bool win_override, thres_override;
-    bool win_append, thres_append;
+    //! should we append _w<window_size> to the saved analysis
+    bool win_append; 
+    //! should we append _t<threshold> to the saved analysis
+    bool thres_append;
 
     //! sequence data
     std::vector<Sequence> the_seqs;