add notes of what i learned about seqcomp and nway

[mussa.git] / flp.hh

diff --git a/flp.hh b/flp.hh
index a34b51a8a7b3a49fd711906b5a3fd66d851b1b30..bbeff41e730076b348d13d2ece648d599c3144c7 100644 (file)
--- a/flp.hh
+++ b/flp.hh
@@ -40,18 +40,31 @@ class FLPs
 
   public:
     FLPs();
+    //! Setup a FLP and reserve space for the match lists
+    /*!
+     * Initialize the all_matches structure with a list of matches
+     * for enough windows for the size of sequence 1
+     */
     void setup(std::string type, int win_size, int hard_thres, int len1, int len2);
     inline void add(int seq1_i, int seq2_i, int a_score, int i2_offset);
     void seqcomp(std::string seq1, std::string seq2, bool is_RC);
   //bool FLPs::match_less(match *match1, match *match2);
   //void FLPs::sort();
+    //! Return all the matches for a particular window?
     std::list<int> matches(int index);
-  //version with int threshold 
+    //! Return all the matches for a particular window abouve threshold
     std::list<int> thres_matches(int index, int thres);
+    //! Return the number of windows for sequence 1
     int win_num();
+    //! Save all the FLPs to save_file_path
     void file_save(std::string save_file_path);
+    //! Load a vector of a lists of FLPs
     void file_load(std::string file_path);
 
+    /*! All of the matches are stored here, it appears each window position
+     *  in sequence 1 gets an entry in the vector, the list contains matches
+     *  between sequence 1 and sequence 2
+     */
     std::vector<std::list<match> > all_matches;
 };
 #endif