add notes of what i learned about seqcomp and nway

stored notes as doxygen comments

diff --git a/flp.cxx b/flp.cxx
index 73527d2c37905c96c8c7e9615a2942453b18f194..879f550c57c285909752b4c97219c922284ea9a6 100644 (file)
--- a/flp.cxx
+++ b/flp.cxx
@@ -82,16 +82,11 @@ FLPs::matches(int index)
   index = abs(index);
   list_i = all_matches[index].begin();
   list_end = all_matches[index].end();
-  //if (list_i == list_end)
-  //cout << "its fuckin empty!!!!";
   while (list_i != list_end)
   {
     these_matches.push_back(list_i->index);
-    //cout << list_i->index << " ";
     ++list_i;
   }
-  //cout << endl;
-
   return these_matches;
 }
 
@@ -106,22 +101,15 @@ FLPs::thres_matches(int index, int thres)
   list_end = all_matches[index].end();
   thres_matches.clear();
 
-  //if (list_i == list_end)
-  //cout << "its fuckin empty!!!!";
   while (list_i != list_end)
   {
     if (list_i->score >= thres)
       thres_matches.push_back(list_i->index);
-    //cout << list_i->index << " ";
-
     ++list_i;
   }
-  //cout << endl;
-
   return thres_matches;
 }
 
-
 void
 FLPs::file_save(string save_file_path)
 {
@@ -166,11 +154,6 @@ FLPs::file_load(string file_path)
   list<match> a_match_list;
   int i;
 
-
-
-
-
-
   data_file.open(file_path.c_str(), ios::in);
 
   getline(data_file,file_data_line);
@@ -225,11 +208,3 @@ FLPs::file_load(string file_path)
   data_file.close();
 }
 
-/*
-      cout << "fee\n";
-      cout << "fie\n";
-      cout << "foe  ";
-      cout << "fum\n";
-*/
-
-

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

diff --git a/gui/ConnView.hh b/gui/ConnView.hh
index cf28ff7fc81e8d9da3cd9df299cd6eae09c72a99..2efaba36c8b0b8f36d61334ca79badb95a333e2b 100644 (file)
--- a/gui/ConnView.hh
+++ b/gui/ConnView.hh
@@ -52,6 +52,7 @@ class ConnView : public Fl_Box
 
   //this data is passed as pointers to the instantiated classes
     std::vector<Sequence> *S;
+    //! Store the nway paths our analysis did, we mostly need the refined paths
     Nway_Paths *P;
 
     int name_pad, y_pad;

diff --git a/mussa_class.hh b/mussa_class.hh
index 334f10f5c2b376593b3cb718016c27532b9e589e..341a3e4f061c9083f9f5ad54fe4029e3eff1ec48 100644 (file)
--- a/mussa_class.hh
+++ b/mussa_class.hh
@@ -51,6 +51,11 @@ class Mussa
     // Private methods
     std::string get_Seqs();
     void seqcomp();
+    /*! actually run the nway comparison
+     *  it appears there are 4 modes, t (trans_path_search), 
+     *  r (radiate_path_search), e (entropy_path_search), and 
+     *  o, (find_paths_r (old recursive analysis))
+     */
     void nway();
 
 

diff --git a/mussa_nway.hh b/mussa_nway.hh
index 32209c4481bfeb01b55281f97490f91ffa885b2f..41fde80046198bb91fbb66b60d24c1f6a4764f73 100644 (file)
--- a/mussa_nway.hh
+++ b/mussa_nway.hh
@@ -38,6 +38,8 @@ class Nway_Paths
 
   public:
     Nway_Paths();
+    //! setup an nway comparison, initialize # of species, window size, 
+    //! threshold
     void setup(int sp_num, int w, int t);
     void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
     void set_soft_thres(int soft_thres);