From 336103ed40931c3317808a0bf9b7e33d502227d7 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Tue, 21 Feb 2006 08:42:03 +0000
Subject: [PATCH] add notes of what i learned about seqcomp and nway stored
 notes as doxygen comments

---
 flp.cxx         | 25 -------------------------
 flp.hh          | 15 ++++++++++++++-
 gui/ConnView.hh |  1 +
 mussa_class.hh  |  5 +++++
 mussa_nway.hh   |  2 ++
 5 files changed, 22 insertions(+), 26 deletions(-)

diff --git a/flp.cxx b/flp.cxx
index 73527d2..879f550 100644
--- 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 a34b51a..bbeff41 100644
--- 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 cf28ff7..2efaba3 100644
--- 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 334f10f..341a3e4 100644
--- 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 32209c4..41fde80 100644
--- 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);
-- 
2.30.2