[project @ 4]

[mussa.git] / mussa_class.hh

diff --git a/mussa_class.hh b/mussa_class.hh
index b80bc3e947b9f577165e892fbe49847dcf0c6e10..06877c735a4990d14e4a0e1503c340cd9448d0ef 100644 (file)
--- a/mussa_class.hh
+++ b/mussa_class.hh
@@ -8,10 +8,11 @@
 class Mussa
 {
   private:
-    string ana_name;
+    string para_file_path, ana_name;
     int seq_num, window, threshold;
     list<string> seq_files, annot_files;
-    list<int> fasta_indices;
+    list<int> fasta_indices, sub_seq_starts, sub_seq_ends;
+    bool win_override, thres_override;
     bool win_append, thres_append;
 
     vector<Sequence> the_Seqs;
@@ -20,12 +21,18 @@ class Mussa
 
   public:
     Mussa();
-    void setup(char * para_file_path);
+    char parse_args(int argc, char **argv);
+    void setup();
     void get_Seqs();
     void seqcomp();
     void nway();
+    void save();
+    void load();
+    void FuckingPieceOfShit(int x_max, int y_max);
+
+    // deprecated - support bridge for python version of mussa
     void save_old();
     void load_old(char * load_file_path, int s_num);
-    void FuckingPieceOfShit(int x_max, int y_max);
+
 };