[project @ 4]

[mussa.git] / sequence.hh

diff --git a/sequence.hh b/sequence.hh
index afbb9da21e65c1454b9d299b19380d119b6e27f5..088eac842f329afe3c2a69d28814fac4c577b4b8 100644 (file)
--- a/sequence.hh
+++ b/sequence.hh
@@ -7,12 +7,20 @@
 #include <list>
 #include <vector>
 #include <string>
-#include <fstream.h>
+#include <fstream>
 #include <stdlib.h>
 #include <algorithm>
 
 // Sequence data class
 
+using namespace std;
+
+struct annot
+{
+  int start, end;
+  string name, type;
+};
+
 class Sequence
 {
   friend class ConnView;
@@ -24,11 +32,6 @@ class Sequence
     string species;
     int species_num; 
 
-    struct annot
-    {
-      int start, end;
-      string name, type;
-    };
 
     list<annot> annots;
 
@@ -37,7 +40,8 @@ class Sequence
 
   public:
     Sequence();
-    void load_fasta(string file_path, int seq_num);
+    void load_fasta(string file_path, int seq_num, 
+                    int start_index, int end_index);
     void load_annot(string file_path);
     string seq();
     const char * c_seq();
@@ -45,6 +49,9 @@ class Sequence
     int len();
     string hdr();
     void set_seq(string a_seq);
+    list<int> find_motif(string a_motif);
   //  string species();
     void clear();
+    void save(fstream &save_file);
+    void load_museq(string load_file_path, int seq_num); 
 };