added rename.seqs command.

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
index d6984952188de368c765bf2997198f1fefb8bce5..5397e02e7c158e5074a7f8e626d813561cc6d9b6 100644 (file)
--- a/groupmap.h
+++ b/groupmap.h
@@ -34,19 +34,25 @@ public:
                for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
                return namesOfGroups;
        }
+    vector<string> getNamesSeqs();
        void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
-       map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
        int getNumSeqs()  {  return groupmap.size();  }
-       vector<string> getNamesSeqs();
        vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
        int getNumSeqs(string); //return the number of seqs in a given group
-                       
+    int getCopy(GroupMap*);
+    int renameSeq(string, string);
+    int print(ofstream&);
+    int print(ofstream&, vector<string>); //print certain groups
+    
+    
+    map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+    
 private:
        vector<string> namesOfGroups;
        MothurOut* m;
        ifstream fileHandle;
        string groupFileName;
-       int index;
+    int index;
        map<string, string>::iterator it;
        void setNamesOfGroups(string); 
        map<string, string> groupmap; //sequence name and groupname