fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
index 75e0fdcf8a7f9f69df01245f6e09e1e9038bde93..d03880d9814fac255613daa381f6d63b4ccfba4a 100644 (file)
--- a/groupmap.h
+++ b/groupmap.h
@@ -5,35 +5,35 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/1/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
+#include "mothur.h"
 #include "utilities.hpp"
 
+/* This class is a representation of the groupfile.  It is used by all the shared commands to determine what group a 
+       certain sequence belongs to. */
 
 class GroupMap {
 public:
+       GroupMap() {};
        GroupMap(string);
        ~GroupMap();
        void readMap();
        int getNumGroups();
        string getGroup(string);
+       void setGroup(string, string);
        vector<string> namesOfGroups;
-       
-       
+       map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays.
+               
 private:
        ifstream fileHandle;
        string groupFileName;
-       int numGroups;
+       int index;
        map<string, string>::iterator it;
        void setNamesOfGroups(string); 
        map<string, string> groupmap; //sequence name and groupname
 };
 
-#endif
\ No newline at end of file
+#endif