X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=e52ada56056e14cf8df6f4a2b7e541d7c8b1fcc7;hb=462fca6d24fd15ca035358ff70bcfae52c3281c3;hp=a3b923cd4da60ce601c58d1553e2a95f6b9f4ab9;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index a3b923c..e52ada5 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -9,28 +9,30 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
 
 /* 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();
+	bool isValidGroup(string);  //return true if string is a valid group
 	string getGroup(string);
+	void setGroup(string, string);
 	vector<string> namesOfGroups;
-		
+	map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays.
+	int getNumSeqs()  {  return groupmap.size();  }
+	vector<string> getNamesSeqs();
+			
 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