X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=a99ad119db44c2fd3bb6f78b696fc2d9ddf170af;hb=5f44783e6d74a9c207492ac244210c915cadc272;hp=263fc845b00f535d6d5db76e79d07470851b4481;hpb=60fdefb3a300b59c3bbeffdca8a5f1f30c6a43af;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 263fc84..a99ad11 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -9,32 +9,35 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#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 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 and libshuff commands.
+	int getNumSeqs()  {  return groupmap.size();  }
+	vector<string> getNamesSeqs();
+	int getNumSeqs(string); //return the number of seqs in a given group
+			
 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
+	map<string, int> seqsPerGroup;  //maps groupname to number of seqs in that group
 };
 
-#endif
\ No newline at end of file
+#endif