X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=d0e43c5b16a8989786146ec2026b18bbd86c8121;hb=2e77272b6f5987bd2bde592bb15262a8c69ea9e0;hp=de69ca4d94c5e98342c666c7de0a768f61a3b267;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index de69ca4..d0e43c5 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -9,11 +9,8 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "mothurout.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. */
@@ -23,20 +20,27 @@ public:
 	GroupMap() {};
 	GroupMap(string);
 	~GroupMap();
-	void readMap();
+	int readMap();
+	int readDesignMap();
 	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.
-		
+	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:
+	MothurOut* m;
 	ifstream fileHandle;
 	string groupFileName;
 	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