X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=d0e43c5b16a8989786146ec2026b18bbd86c8121;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=e52ada56056e14cf8df6f4a2b7e541d7c8b1fcc7;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index e52ada5..d0e43c5 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -10,6 +10,7 @@
  */
 
 #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. */
@@ -19,23 +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