X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=8a1cfff6f660e0042f8a44784e8abff7864c5c2e;hb=8ef6687c1f586285d01c000cc5e359bf9c07c717;hp=54225e22a0ffab29c3ef7081aec8e75257d6d2d7;hpb=c5c3ba0fa9d18707c9c9ce692cff061b6f882e44;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 54225e2..8a1cfff 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. */
@@ -19,22 +20,26 @@ 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.
+	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