X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=54085a19bab041d0caf17981c8c6c81f05a0c8b9;hb=15cde0905641f8adddc1cc704f8c064f760e7461;hp=20048a59a5f5aaa3658dd5697f26e3f255a978e1;hpb=7e0cf6431e287072c40b2c10c9e08199fce29ef4;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 20048a5..54085a1 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -10,7 +10,7 @@
  */
 
 #include "mothur.h"
-#include "utilities.hpp"
+#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. */
@@ -20,21 +20,28 @@ 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();
+	vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
+	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