X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=bdcd61e7c763cc10e31088d3292064887a8070a8;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=29c174134eee5689e5210775dbde2f220010d551;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 29c1741..bdcd61e 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -17,11 +17,13 @@
 
 class GroupMap {
 public:
-	GroupMap() {};
+	GroupMap() { m = MothurOut::getInstance(); }
 	GroupMap(string);
 	~GroupMap();
 	int readMap();
+    int readMap(string);
 	int readDesignMap();
+    int readDesignMap(string);
 	int getNumGroups();
 	bool isValidGroup(string);  //return true if string is a valid group
 	string getGroup(string);
@@ -32,19 +34,22 @@ public:
 		for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
 		return namesOfGroups;
 	}
+    vector<string> getNamesSeqs();
 	void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
-	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
-			
+    int getCopy(GroupMap*);
+    
+    
+    map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+    
 private:
 	vector<string> namesOfGroups;
 	MothurOut* m;
 	ifstream fileHandle;
 	string groupFileName;
-	int index;
+    int index;
 	map<string, string>::iterator it;
 	void setNamesOfGroups(string); 
 	map<string, string> groupmap; //sequence name and groupname