X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=078cdb7699f53192b526ab3979036d5144b968e1;hb=cd10743907df223b7dd5b3a3deb20fde758b8ed7;hp=b744490d760d108df3ef7780cb35bcae918b9dd2;hpb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index b744490..078cdb7 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -39,16 +39,15 @@ class FullMatrix {
 		void setBounds();  //requires globaldata->Groups to be filled
 		vector<float> getMins(int); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
 		void getDist(vector<float>&);  //fills a vector with the valid distances for the integral form.
-		void shuffle(int);  //shuffles the sequences in the box passed in.
+		void shuffle(string, string);  //shuffles the sequences in the groups passed in.
 		void restore();  //unshuffles the matrix.
-				
-		
-	void printMinsForRows(ostream&);
+	
 	private:
 		void sortGroups(int, int);  //this function sorts the sequences within the matrix.
 		void getBounds(int&, string);
 		void readSquareMatrix(ifstream&);  
 		void readLTMatrix(ifstream&);
+		void printMinsForRows(ostream&);
 		
 		map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
 		map<int, Swap> restoreIndex; //a map of the swaps made so you can undo them in restore.