libshuff and updated help to include libshuff and modifications to read.dist.

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index b744490d760d108df3ef7780cb35bcae918b9dd2..078cdb7699f53192b526ab3979036d5144b968e1 100644 (file)
--- 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.