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.