- 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.
- map<int, Names>::iterator it;
- map<int, Swap>::reverse_iterator it2;
-
- vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
- vector<float> minsForRows; //vector< minimum distance for that subrow> - one for each comparison.
- vector<int> bounds; //bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find upper bound of C because its numSeqs.
-
- GroupMap* groupmap; //maps sequences to groups they belong to.
- GlobalData* globaldata;
- int numSeqs, numGroups, numUserGroups;
- bool square;
-
+private:
+ vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
+ int readSquareMatrix(ifstream&);
+ int readLTMatrix(ifstream&);
+ vector<Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
+ vector<int> sizes;
+ vector<string> groups;
+
+ void sortGroups(int, int); //this function sorts the sequences within the matrix.
+ void swapRows(int, int);
+
+ GroupMap* groupmap; //maps sequences to groups they belong to.
+ int numSeqs;
+ int numGroups;
+ int numUserGroups;
+ bool sim;
+ MothurOut* m;