#include "globaldata.hpp"
#include "progress.hpp"
-using namespace std;
+
+struct Names {
+ string seqName;
+ string groupName;
+};
class FullMatrix {
- public:
- FullMatrix(){};
- FullMatrix(ifstream&);
- ~FullMatrix(){};
+public:
+ FullMatrix(){ m = MothurOut::getInstance(); }
+ FullMatrix(ifstream&);
+ ~FullMatrix(){};
- int getNumSeqs();
- void printMatrix(ostream&);
+ int getNumSeqs();
+ vector<int> getSizes();
+ vector<string> getGroups();
+ void setGroups(vector<string> names) { groups = names; }
+ void setSizes(vector<int> s) { sizes = s; }
+ int getNumGroups();
+ void printMatrix(ostream&);
+ float get(int, int);
+ Names getRowInfo(int row) { return index[row]; }
- private:
- void sortGroups(); //this function sorts the sequences within the matrix.
- void quicksort(int, int, int);//row of matrix, low, high and row number
- void readSquareMatrix(ifstream&);
- void readLTMatrix(ifstream&);
- vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
- map<int, string> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
- GroupMap* groupmap; //maps sequences to groups they belong to.
- GlobalData* globaldata;
- int numSeqs;
- 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;
+ GlobalData* globaldata;
+ MothurOut* m;
};
-#endif
\ No newline at end of file
+#endif