using namespace std;
struct Names {
- string groupname;
string seqName;
+ string groupName;
};
-
class FullMatrix {
- public:
- FullMatrix(){};
- FullMatrix(ifstream&);
- ~FullMatrix(){};
+public:
+ FullMatrix(){};
+ FullMatrix(ifstream&);
+ ~FullMatrix(){};
- int getNumSeqs();
- void printMatrix(ostream&);
+ int getNumSeqs();
+ vector<int> getSizes();
+ vector<string> getGroups();
+ int getNumGroups();
+ void printMatrix(ostream&);
+ float get(int, int);
- private:
- void sortGroups(int, int); //this function sorts the sequences within the matrix.
- 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, Names> 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.
+ void readSquareMatrix(ifstream&);
+ void 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.
+
+
+ GroupMap* groupmap; //maps sequences to groups they belong to.
+ int numSeqs;
+ int numGroups;
+ int numUserGroups;
+ GlobalData* globaldata;
};
#endif
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