fixed some bugs

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 43bde963ca3396241a26771771189cb27c2df617..95c472fd4f1951f5bbee064a764eb6016a2ed956 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -14,39 +14,41 @@
 #include "globaldata.hpp"
 #include "progress.hpp"
 
-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&);
-               void getMinsForRowsVectors();  //requires globaldata->Groups to be filled
+       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 getBounds(int&, string);
-               void readSquareMatrix(ifstream&);  
-               void readLTMatrix(ifstream&);
-               vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-               vector< vector<float> > minsForRows;  //vector< minimum distance for that subrow> -one for each comparison.
-               map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
-               map<int, Names>::iterator it;
-               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.
+       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
\ No newline at end of file