changing command name classify.shared to classifyrf.shared

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 5912b6ccc0ea323bf905bd0e9f301631276c4490..9de7ead566d4d5446b5ea405b5e3c7eb24991cc0 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,10 +11,8 @@
 
 #include "mothur.h"
 #include "groupmap.h"
-#include "globaldata.hpp"
 #include "progress.hpp"
 
-using namespace std;
 
 struct Names {
        string          seqName;
@@ -24,32 +22,37 @@ struct Names {
 class FullMatrix {
        
 public:
-       FullMatrix(){};
-       FullMatrix(ifstream&);
+       //FullMatrix(){ m = MothurOut::getInstance(); }
+       FullMatrix(ifstream&, GroupMap*, bool);
        ~FullMatrix(){};
        
        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:
        vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-       void readSquareMatrix(ifstream&);  
-       void readLTMatrix(ifstream&);
+       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 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;
+       bool sim;
+       MothurOut* m;
 };
 
-#endif
\ No newline at end of file
+#endif