fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 389816abd70d40ce47ec324ce5d830bee77feff9..f3ad0e73dfb2615e4fbeb5bbd96f1a025c6a0ae6 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,21 +11,32 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "globaldata.hpp"
+#include "progress.hpp"
+
+using namespace std;
 
 class FullMatrix {
        
-public:
-       FullMatrix(){};
-       FullMatrix(ifstream&);
-       ~FullMatrix(){};
+       public:
+               FullMatrix(){};
+               FullMatrix(ifstream&);
+               ~FullMatrix(){};
        
-       int getNumSeqs();
+               int getNumSeqs();
+               void printMatrix(ostream&);
        
-private:
-       void sortGroups();  //this function sorts the sequences within the matrix.  
-       vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-       GroupMap* groupmap;  //maps sequences to groups they belong to.
-       int numSeqs;
+       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;
 
 };