X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=f3ad0e73dfb2615e4fbeb5bbd96f1a025c6a0ae6;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=4fe11451ea7bc612e1b50397bd82328bbe2195c3;hpb=8aaea67a29205b8d3fe787d94d0dc5987858d2e6;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index 4fe1145..f3ad0e7 100644
--- 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;
 
 };