X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=9de7ead566d4d5446b5ea405b5e3c7eb24991cc0;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=15fee6e04a97416f3ad734c4f81fe75a6eb598ec;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index 15fee6e..9de7ead 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,7 +11,6 @@
 
 #include "mothur.h"
 #include "groupmap.h"
-#include "globaldata.hpp"
 #include "progress.hpp"
 
 
@@ -23,8 +22,8 @@ struct Names {
 class FullMatrix {
 	
 public:
-	FullMatrix(){ m = MothurOut::getInstance(); }
-	FullMatrix(ifstream&);
+	//FullMatrix(){ m = MothurOut::getInstance(); }
+	FullMatrix(ifstream&, GroupMap*, bool);
 	~FullMatrix(){};
 	
 	int getNumSeqs();
@@ -39,8 +38,8 @@ public:
 	
 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;
@@ -52,7 +51,7 @@ private:
 	int numSeqs;
 	int numGroups;
 	int numUserGroups;
-	GlobalData* globaldata;
+	bool sim;
 	MothurOut* m;
 };