X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=fe61307552b67bdc4567d00025e1a1401a9e70f3;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;p=mothur.git

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index fe61307..4451d66 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -11,11 +11,9 @@
 
 /**************************************************************************/
 //This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle) {
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
 	try{
 		m = MothurOut::getInstance();
-		globaldata = GlobalData::getInstance();
-		groupmap = globaldata->gGroupmap;
 		
 		string name, group;
 		
@@ -45,7 +43,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				
 				for(int i=0;i<numSeqs;i++){
 					filehandle >> matrix[0][i];
-					if (globaldata->sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
+					if (sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
 				}
 				break;
 			}
@@ -95,7 +93,7 @@ int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 				if (m->control_pressed) { delete reading;  return 0; }
 				
 				filehandle >> matrix[i][j];
-				if (globaldata->sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
+				if (sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
 				
 				count++;
 				reading->update(count);
@@ -139,7 +137,7 @@ int FullMatrix::readLTMatrix(ifstream& filehandle) {
 				if (m->control_pressed) { delete reading;  return 0; }
 				
 				filehandle >> distance;
-				if (globaldata->sim) {  distance = 1.0 - distance;  }
+				if (sim) {  distance = 1.0 - distance;  }
 				
 				matrix[i][j] = distance;  matrix[j][i] = distance;