X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=8091554e946668fa47259f8157fb6bd489fb8b38;hpb=1f78a8c454a636f19b4711bd52782ea1e3e81d3d;p=mothur.git

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 8091554..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;
 			}
@@ -56,7 +54,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				break;
 			}
 		}
-	cout << "here" << endl;	
+	
 		//read rest of matrix
 		if (square == true) {  readSquareMatrix(filehandle); }
 		else {  readLTMatrix(filehandle); }
@@ -74,7 +72,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 /**************************************************************************/
 int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 	try {
-	cout << "square" << endl;
+	
 		Progress* reading;
 		reading = new Progress("Reading matrix:     ", numSeqs * numSeqs);
 		
@@ -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);
@@ -117,7 +115,7 @@ int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 /**************************************************************************/
 int FullMatrix::readLTMatrix(ifstream& filehandle) {
 	try {
-	cout << "lt" << endl;	
+		
 		Progress* reading;
 		reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
 		
@@ -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;