X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hp=72866491648e1fb02f681c1ca5842fdbba8e58a2;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 7286649..4451d66 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -11,15 +11,14 @@
 
 /**************************************************************************/
 //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;
-		filehandle >> numSeqs >> name;
 		
+		filehandle >> numSeqs >> name;
+	
 		//make the matrix filled with zeros
 		matrix.resize(numSeqs); 
 		for(int i = 0; i < numSeqs; i++) {
@@ -44,6 +43,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				
 				for(int i=0;i<numSeqs;i++){
 					filehandle >> matrix[0][i];
+					if (sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
 				}
 				break;
 			}
@@ -54,7 +54,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				break;
 			}
 		}
-		
+	
 		//read rest of matrix
 		if (square == true) {  readSquareMatrix(filehandle); }
 		else {  readLTMatrix(filehandle); }
@@ -93,6 +93,7 @@ int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 				if (m->control_pressed) { delete reading;  return 0; }
 				
 				filehandle >> matrix[i][j];
+				if (sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
 				
 				count++;
 				reading->update(count);
@@ -114,6 +115,7 @@ int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 /**************************************************************************/
 int FullMatrix::readLTMatrix(ifstream& filehandle) {
 	try {
+		
 		Progress* reading;
 		reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
 		
@@ -135,8 +137,10 @@ int FullMatrix::readLTMatrix(ifstream& filehandle) {
 				if (m->control_pressed) { delete reading;  return 0; }
 				
 				filehandle >> distance;
-		
+				if (sim) {  distance = 1.0 - distance;  }
+				
 				matrix[i][j] = distance;  matrix[j][i] = distance;
+				
 				count++;
 				reading->update(count);
 			}