X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuff.cpp;h=5f1bdefe6ea95e36c6b30800a690af2ceecb1fbb;hp=e6c83f7a42b20cb674675fd6608f9da5dd9f7fa6;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=9354b70bb84f6dd52ff4a1955754bcbf7edeedbf

diff --git a/libshuff.cpp b/libshuff.cpp
index e6c83f7..5f1bdef 100644
--- a/libshuff.cpp
+++ b/libshuff.cpp
@@ -17,13 +17,14 @@ void swap(int& i,int& j){	int t = i;  i = j;  j = t;	}
 
 Libshuff::Libshuff(FullMatrix* D, int it, float step, float co) : matrix(D), iters(it), stepSize(step), cutOff(co){
 	try{
+		m = MothurOut::getInstance();
 		groupNames = matrix->getGroups();
 		groupSizes = matrix->getSizes();
 		numGroups = matrix->getNumGroups();
 		initializeGroups(matrix);
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "Libshuff");
+		m->errorOut(e, "Libshuff", "Libshuff");
 		exit(1);
 	}
 }
@@ -49,7 +50,7 @@ void Libshuff::initializeGroups(FullMatrix* matrix){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "initializeGroups");
+		m->errorOut(e, "Libshuff", "initializeGroups");
 		exit(1);
 	}
 }
@@ -64,7 +65,6 @@ vector<vector<vector<double> > > Libshuff::getSavedMins(){
 
 vector<double> Libshuff::getMinX(int x){
 	try{
-
 		vector<double> minX(groupSizes[x], 0);
 		for(int i=0;i<groupSizes[x];i++){
 			minX[i] = (groupSizes[x] > 1 ? (i==0 ? matrix->get(groups[x][0], groups[x][1]) : matrix->get(groups[x][i], groups[x][0])) : 0.0); //get the first value in row i of this block
@@ -79,7 +79,7 @@ vector<double> Libshuff::getMinX(int x){
 		return minX;
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "getMinX");
+		m->errorOut(e, "Libshuff", "getMinX");
 		exit(1);
 	}
 }
@@ -100,7 +100,7 @@ vector<double> Libshuff::getMinXY(int x, int y){
 		return minXY;
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "getMinXY");
+		m->errorOut(e, "Libshuff", "getMinXY");
 		exit(1);
 	}
 }
@@ -126,7 +126,7 @@ void Libshuff::randomizeGroups(int x, int y){
 		for(int k=0;k<groupSizes[y];k++)	{	groups[y][k]=v[index++];	}
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "randomizeGroups");
+		m->errorOut(e, "Libshuff", "randomizeGroups");
 		exit(1);
 	}
 }