X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuff.cpp;h=5f1bdefe6ea95e36c6b30800a690af2ceecb1fbb;hp=002cd52d2aff36d8ac70d4ed9b919d8a8d0a2033;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/libshuff.cpp b/libshuff.cpp
index 002cd52..5f1bdef 100644
--- a/libshuff.cpp
+++ b/libshuff.cpp
@@ -17,14 +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);
 	}
 }
@@ -43,13 +43,14 @@ void Libshuff::initializeGroups(FullMatrix* matrix){
 		}
 		int index=0;
 		for(int i=0;i<numGroups;i++){
+
 			for(int j=0;j<groupSizes[i];j++){
 				savedGroups[i][j] = groups[i][j] = index++;
 			}
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "initializeGroups");
+		m->errorOut(e, "Libshuff", "initializeGroups");
 		exit(1);
 	}
 }
@@ -66,7 +67,8 @@ 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);
+			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
+			//minX[i] = matrix->get(groups[x][i], groups[x][0]);
 			for(int j=0;j<groupSizes[x];j++){
 				if(i != j)	{
 					double dx = matrix->get(groups[x][i], groups[x][j]);
@@ -77,7 +79,7 @@ vector<double> Libshuff::getMinX(int x){
 		return minX;
 	}
 	catch(exception& e) {
-		errorOut(e, "Libshuff", "getMinX");
+		m->errorOut(e, "Libshuff", "getMinX");
 		exit(1);
 	}
 }
@@ -98,7 +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);
 	}
 }
@@ -124,7 +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);
 	}
 }