X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuff.cpp;h=5f1bdefe6ea95e36c6b30800a690af2ceecb1fbb;hp=b7e5f27007f4fe33fd2e4d43ff8ea50a2399c130;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=197c6d3303439582502840980d6a85cf3aab2314

diff --git a/libshuff.cpp b/libshuff.cpp
index b7e5f27..5f1bdef 100644
--- a/libshuff.cpp
+++ b/libshuff.cpp
@@ -17,21 +17,16 @@ 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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function Libshuff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Libshuff", "Libshuff");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Libshuff class function Libshuff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-	
 }
 
 /***********************************************************************/
@@ -48,20 +43,16 @@ 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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function initializeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Libshuff", "initializeGroups");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Libshuff class function initializeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-	
 }
 
 /***********************************************************************/
@@ -76,7 +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]);
@@ -87,14 +79,9 @@ vector<double> Libshuff::getMinX(int x){
 		return minX;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function getMinX. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Libshuff", "getMinX");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Libshuff class function getMinX. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-	
 }
 
 /***********************************************************************/
@@ -113,13 +100,9 @@ vector<double> Libshuff::getMinXY(int x, int y){
 		return minXY;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function getMinXY. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Libshuff", "getMinXY");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Libshuff class function getMinXY. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -143,13 +126,9 @@ void Libshuff::randomizeGroups(int x, int y){
 		for(int k=0;k<groupSizes[y];k++)	{	groups[y][k]=v[index++];	}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Libshuff class Function randomizeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Libshuff", "randomizeGroups");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Libshuff class function randomizeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/