X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sparsematrix.cpp;h=3a0ec6521720c1f89eb7c54ce47f60a2f81d364a;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=8a873f74c2441c4dd50f20450ebe4882227ce32b;hpb=1b9d0a66e4737f31d16824fe93944880b9edc530;p=mothur.git

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index 8a873f7..3a0ec65 100644
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -5,7 +5,7 @@
 
 /***********************************************************************/
 
-SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){}
+SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){  m = MothurOut::getInstance();  }
 
 /***********************************************************************/
 
@@ -34,7 +34,7 @@ MatData SparseMatrix::rmCell(MatData data){
 	//  clustering and the clustering algorithm updates smallDist
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "rmCell");
+		m->errorOut(e, "SparseMatrix", "rmCell");
 		exit(1);
 	}
 }
@@ -50,7 +50,7 @@ void SparseMatrix::addCell(PCell value){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "addCell");
+		m->errorOut(e, "SparseMatrix", "addCell");
 		exit(1);
 	}
 }
@@ -66,7 +66,7 @@ void SparseMatrix::clear(){
 		smallDist = 1e6;
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "clear");
+		m->errorOut(e, "SparseMatrix", "clear");
 		exit(1);
 	}
 }
@@ -97,7 +97,7 @@ void SparseMatrix::print(){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "print");
+		m->errorOut(e, "SparseMatrix", "print");
 		exit(1);
 	}
 }
@@ -108,15 +108,15 @@ void SparseMatrix::print(ListVector* list){
 	try {
 		int index = 0;
 	
-		mothurOutEndLine(); mothurOut("Index\tRow\tColumn\tDistance"); mothurOutEndLine();
+		m->mothurOutEndLine(); m->mothurOut("Index\tRow\tColumn\tDistance"); m->mothurOutEndLine();
 	
 		for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-			mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
+			m->mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); m->mothurOutEndLine();
 			index++;
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "print");
+		m->errorOut(e, "SparseMatrix", "print");
 		exit(1);
 	}
 }
@@ -136,7 +136,7 @@ PCell* SparseMatrix::getSmallestCell(){
 	//	if the mins vector is empty go here...
 		if(mins.empty()){		
 			mins.clear();
-		
+	
 			smallDist = begin()->dist;  //set the first candidate small distance
 		
 			for(MatData currentCell=begin();currentCell!=end();currentCell++){
@@ -153,7 +153,7 @@ PCell* SparseMatrix::getSmallestCell(){
 				}
 
 			}
-//			random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
+			random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
 
 			for(int i=0;i<mins.size();i++){
 				mins[i]->vectorMap = &mins[i];  //assign vectorMap to the address for the container
@@ -168,7 +168,7 @@ PCell* SparseMatrix::getSmallestCell(){
 		return smallCell;
 	}
 	catch(exception& e) {
-		errorOut(e, "SparseMatrix", "getSmallestCell");
+		m->errorOut(e, "SparseMatrix", "getSmallestCell");
 		exit(1);
 	}
 }