X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sparsematrix.cpp;h=3a0ec6521720c1f89eb7c54ce47f60a2f81d364a;hp=fc10d27e4193dfcce4ecde200416157876c9ad14;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index fc10d27..3a0ec65 100644
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -2,13 +2,10 @@
 #include "sparsematrix.hpp"
 #include "listvector.hpp"
 
-using namespace std;
-
-typedef list<PCell>::iterator MatData;
 
 /***********************************************************************/
 
-SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){};
+SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){  m = MothurOut::getInstance();  }
 
 /***********************************************************************/
 
@@ -24,26 +21,22 @@ float SparseMatrix::getSmallDist(){
 
 /***********************************************************************/
 
-void SparseMatrix::rmCell(MatData data){
+MatData SparseMatrix::rmCell(MatData data){
 	try {
 		if(data->vectorMap != NULL ){
 			*(data->vectorMap) = NULL;
 			data->vectorMap = NULL;
 		}
-		matrix.erase(data);		
+		data = matrix.erase(data);		
 		numNodes--;
-	
+		return(data);
 	//  seems like i should be updating smallDist here, but the only time we remove cells is when
 	//  clustering and the clustering algorithm updates smallDist
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "rmCell");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -57,13 +50,9 @@ void SparseMatrix::addCell(PCell value){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "addCell");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -77,13 +66,9 @@ void SparseMatrix::clear(){
 		smallDist = 1e6;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "clear");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -112,13 +97,9 @@ void SparseMatrix::print(){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -127,21 +108,17 @@ void SparseMatrix::print(ListVector* list){
 	try {
 		int index = 0;
 	
-		cout << endl << "Index\tRow\tColumn\tDistance" << endl;
+		m->mothurOutEndLine(); m->mothurOut("Index\tRow\tColumn\tDistance"); m->mothurOutEndLine();
 	
 		for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-			cout << index << '\t' << list->get(currentCell->row)  << '\t' << list->get(currentCell->column) << '\t' << currentCell->dist << endl;
+			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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -159,7 +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++){
@@ -191,13 +168,9 @@ PCell* SparseMatrix::getSmallestCell(){
 		return smallCell;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SparseMatrix", "getSmallestCell");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SparseMatrix class function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/