X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ordervector.cpp;h=a6dff32386beb1cfeae07a1aa9f01decee5ea0f1;hp=8732c8a614eed4ce29d882f0abeea13693d81340;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/ordervector.cpp b/ordervector.cpp
index 8732c8a..a6dff32 100644
--- a/ordervector.cpp
+++ b/ordervector.cpp
@@ -7,12 +7,8 @@
  *
  */
 
-using namespace std;
-
 #include "ordervector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
+
 
 /***********************************************************************/
 
@@ -20,7 +16,7 @@ OrderVector::OrderVector() : DataVector() {}
 
 /***********************************************************************/
 
-//OrderVector::OrderVector(int ns) : DataVector(), data(ns, -1) {};
+//OrderVector::OrderVector(int ns) : DataVector(), data(ns, -1) {}
 
 /***********************************************************************/
 
@@ -51,11 +47,7 @@ OrderVector::OrderVector(ifstream& f) : DataVector() {
 		updateStats();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function OrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OrderVector class function OrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OrderVector", "OrderVector");
 		exit(1);
 	}
 }
@@ -81,7 +73,14 @@ int OrderVector::getMaxRank(){
 	if(needToUpdate == 1){	updateStats();	}
 	return maxRank;
 }
+/***********************************************************************/
 
+void OrderVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+}
 /***********************************************************************/
 
 
@@ -120,11 +119,7 @@ void OrderVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OrderVector", "print");
 		exit(1);
 	}
 }
@@ -141,19 +136,15 @@ void OrderVector::print(string prefix, ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OrderVector", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
 
 void OrderVector::resize(int){
-	cout << "resize() did nothing in class OrderVector";
+	m->mothurOut("resize() did nothing in class OrderVector");
 }
 
 /***********************************************************************/
@@ -195,13 +186,9 @@ RAbundVector OrderVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OrderVector", "getRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -248,13 +235,9 @@ void OrderVector::updateStats(){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OrderVector", "updateStats");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/