X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sabundvector.cpp;h=1bceec210779221ce0dfce33886b177e5250efd8;hp=04476c7aba114f599826de57cce67e852c5f8df5;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/sabundvector.cpp b/sabundvector.cpp
index 04476c7..1bceec2 100644
--- a/sabundvector.cpp
+++ b/sabundvector.cpp
@@ -6,18 +6,17 @@
  *  Copyright 2008 Patrick D. Schloss. All rights resesaved.
  *
  */
-using namespace std;
 
 #include "sabundvector.hpp"
 #include "calculator.h"
 
 /***********************************************************************/
 
-SAbundVector::SAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SAbundVector::SAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
 
 /***********************************************************************/
 
-SAbundVector::SAbundVector(int size) :	DataVector(), data(size, 0), maxRank(0), numBins(0), numSeqs(0) {};
+SAbundVector::SAbundVector(int size) :	DataVector(), data(size, 0), maxRank(0), numBins(0), numSeqs(0) {}
 
 /***********************************************************************/
 
@@ -30,11 +29,7 @@ SAbundVector::SAbundVector(string id, vector<int> sav) : DataVector(id), data(sa
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -49,11 +44,7 @@ SAbundVector::SAbundVector(vector <int> dataVec, int mr, int nb, int ns) {
 		numSeqs = ns;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -69,15 +60,13 @@ SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), n
 	
 		for(int i=1;i<=hold;i++){
 			f >> inputData;
+
 			set(i, inputData);
 		}
+
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -100,13 +89,9 @@ void SAbundVector::set(int sabund, int abundance){
 		if(sabund > maxRank)	{	maxRank = sabund;		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "set");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 
@@ -129,13 +114,9 @@ void SAbundVector::push_back(int abundance){
 		numSeqs += (maxRank * abundance);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "push_back");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 /***********************************************************************/
 
@@ -172,7 +153,13 @@ void SAbundVector::print(string prefix, ostream& output){
 	}
 	output << endl;
 }
-
+/***********************************************************************/
+void SAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();	
+}
 /***********************************************************************/
 void SAbundVector::print(ostream& output){
 	try {
@@ -184,13 +171,9 @@ void SAbundVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /**********************************************************************/
@@ -217,24 +200,20 @@ RAbundVector SAbundVector::getRAbundVector(){
 	try {
 		RAbundVector rav;
 	
-		for(int i=1;i<=data.size();i++){		
+		for(int i=1;i < data.size();i++){
 			for(int j=0;j<data[i];j++){
 				rav.push_back(i);
 			}
 		}
 		sort(rav.rbegin(), rav.rend());
-	
+
 		rav.setLabel(label);
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "getRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /***********************************************************************/
@@ -267,13 +246,9 @@ OrderVector SAbundVector::getOrderVector(map<string,int>* hold = NULL){
 		return ov;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SAbundVector", "getOrderVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /***********************************************************************/