X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rabundvector.cpp;h=6cbaa0d896ad7d47105873c67cdc6d003329b83a;hp=471c7e26fa587f5e18dd8a903a31c30c6efc0192;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8

diff --git a/rabundvector.cpp b/rabundvector.cpp
index 471c7e2..6cbaa0d 100644
--- a/rabundvector.cpp
+++ b/rabundvector.cpp
@@ -41,11 +41,7 @@ RAbundVector::RAbundVector(string id, vector<int> rav) : DataVector(id), data(ra
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "RAbundVector");
 		exit(1);
 	}
 }
@@ -60,17 +56,11 @@ RAbundVector::RAbundVector(vector<int> rav, int mr, int nb, int ns) {
 		data = rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "RAbundVector");
 		exit(1);
 	}
 }
 
-
-
 /***********************************************************************/
 
 
@@ -88,11 +78,7 @@ RAbundVector::RAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0),
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "RAbundVector");
 		exit(1);
 	}
 }
@@ -117,11 +103,7 @@ void RAbundVector::set(int binNumber, int newBinSize){
 		numSeqs += (newBinSize - oldBinSize);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "set");
 		exit(1);
 	}
 }
@@ -132,7 +114,15 @@ int RAbundVector::get(int index){
 	return data[index];
 	
 }
+/***********************************************************************/
 
+void RAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+	
+}
 /***********************************************************************/
 
 void RAbundVector::push_back(int binSize){
@@ -147,11 +137,7 @@ void RAbundVector::push_back(int binSize){
 		numSeqs += binSize;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "push_back");
 		exit(1);
 	}
 }
@@ -215,6 +201,19 @@ vector<int>::reverse_iterator RAbundVector::rend(){
 	return data.rend();					
 }
 
+/***********************************************************************/
+void RAbundVector::nonSortedPrint(ostream& output){
+	try {	
+		output << label << '\t' << numBins << '\t';
+	
+		for(int i=0;i<numBins;i++){		output << data[i] << '\t';		}
+		output << endl;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RAbundVector", "nonSortedPrint");
+		exit(1);
+	}
+}
 /***********************************************************************/
 void RAbundVector::print(string prefix, ostream& output){
 	try {	
@@ -227,15 +226,12 @@ void RAbundVector::print(string prefix, ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "print");
 		exit(1);
 	}
 }
 
+
 /***********************************************************************/
 void RAbundVector::print(ostream& output){
 	try {
@@ -248,11 +244,7 @@ void RAbundVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "print");
 		exit(1);
 	}
 }
@@ -295,11 +287,7 @@ SAbundVector RAbundVector::getSAbundVector() {
 		return sav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "getSAbundVector");
 		exit(1);
 	}
 }
@@ -309,23 +297,20 @@ SAbundVector RAbundVector::getSAbundVector() {
 OrderVector RAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
 	try {
 		OrderVector ov;
-	
+
 		for(int i=0;i<data.size();i++){
 			for(int j=0;j<data[i];j++){
 				ov.push_back(i);
 			}
 		}
 		random_shuffle(ov.begin(), ov.end());
-
 		ov.setLabel(label);	
+		ov.getNumBins();
+
 		return ov;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RAbundVector", "getOrderVector");
 		exit(1);
 	}
 }