X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=2df67b8d19b1861714aba2746e3326256cdfe2ae;hb=7837a9bfdfccdc26360987a44c389832fdb82651;hp=218ed8709dd6ce4b624c233c4d60aa8c3cb4a27f;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 218ed87..2df67b8 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -57,6 +57,8 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			}
 		}
 		
+		gobble(f); 
+		
 		if (f.eof() != true) { f >> nextLabel; }
 		
 		//read the rest of the groups info in
@@ -79,6 +81,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 				}
 			}
 			
+			gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 
@@ -93,11 +96,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
 		exit(1);
 	}
 }
@@ -167,11 +166,7 @@ void SharedOrderVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "print");
 		exit(1);
 	}
 }
@@ -180,7 +175,7 @@ void SharedOrderVector::print(ostream& output){
 /***********************************************************************/
 
 void SharedOrderVector::resize(int){
-	cout << "resize() did nothing in class SharedOrderVector";
+	m->mothurOut("resize() did nothing in class SharedOrderVector");
 }
 
 /***********************************************************************/
@@ -223,13 +218,9 @@ RAbundVector SharedOrderVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "getRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 /***********************************************************************/
 
@@ -247,11 +238,7 @@ OrderVector SharedOrderVector::getOrderVector(map<string,int>* nameMap = NULL) {
 		return ov;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "getOrderVector");
 		exit(1);
 	}
 }
@@ -281,14 +268,9 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
 		return sharedRav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
-	
 }
 /***********************************************************************/
 vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
@@ -303,14 +285,9 @@ vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
 		return lookup;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	
 }
 /***********************************************************************/
 SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
@@ -321,14 +298,9 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
 				
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	
 }
 
 /***********************************************************************/
@@ -361,13 +333,9 @@ void SharedOrderVector::updateStats(){
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOrderVector", "updateStats");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedOrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/