X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=2df67b8d19b1861714aba2746e3326256cdfe2ae;hb=905cc2b0bd18c5ce611b048d785e93859865a5ea;hp=08692de4ca3fec388ff31407aeee1c0a4d04dd61;hpb=37519fc35c0eb1523e84227517694c4015847c6d;p=mothur.git

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 08692de..2df67b8 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -7,9 +7,6 @@
  *
  */
 
-using namespace std;
-
-
 #include "sharedordervector.h"
 #include "sharedutilities.h"
 
@@ -36,7 +33,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 		
 		if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
 		
-		int num, inputData, pos, count;
+		int num, inputData, count;
 		count = 0;  numSeqs = 0;
 		string holdLabel, nextLabel, groupN;
 		individual newguy;
@@ -60,8 +57,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			}
 		}
 		
-		//save position in file in case next line is a new label.
-		pos = f.tellg();
+		gobble(f); 
 		
 		if (f.eof() != true) { f >> nextLabel; }
 		
@@ -85,15 +81,14 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 				}
 			}
 			
-			//save position in file in case next line is a new label.
-			pos = f.tellg();
-	
+			gobble(f);
+				
 			if (f.eof() != true) { f >> nextLabel; }
 
 		}
 		
 		//put file pointer back since you are now at a new distance label
-		f.seekg(pos, ios::beg);
+		for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
 	
 		if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
 		
@@ -101,11 +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);
 	}
 }
@@ -175,11 +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);
 	}
 }
@@ -188,7 +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");
 }
 
 /***********************************************************************/
@@ -231,13 +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);
-	}	
 }
 /***********************************************************************/
 
@@ -255,11 +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);
 	}
 }
@@ -289,14 +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";
+		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);
-	}
-	
 }
 /***********************************************************************/
 vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
@@ -311,14 +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";
-		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);
 	}
-	
 }
 /***********************************************************************/
 SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
@@ -329,14 +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";
-		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", "getSharedSAbundVector");
 		exit(1);
 	}
-	
 }
 
 /***********************************************************************/
@@ -369,13 +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);
-	}	
 }
 
 /***********************************************************************/