X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.cpp;h=e123298930f706f9bf19d267e0ee17a5ddb41243;hb=c4fb347858dd8cfea4d2933f429fff4130dca65b;hp=3af7cfe93f2d2b6dba45ab7b9ae5cd8c17184255;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/listvector.cpp b/listvector.cpp
index 3af7cfe..e123298 100644
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -7,25 +7,20 @@
  *
  */
 
-using namespace std;
 
-#include <map>
-#include <exception>
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
 #include "listvector.hpp"
 
 
 /***********************************************************************/
 
-ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
 
 /***********************************************************************/
 
-ListVector::ListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){};
+ListVector::ListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){}
 
 /***********************************************************************/
 
@@ -41,11 +36,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -64,13 +55,11 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 			f >> inputData;
 			set(i, inputData);
 		}
+		
+		gobble(f);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -90,11 +79,7 @@ void ListVector::set(int binNumber, string seqNames){
 		numSeqs += (nNames_new - nNames_old);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "set");
 		exit(1);
 	}
 }
@@ -119,11 +104,7 @@ void ListVector::push_back(string seqNames){
 		numSeqs += nNames;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector 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 ListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "push_back");
 		exit(1);
 	}
 }
@@ -163,11 +144,7 @@ void ListVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "print");
 		exit(1);
 	}
 }
@@ -198,11 +175,7 @@ RAbundVector ListVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -223,41 +196,11 @@ SAbundVector ListVector::getSAbundVector(){
 		return sav;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "getSAbundVector");
 		exit(1);
 	}
 }
 
-/***********************************************************************/
-SharedOrderVector* ListVector::getSharedOrderVector(){
-	globaldata = GlobalData::getInstance();
-	string groupName, names, name;
-	groupmap = globaldata->gGroupmap;
-	SharedOrderVector* order;
-	order = new SharedOrderVector();
-	order->setLabel(label);
-	
-	for(int i=0;i<numBins;i++){
-		int binSize = getNumNames(get(i));	//find number of individual in given bin	
-		names = get(i);
-		while (names.find_first_of(',') != -1) { 
-			name = names.substr(0,names.find_first_of(','));
-			names = names.substr(names.find_first_of(',')+1, names.length());
-			groupName = groupmap->getGroup(name);
-			order->push_back(i, binSize, groupName);  //i represents what bin you are in
-		}
-		//get last name
-		groupName = groupmap->getGroup(names);
-		order->push_back(i, binSize, groupName);
-	}
-	random_shuffle(order->begin(), order->end());
-	return order;
-}
-
 /***********************************************************************/
 
 OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
@@ -295,7 +238,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 					}
 					else{
 						if(orderMap->count(seqName) == 0){
-							cerr << seqName << " not found, check *.names file\n";
+							mothurOut(seqName + " not found, check *.names file\n");
 							exit(1);
 						}
 					
@@ -305,7 +248,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 				}
 			
 				if(orderMap->count(seqName) == 0){
-					cerr << seqName << " not found, check *.names file\n";
+					mothurOut(seqName + " not found, check *.names file\n");
 					exit(1);
 				}
 				ov.set((*orderMap)[seqName], i);	
@@ -318,11 +261,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ListVector", "getOrderVector");
 		exit(1);
 	}
 }