X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.cpp;h=9369a12280b35cd41a6a6e3548258f27ebb36b5c;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=3af7cfe93f2d2b6dba45ab7b9ae5cd8c17184255;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/listvector.cpp b/listvector.cpp
index 3af7cfe..9369a12 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){}
 
 /***********************************************************************/
 
@@ -33,7 +28,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 	try {
 		for(int i=0;i<data.size();i++){
 			if(data[i] != ""){
-				int binSize = getNumNames(data[i]);
+				int binSize = m->getNumNames(data[i]);
 				numBins = i+1;
 				if(binSize > maxRank)	{	maxRank = binSize;	}
 				numSeqs += binSize;
@@ -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";
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -64,13 +55,10 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 			f >> inputData;
 			set(i, inputData);
 		}
+		m->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";
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -79,9 +67,9 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 
 void ListVector::set(int binNumber, string seqNames){
 	try {
-		int nNames_old = getNumNames(data[binNumber]);
+		int nNames_old = m->getNumNames(data[binNumber]);
 		data[binNumber] = seqNames;
-		int nNames_new = getNumNames(seqNames);
+		int nNames_new = m->getNumNames(seqNames);
 	
 		if(nNames_old == 0)			{	numBins++;				}
 		if(nNames_new == 0)			{	numBins--;				}
@@ -90,11 +78,7 @@ 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";
+		m->errorOut(e, "ListVector", "set");
 		exit(1);
 	}
 }
@@ -110,7 +94,7 @@ string ListVector::get(int index){
 void ListVector::push_back(string seqNames){
 	try {
 		data.push_back(seqNames);
-		int nNames = getNumNames(seqNames);
+		int nNames = m->getNumNames(seqNames);
 	
 		numBins++;
 	
@@ -119,11 +103,7 @@ 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";
+		m->errorOut(e, "ListVector", "push_back");
 		exit(1);
 	}
 }
@@ -163,11 +143,7 @@ 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";
+		m->errorOut(e, "ListVector", "print");
 		exit(1);
 	}
 }
@@ -180,7 +156,7 @@ RAbundVector ListVector::getRAbundVector(){
 		RAbundVector rav;
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);
+			int binSize = m->getNumNames(data[i]);
 			rav.push_back(binSize);
 		}
 	
@@ -198,11 +174,7 @@ 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";
+		m->errorOut(e, "ListVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -214,7 +186,7 @@ SAbundVector ListVector::getSAbundVector(){
 		SAbundVector sav(maxRank+1);
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);	
+			int binSize = m->getNumNames(data[i]);	
 			sav.set(binSize, sav.get(binSize) + 1);	
 		}
 		sav.set(0, 0);
@@ -223,41 +195,11 @@ 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";
+		m->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){
@@ -267,7 +209,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 			OrderVector ov;
 		
 			for(int i=0;i<data.size();i++){
-				int binSize = getNumNames(data[i]);		
+				int binSize = m->getNumNames(data[i]);		
 				for(int j=0;j<binSize;j++){
 					ov.push_back(i);
 				}
@@ -295,7 +237,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 					}
 					else{
 						if(orderMap->count(seqName) == 0){
-							cerr << seqName << " not found, check *.names file\n";
+							m->mothurOut(seqName + " not found, check *.names file\n");
 							exit(1);
 						}
 					
@@ -305,7 +247,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 				}
 			
 				if(orderMap->count(seqName) == 0){
-					cerr << seqName << " not found, check *.names file\n";
+					m->mothurOut(seqName + " not found, check *.names file\n");
 					exit(1);
 				}
 				ov.set((*orderMap)[seqName], i);	
@@ -318,11 +260,7 @@ 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";
+		m->errorOut(e, "ListVector", "getOrderVector");
 		exit(1);
 	}
 }