X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.cpp;h=9369a12280b35cd41a6a6e3548258f27ebb36b5c;hb=3cd964b03f04bc569c4a7d0b99be9908c54c1d44;hp=e123298930f706f9bf19d267e0ee17a5ddb41243;hpb=30b3ffcd1cfd08e7144ae721bb53e27eb3f7a5d1;p=mothur.git

diff --git a/listvector.cpp b/listvector.cpp
index e123298..9369a12 100644
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -28,7 +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;
@@ -36,7 +36,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "ListVector");
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -55,11 +55,10 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 			f >> inputData;
 			set(i, inputData);
 		}
-		
-		gobble(f);
+		m->gobble(f);
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "ListVector");
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -68,9 +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--;				}
@@ -79,7 +78,7 @@ void ListVector::set(int binNumber, string seqNames){
 		numSeqs += (nNames_new - nNames_old);
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "set");
+		m->errorOut(e, "ListVector", "set");
 		exit(1);
 	}
 }
@@ -95,7 +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++;
 	
@@ -104,7 +103,7 @@ void ListVector::push_back(string seqNames){
 		numSeqs += nNames;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "push_back");
+		m->errorOut(e, "ListVector", "push_back");
 		exit(1);
 	}
 }
@@ -144,7 +143,7 @@ void ListVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "print");
+		m->errorOut(e, "ListVector", "print");
 		exit(1);
 	}
 }
@@ -157,7 +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);
 		}
 	
@@ -175,7 +174,7 @@ RAbundVector ListVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getRAbundVector");
+		m->errorOut(e, "ListVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -187,7 +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);
@@ -196,7 +195,7 @@ SAbundVector ListVector::getSAbundVector(){
 		return sav;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getSAbundVector");
+		m->errorOut(e, "ListVector", "getSAbundVector");
 		exit(1);
 	}
 }
@@ -210,7 +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);
 				}
@@ -238,7 +237,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 					}
 					else{
 						if(orderMap->count(seqName) == 0){
-							mothurOut(seqName + " not found, check *.names file\n");
+							m->mothurOut(seqName + " not found, check *.names file\n");
 							exit(1);
 						}
 					
@@ -248,7 +247,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 				}
 			
 				if(orderMap->count(seqName) == 0){
-					mothurOut(seqName + " not found, check *.names file\n");
+					m->mothurOut(seqName + " not found, check *.names file\n");
 					exit(1);
 				}
 				ov.set((*orderMap)[seqName], i);	
@@ -261,7 +260,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getOrderVector");
+		m->errorOut(e, "ListVector", "getOrderVector");
 		exit(1);
 	}
 }