X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sabundvector.cpp;h=0b3dde6fe9312b72d2f08a716b5b61ee01cca64d;hp=b70c642643cfd746e63c236e328feb8e37d74a44;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/sabundvector.cpp b/sabundvector.cpp
index b70c642..0b3dde6 100644
--- a/sabundvector.cpp
+++ b/sabundvector.cpp
@@ -29,7 +29,7 @@ SAbundVector::SAbundVector(string id, vector<int> sav) : DataVector(id), data(sa
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "SAbundVector");
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -44,7 +44,7 @@ SAbundVector::SAbundVector(vector <int> dataVec, int mr, int nb, int ns) {
 		numSeqs = ns;
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "SAbundVector");
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -54,7 +54,7 @@ SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), n
 	try {
 		int hold;
 		f >> label >> hold;
-	
+        
 		data.assign(hold+1, 0);
 		int inputData;
 	
@@ -62,9 +62,10 @@ SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), n
 			f >> inputData;
 			set(i, inputData);
 		}
+
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "SAbundVector");
+		m->errorOut(e, "SAbundVector", "SAbundVector");
 		exit(1);
 	}
 }
@@ -87,7 +88,7 @@ void SAbundVector::set(int sabund, int abundance){
 		if(sabund > maxRank)	{	maxRank = sabund;		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "set");
+		m->errorOut(e, "SAbundVector", "set");
 		exit(1);
 	}
 }
@@ -112,7 +113,7 @@ void SAbundVector::push_back(int abundance){
 		numSeqs += (maxRank * abundance);
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "push_back");
+		m->errorOut(e, "SAbundVector", "push_back");
 		exit(1);
 	}
 }
@@ -151,7 +152,13 @@ void SAbundVector::print(string prefix, ostream& output){
 	}
 	output << endl;
 }
-
+/***********************************************************************/
+void SAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();	
+}
 /***********************************************************************/
 void SAbundVector::print(ostream& output){
 	try {
@@ -163,7 +170,7 @@ void SAbundVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "print");
+		m->errorOut(e, "SAbundVector", "print");
 		exit(1);
 	}
 }
@@ -192,18 +199,18 @@ RAbundVector SAbundVector::getRAbundVector(){
 	try {
 		RAbundVector rav;
 	
-		for(int i=1;i<=data.size();i++){		
+		for(int i=1;i < data.size();i++){
 			for(int j=0;j<data[i];j++){
 				rav.push_back(i);
 			}
 		}
 		sort(rav.rbegin(), rav.rend());
-	
+
 		rav.setLabel(label);
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "getRAbundVector");
+		m->errorOut(e, "SAbundVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -238,7 +245,7 @@ OrderVector SAbundVector::getOrderVector(map<string,int>* hold = NULL){
 		return ov;
 	}
 	catch(exception& e) {
-		errorOut(e, "SAbundVector", "getOrderVector");
+		m->errorOut(e, "SAbundVector", "getOrderVector");
 		exit(1);
 	}
 }