X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsabundvector.cpp;h=efd14bcc249207ac4181fc552b8a918d57144083;hp=8282f66878e9f29324b136b243956c5a33f07243;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
index 8282f66..efd14bc 100644
--- a/sharedsabundvector.cpp
+++ b/sharedsabundvector.cpp
@@ -13,7 +13,7 @@
 
 /***********************************************************************/
 
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
+SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){  }
 
 /***********************************************************************/
 
@@ -45,7 +45,7 @@ void SharedSAbundVector::set(int bin, int abundance, string groupName){
 		if(bin > maxRank)	{	maxRank = bin;		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "set");
+		m->errorOut(e, "SharedSAbundVector", "set");
 		exit(1);
 	}
 }
@@ -79,7 +79,7 @@ void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
 		numSeqs += (maxRank * abundance);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "push_back");
+		m->errorOut(e, "SharedSAbundVector", "push_back");
 		exit(1);
 	}
 }
@@ -107,7 +107,7 @@ void SharedSAbundVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "print");
+		m->errorOut(e, "SharedSAbundVector", "print");
 		exit(1);
 	}
 }
@@ -143,7 +143,7 @@ RAbundVector SharedSAbundVector::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].abundance;j++){
 				rav.push_back(i);
 			}
@@ -154,7 +154,7 @@ RAbundVector SharedSAbundVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "getRAbundVector");
+		m->errorOut(e, "SharedSAbundVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -170,7 +170,7 @@ SAbundVector SharedSAbundVector::getSAbundVector(){
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "getSAbundVector");
+		m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
 		exit(1);
 	}
 }
@@ -191,11 +191,9 @@ SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
 	try {
 		SharedRAbundVector rav;
 		
-		int binNumber = 0;
-		for(int i=1;i<=data.size();i++){		
+		for(int i=1;i<data.size();i++){		
 			for(int j=0;j<data[i].abundance;j++){
-				rav.push_back(i, binNumber, data[i].group);
-				binNumber++;
+				rav.push_back(i, data[i].group);
 			}
 		}
 		sort(rav.rbegin(), rav.rend(), compareMembers);
@@ -206,7 +204,7 @@ SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
+		m->errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
 		exit(1);
 	}
 }
@@ -232,10 +230,19 @@ SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
 		return ov;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "getSharedOrderVector");
+		m->errorOut(e, "SharedSAbundVector", "getSharedOrderVector");
 		exit(1);
 	}
 }
+/***********************************************************************/
+
+void SharedSAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+}
+
 /***********************************************************************/
 OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
 	try {
@@ -259,7 +266,7 @@ OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
 		return ov;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSAbundVector", "getOrderVector");
+		m->errorOut(e, "SharedSAbundVector", "getOrderVector");
 		exit(1);
 	}
 }