X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=51e277a659ce33789482ea837db6c7a6d0075b25;hb=c47e480b743d1c242b8c527b6d12f992c68b8c2c;hp=7952859bccb3048bd796bdb05f74d2d920ed9c05;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 7952859..51e277a 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -59,8 +59,9 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 //reads a shared file
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
-		m->namesOfGroups.clear();
-				
+		m->clearAllGroups();
+		vector<string> allGroups;
+		
 		int num, inputData, count;
 		count = 0;  
 		string holdLabel, nextLabel, groupN;
@@ -112,7 +113,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		lookup[0]->setLabel(label);
 		lookup[0]->setGroup(groupN);
 		
-		m->namesOfGroups.push_back(groupN);
+		allGroups.push_back(groupN);
 		
 		//fill vector.  data = first sharedrabund in file
 		for(int i=0;i<num;i++){
@@ -133,7 +134,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			f >> groupN >> num;
 			count++;
 			
-			m->namesOfGroups.push_back(groupN);
+			allGroups.push_back(groupN);
 			
 			//add new vector to lookup
 			temp = new SharedRAbundVector();
@@ -152,7 +153,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 				
 			if (f.eof() != true) { f >> nextLabel; }
 		}
-			m->saveNextLabel = nextLabel;
+		m->saveNextLabel = nextLabel;
+		m->setAllGroups(allGroups);
 		
 	}
 	catch(exception& e) {
@@ -393,7 +395,7 @@ int SharedRAbundVector::getGroupIndex()  { return index; }
 void SharedRAbundVector::setGroupIndex(int vIndex)	{ index = vIndex; }
 /***********************************************************************/
 int SharedRAbundVector::getNumBins(){
-	return numBins;
+		return numBins;
 }
 
 /***********************************************************************/
@@ -418,12 +420,15 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		SharedUtil* util;
 		util = new SharedUtil();
 		
-		util->setGroups(m->Groups, m->namesOfGroups);
+		vector<string> Groups = m->getGroups();
+		vector<string> allGroups = m->getAllGroups();
+		util->setGroups(Groups, allGroups);
+		m->setGroups(Groups);
 		
 		bool remove = false;
 		for (int i = 0; i < lookup.size(); i++) {
 			//if this sharedrabund is not from a group the user wants then delete it.
-			if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) { 
+			if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) { 
 				remove = true;
 				delete lookup[i]; lookup[i] = NULL;
 				lookup.erase(lookup.begin()+i);