X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=6dfcb97f0aff013d15c1c641e93a24b0d7b229a3;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=f2d8e07f81320d58b500287dc66df8e068246ee5;hpb=87537e4ee46cae9b7041ae0ed4dbbc229936d37c;p=mothur.git

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index f2d8e07..6dfcb97 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -16,32 +16,30 @@
 
 /***********************************************************************/
 
-SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; }
+SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
 
 /***********************************************************************/
 
-SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; }
+SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
 
 /***********************************************************************/
 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
-		globaldata = GlobalData::getInstance();
-
 		//set up groupmap for later.
-		groupmap = new GroupMap(globaldata->getGroupFile());
-		groupmap->readMap();
+		groupmap = new GroupMap(m->getGroupFile());
+		groupmap->readMap(); 
 
 		int hold;
 		string inputData;
 		f >> label >> hold;
 	
 		data.assign(hold, "");
-	
+		
 		for(int i=0;i<hold;i++){
 			f >> inputData;
 			set(i, inputData);
 		}
-	
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedListVector", "SharedListVector");
@@ -61,6 +59,8 @@ void SharedListVector::set(int binNumber, string seqNames){
 		if(nNames_new > maxRank)	{	maxRank = nNames_new;	}
 	
 		numSeqs += (nNames_new - nNames_old);
+		
+			 
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedListVector", "set");
@@ -266,17 +266,20 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 		vector<SharedRAbundVector*> lookup;  //contains just the groups the user selected
 		map<string, SharedRAbundVector*> finder;  //contains all groups in groupmap
 		string group, names, name;
-	
-		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+		
+		vector<string> Groups = m->getGroups();
+		vector<string> allGroups = groupmap->getNamesOfGroups();
+		util->setGroups(Groups, allGroups);
+		m->setGroups(Groups);
 		delete util;
 
-		for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+		for (int i = 0; i < allGroups.size(); i++) {
 			SharedRAbundVector* temp = new SharedRAbundVector(data.size());
-			finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
-			finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
-			finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-			if (m->inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
-				lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+			finder[allGroups[i]] = temp;
+			finder[allGroups[i]]->setLabel(label);
+			finder[allGroups[i]]->setGroup(allGroups[i]);
+			if (m->inUsersGroups(allGroups[i], m->getGroups())) {  //if this group is in user groups
+				lookup.push_back(finder[allGroups[i]]);
 			}
 		}