X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=5e36299505246ecbdbae8c64822a59e916f54dcc;hb=8c548985e92f5be0bde10eddea89a6ae888b73da;hp=4ed479555ab7ac66a75e789e71f9be5053ec3ae2;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 4ed4795..5e36299 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -15,20 +15,13 @@
 RareFactSharedCommand::RareFactSharedCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
-		string fileNameRoot, groups;
+		string fileNameRoot;
 		fileNameRoot = getRootName(globaldata->inputFileName);
-		groupmap = globaldata->gGroupmap;
-		
-		//initialize groups for label
-		groups = "";
-		for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
-			groups = groups + groupmap->namesOfGroups[i];
-		}
-		
+				
 		int i;
 		for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
 			if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-				rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"sharedObserved", groups)));
+				rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
 			}
 		}
 	}
@@ -61,8 +54,8 @@ int RareFactSharedCommand::execute(){
 		read->read(&*globaldata); 
 		
 		input = globaldata->ginput;
-		list = globaldata->glist;
-		order = list->getSharedOrderVector();
+		SharedList = globaldata->gSharedList;
+		order = SharedList->getSharedOrderVector();
 		
 		while(order != NULL){
 		
@@ -78,9 +71,9 @@ int RareFactSharedCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 			}
 			
-			list = input->getListVector(); //get new list vector to process
-			if (list != NULL) {
-				order = list->getSharedOrderVector(); //gets new order vector with group info.
+			SharedList = input->getSharedListVector(); //get new list vector to process
+			if (SharedList != NULL) {
+				order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 				count++;
 			}else {
 				break;