X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectdisplay.h;h=781cea1824dc77cb445819c94aed3173786baa94;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=d33efe9792332902559d4a600bc3c5581b557185;hpb=dfae916a398508554d35c6b3c8002b69becb53be;p=mothur.git

diff --git a/collectdisplay.h b/collectdisplay.h
index d33efe9..781cea1 100644
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -30,8 +30,12 @@ public:
 		//figure out what groups are being compared in getValues
 		//because we randomizes the order we need to put the results in the correct column in the output file
 		int group1Index, group2Index, pos;
-		group1Index = shared[0]->getGroupIndex();
-		group2Index = shared[1]->getGroupIndex();
+		
+		vector<string> mGroups = m->getGroups();
+		for (int i = 0; i < mGroups.size(); i++) {
+			if (shared[0]->getGroup() == mGroups[i]) { group1Index = i; }
+			if (shared[1]->getGroup() == mGroups[i]) { group2Index = i; }
+		}
 		
 		numGroupComb = 0;
 		int n = 1;
@@ -46,7 +50,7 @@ public:
 			}
 			n++;
 		}
-		
+			
 		if ((estimate->getMultiple() == true) && all) { 
 			numGroupComb++; 
 			groupData.resize((numGroupComb*data.size()), 0);
@@ -81,6 +85,7 @@ public:
 	
 	
 	bool isCalcMultiple()	{ return estimate->getMultiple(); }
+	bool calcNeedsAll()     { return estimate->getNeedsAll(); }
 	bool hasLciHci()	{
 		if (estimate->getCols() == 3) { return true; } 
 		else{ return false; }