X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectdisplay.h;h=781cea1824dc77cb445819c94aed3173786baa94;hp=15cc5a75a1f32edac6d234ea934ceffdad608301;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63

diff --git a/collectdisplay.h b/collectdisplay.h
index 15cc5a7..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);
@@ -72,14 +76,20 @@ public:
 			output->output(numSeqs, groupData);	
 		}
 	};
-	
+									
 	void init(string s)		{	output->initFile(s);	};
 	void reset()			{	output->resetFile();	};
 	void close()			{	output->resetFile();	};
 	void setAll(bool a)		{	all = a;				}
 	bool getAll()			{	return all;				}
 	
-	bool isCalcMultiple() { return estimate->getMultiple(); }
+	
+	bool isCalcMultiple()	{ return estimate->getMultiple(); }
+	bool calcNeedsAll()     { return estimate->getNeedsAll(); }
+	bool hasLciHci()	{
+		if (estimate->getCols() == 3) { return true; } 
+		else{ return false; } 
+	}
 	
 	string getName()	{  return estimate->getName();  }