X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectdisplay.h;h=781cea1824dc77cb445819c94aed3173786baa94;hp=110d816f1718f374c5dca22afd4c65502ac889fa;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8

diff --git a/collectdisplay.h b/collectdisplay.h
index 110d816..781cea1 100644
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -15,6 +15,8 @@ class CollectDisplay : public Display {
 public:
 	CollectDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file) {timesCalled = 0;};
 	~CollectDisplay()	{	delete estimate; delete output;		}
+	
+	
 	void update(SAbundVector* rank){
 		nSeqs=rank->getNumSeqs();
 		data = estimate->getValues(rank);
@@ -26,10 +28,14 @@ public:
 		data = estimate->getValues(shared);  //passes estimators a shared vector from each group to be compared
 		
 		//figure out what groups are being compared in getValues
-		//because the jumble parameter randomizes the order we need to put the results in the correct column in the output file
+		//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;
@@ -44,8 +50,8 @@ public:
 			}
 			n++;
 		}
-		
-		if (estimate->getMultiple() == true) { 
+			
+		if ((estimate->getMultiple() == true) && all) { 
 			numGroupComb++; 
 			groupData.resize((numGroupComb*data.size()), 0);
 			//is this the time its called with all values
@@ -70,18 +76,33 @@ public:
 			output->output(numSeqs, groupData);	
 		}
 	};
-	
+									
 	void init(string s)		{	output->initFile(s);	};
 	void reset()			{	output->resetFile();	};
 	void close()			{	output->resetFile();	};
-	bool isCalcMultiple() { return estimate->getMultiple(); }
+	void setAll(bool a)		{	all = a;				}
+	bool getAll()			{	return all;				}
+	
+	
+	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();  }
+	
 	
 private:
+	
 	Calculator* estimate;
 	FileOutput* output;
 	int nSeqs, timesCalled, numGroupComb;
 	vector<double> data;
 	vector<double> groupData;
+	bool all;
+	
 };
 
 /***********************************************************************/