X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectdisplay.h;h=7e40ad7359c7553a033ee03645ad6eb2421012ae;hb=ec453945974b5c72af0bea042e3517312566d592;hp=71275737d24a437f09a97eefa528e7f30ed4a134;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/collectdisplay.h b/collectdisplay.h
index 7127573..7e40ad7 100644
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -6,7 +6,7 @@
 #include "calculator.h"
 #include "fileoutput.h"
 #include "display.h"
-#include <vector>
+
 
 using namespace std;
 
@@ -23,32 +23,69 @@ public:
 		output->output(nSeqs, data);	
 	};
 	
-	void update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroupComb){
+	void update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroups){
 		timesCalled++;
-		data = estimate->getValues(shared1, shared2);  //passes estimators a shared vector from each group to be compared
-		//fills groupdata with datas info
-		for (int i = 0; i < data.size(); i++) {
-			groupData.push_back(data[i]);
+		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
+		int group1Index, group2Index, pos;
+		group1Index = shared[0]->getGroupIndex();
+		group2Index = shared[1]->getGroupIndex();
+		
+		numGroupComb = 0;
+		int n = 1;
+		for (int i = 0; i < (numGroups - 1); i++) {
+			for (int l = n; l < numGroups; l++) {
+				if ((group1Index == i) && (group2Index == l)) {
+					pos = numGroupComb;  //pos tells you which column in the output file you are in
+				}else if ((group1Index == l) && (group2Index == i)) {
+					pos = numGroupComb;
+				}
+				numGroupComb++;
+			}
+			n++;
+		}
+		
+		if (estimate->getMultiple() == true) { 
+			numGroupComb++; 
+			groupData.resize((numGroupComb*data.size()), 0);
+			//is this the time its called with all values
+			if  ((timesCalled % numGroupComb) == 0) { 
+				//last spot
+				pos = ((groupData.size()-1) * data.size());
+			}
+			//fills groupdata with datas info
+			for (int i = 0; i < data.size(); i++) {
+				groupData[pos+i] = data[i];
+			}
+		}else {
+			groupData.resize((numGroupComb*data.size()), 0);
+			//fills groupdata with datas info
+			for (int i = 0; i < data.size(); i++) {
+				groupData[pos+i] = data[i];
+			}
 		}
+		
 		//when you get all your groups info then output
 		if ((timesCalled % numGroupComb) == 0) {
 			output->output(numSeqs, groupData);	
-			groupData.clear();
 		}
 	};
 	
 	void init(string s)		{	output->initFile(s);	};
 	void reset()			{	output->resetFile();	};
 	void close()			{	output->resetFile();	};
+	bool isCalcMultiple() { return estimate->getMultiple(); }
 	
 private:
 	Calculator* estimate;
 	FileOutput* output;
-	int nSeqs, timesCalled;
+	int nSeqs, timesCalled, numGroupComb;
 	vector<double> data;
 	vector<double> groupData;
 };
 
 /***********************************************************************/
 
-#endif
\ No newline at end of file
+#endif