X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectdisplay.h;fp=collectdisplay.h;h=fc405dfa0d7dbfd8885d5c21ec9b1d879f2f4126;hb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;hp=367a188dfb8de90c2e464cb70cc4a7b1b826ccfe;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/collectdisplay.h b/collectdisplay.h
index 367a188..fc405df 100644
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -23,17 +23,40 @@ public:
 		output->output(nSeqs, data);	
 	};
 	
-	void update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroupComb){
+	void update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroups){
 		timesCalled++;
 		data = estimate->getValues(shared1, shared2);  //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 = shared1->getGroupIndex();
+		group2Index = shared2->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++;
+		}
+
+		groupData.resize((numGroupComb*data.size()), 0);
+		
 		//fills groupdata with datas info
 		for (int i = 0; i < data.size(); i++) {
-			groupData.push_back(data[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();
 		}
 	};
 	
@@ -44,7 +67,7 @@ public:
 private:
 	Calculator* estimate;
 	FileOutput* output;
-	int nSeqs, timesCalled;
+	int nSeqs, timesCalled, numGroupComb;
 	vector<double> data;
 	vector<double> groupData;
 };