X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collect.cpp;h=ec5366b627d8e8f776ffd00c0bb63f98a748f4bc;hb=df905918ace8537273616b4120d404ebd29dc9cc;hp=fa6f677a3be5c5f9d0e535acdc870aaae226c016;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;p=mothur.git

diff --git a/collect.cpp b/collect.cpp
index fa6f677..ec5366b 100644
--- a/collect.cpp
+++ b/collect.cpp
@@ -88,16 +88,17 @@ try {
                 //initialize labels for output
                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
                 getGroupComb();
-                groupLabel = ""; 
-                for (int s = 0; s < groupComb.size(); s++) {
-                        groupLabel = groupLabel + label + groupComb[s] + "\t";
-                }
-				
-				//for multi displays
-				string groupLabelAll = groupLabel + label + "all\t";
 				
                 for(int i=0;i<displays.size();i++){
                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
+						bool hasLciHci = displays[i]->hasLciHci();
+						groupLabel = "";
+						for (int s = 0; s < groupComb.size(); s++) {
+							if (hasLciHci) {  groupLabel = groupLabel + label + groupComb[s] + "\t" + label + groupComb[s] + "lci\t" + label + groupComb[s] + "hci\t"; }
+							else{  groupLabel = groupLabel + label + groupComb[s] + "\t";  }
+						}
+
+						string groupLabelAll = groupLabel + label + "all\t"; 
 						if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) {   displays[i]->init(groupLabelAll); }
 						else {  displays[i]->init(groupLabel);  }           
                 }
@@ -131,17 +132,25 @@ try {
 								//how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 
                                 int n = 1;
+								bool pair = true;
                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                         for (int l = n; l < lookup.size(); l++) {
 												subset.clear(); //clear out old pair of sharedrabunds
 												//add new pair of sharedrabund vectors
 												subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-                                                ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
+											
+												//load subset with rest of lookup for those calcs that need everyone to calc for a pair
+												for (int w = 0; w < lookup.size(); w++) {
+													if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+												}
+											
+                                                ccd->updateSharedData(subset, i+1, globaldata->Groups.size(), pair);
                                         }
                                         n++;
                                 }
 								//if this is a calculator that can do multiples then do them
-								ccd->updateSharedData(lookup, i+1, globaldata->Groups.size()); 
+								pair = false;
+								ccd->updateSharedData(lookup, i+1, globaldata->Groups.size(), pair); 
                         }
                         totalNumSeq = i+1;
                 }
@@ -150,17 +159,25 @@ try {
                 if(numSeqs % increment != 0){
                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
                         int n = 1;
+						bool pair = true;
                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                 for (int l = n; l < lookup.size(); l++) {
 										subset.clear(); //clear out old pair of sharedrabunds
 										//add new pair of sharedrabund vectors
 										subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-										ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
+									
+										//load subset with rest of lookup for those calcs that need everyone to calc for a pair
+										for (int w = 0; w < lookup.size(); w++) {
+											if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+										}
+									
+										ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size(), pair);
                                 }
                                 n++;
                         }
 						//if this is a calculator that can do multiples then do them
-						ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size()); 
+						pair = false;
+						ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size(), pair); 
                 }
                 
                 //resets output files