fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it,...

[mothur.git] / collect.cpp

diff --git a/collect.cpp b/collect.cpp
index 79e997de38bc8938bbcdb72d7134a566a7b9a2bb..ec5366b627d8e8f776ffd00c0bb63f98a748f4bc 100644 (file)
--- a/collect.cpp
+++ b/collect.cpp
@@ -132,17 +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;
                 }
@@ -151,17 +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