added check for positive values in pairwise.seqs gap extend, gap open and mismatch...

[mothur.git] / cooccurrencecommand.cpp

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 6864f799f99a1533766f7350f0a6d8a409fe2876..e6c92594f49d8ab038abdb1587983ece722e5592 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -279,7 +279,6 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
         vector<int> rowtotal; rowtotal.resize(numOTUS, 0);
         
-        int rowcount = 0;
         for (int i = 0; i < thisLookUp.size(); i++) {
                        for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
                                if (m->control_pressed) { return 0; }                   
@@ -288,12 +287,10 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                                if(abund > 0) {
                                    initmatrix[i][j] = 1;
                     co_matrix[j][i] = 1;
-                    rowcount++;
-                    columntotal[j]++;
+                    rowtotal[j]++;
+                    columntotal[i]++;
                                }
                        }
-            rowtotal[i] = rowcount;
-            rowcount = 0;
         }
         
         //nrows is ncols of inital matrix. All the functions need this value. They assume the transposition has already taken place and nrows and ncols refer to that matrix.