X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cooccurrencecommand.cpp;h=75b87fae4303f161a1f75fb632e831672a80e29d;hb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;hp=cfde0a906d7a3138160205623bd42b59f9c2918f;hpb=4b5845a9cb928110bd1e9ec8368727b0198ce49b;p=mothur.git

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index cfde0a9..75b87fa 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -412,7 +412,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         }
 
         //populate null matrix from probability matrix, do this a lot.
-        for(int h=0;h<runs;h++){
+        for(int k=0;k<runs;k++){
             nullmatrix.clear();
             //zero-fill the null matrix
             nullmatrix.assign(nrows, vector<int>(ncols, 0));
@@ -458,7 +458,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                         randnum = rand() / double(RAND_MAX);
                         for(int j=0;j<ncols;j++) {
                             current = probabilityMatrix[ncols * i + j];
-                            if((randnum <= current && randnum > previous && nullmatrix[i][j] != 1) || (previous==current)){
+                            if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
                                 nullmatrix[i][j] = 1;
                                 count++;
                                 previous = 0.0;
@@ -494,6 +494,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
             //swap_checkerboards takes the original matrix and swaps checkerboards
             else if(matrix == "sim9") {
                 trial.swap_checkerboards (co_matrix, ncols, nrows);
+                nullmatrix = co_matrix;
             }
             else {
                 m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true;