From 696633b3cf5f0b6928216069a780fccc87a69f0b Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Tue, 1 May 2012 08:20:19 -0400
Subject: [PATCH 1/1] changes while testing

---
 cooccurrencecommand.cpp | 4 ++--
 trialswap2.h            | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index cfde0a9..8c763e2 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;
diff --git a/trialswap2.h b/trialswap2.h
index 4c03278..924938b 100644
--- a/trialswap2.h
+++ b/trialswap2.h
@@ -21,7 +21,7 @@ public:
     
     double calc_pvalue_lessthan (vector<double>, double);
     double calc_pvalue_greaterthan (vector<double>, double);
-    int swap_checkerboards (vector<vector<int> > &, vector<int>, vector<int>, int, int);
+    int swap_checkerboards (vector<vector<int> > &, int, int);
     int calc_combo (int, int, vector<vector<int> > &);
     double calc_vratio (int, int, vector<int>, vector<int>);
     int calc_checker (vector<vector<int> > &, vector<int>, int, int);
-- 
2.39.2