From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Mon, 30 Apr 2012 17:33:04 +0000 (-0400)
Subject: fixed rowtotal and columntotal
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=5d5ce917adda39d712a4d5ac0932671db1426393

fixed rowtotal and columntotal
---

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index f9db5be..465ddce 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -277,8 +277,8 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
         vector<int> rowtotal; rowtotal.resize(numOTUS, 0);
         
-        for (int i = 0; i < thisLookUp.size(); i++) {
-            for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
+        for (int i = 0; i < thisLookUp.size(); i++) { //nrows in the shared file
+            for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) { //cols of original shared file
                 if (m->control_pressed) { return 0; }
                 int abund = thisLookUp[i]->getAbundance(j);
                 
@@ -296,8 +296,6 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         int ncols = thisLookUp.size();//groups
         double initscore = 0.0;
         
-        vector<int> columntotal; columntotal.resize(ncols, 0);
-        vector<int> rowtotal; rowtotal.resize(nrows, 0);
         vector<double> stats;
         double probabilityMatrix[ncols * nrows];
         vector<vector<int> > nullmatrix(nrows, vector<int>(ncols, 0));
diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 3822f54..c51a5b7 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -192,7 +192,7 @@ int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatr
     }
 }
 /**************************************************************************************************/
-int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix)
+int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix,  vector<int> rowtotal, vector<int> columntotal, int ncols, int nrows)
 {
     try {
         int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
diff --git a/trialswap2.h b/trialswap2.h
index 7b90663..2bd6939 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);
-    void swap_checkerboards (vector<vector<int> > &co_matrix, vector<int> rowtotal, vector<int> columntotal, int ncols, int nrows);
+    void swap_checkerboards (vector<vector<int> > &, vector<int>, 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);