added modify names parameter to set.dir

[mothur.git] / jackknife.cpp

diff --git a/jackknife.cpp b/jackknife.cpp
index 1082465756916c6bebca1e74114f6989ed14ac33..8f0629832208e797efbdc815e619bab28ed49046 100644 (file)
--- a/jackknife.cpp
+++ b/jackknife.cpp
@@ -12,7 +12,7 @@
 /***********************************************************************/
 void Jackknife::getAMatrix(void){
        try {
-               vector<vector<double> > B = binomial(maxOrder);
+               vector<vector<double> > B = m->binomial(maxOrder);
 
                aMat.resize(maxOrder+1);
 
@@ -25,7 +25,7 @@ void Jackknife::getAMatrix(void){
                }
        }
        catch(exception& e) {
-               errorOut(e, "Jackknife", "getAMatrix");
+               m->errorOut(e, "Jackknife", "getAMatrix");
                exit(1);
        }
 }
@@ -53,7 +53,7 @@ double Jackknife::CN(double z){
                return n;
        }
        catch(exception& e) {
-               errorOut(e, "Jackknife", "CN");
+               m->errorOut(e, "Jackknife", "CN");
                exit(1);
        }
 }
@@ -67,7 +67,7 @@ EstOutput Jackknife::getValues(SAbundVector* rank){
        
                double jack, jacklci, jackhci;
        
-               double maxRank = (double)rank->getMaxRank();
+               int maxRank = (double)rank->getMaxRank();
                int S = rank->getNumBins();
 
                double N[maxOrder+1];
@@ -122,7 +122,7 @@ EstOutput Jackknife::getValues(SAbundVector* rank){
                        }
                        ci = 1.96 * sqrt(ci - jack);
                }
-               else if(k=1){
+               else if(k==1){
                        jack = N[1];
                        ci = 1.96*sqrt(variance[1]);
                }else{
@@ -144,7 +144,7 @@ EstOutput Jackknife::getValues(SAbundVector* rank){
                return data;
        }
        catch(exception& e) {
-               errorOut(e, "Jackknife", "getValues");
+               m->errorOut(e, "Jackknife", "getValues");
                exit(1);
        }
 }