fixed a bug in calculating the # of ambig bases

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 194aa33d457fd088e7f367c245e1a8b493a1de49..b632acede61e9f06c576ea236e7eac4b7c896153 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -12,10 +12,9 @@
  
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
@@ -33,10 +32,12 @@ public:
 private:
        void createTree(ostream*);
        void printSims();
+       void process(SharedOrderVector*);
+       
        
        GlobalData* globaldata;
        SharedUtil* util;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        TreeMap* tmap;
        Tree* t;
        vector<Calculator*> treeCalculators;
@@ -45,7 +46,6 @@ private:
        map<int, int> index;  //maps row in simMatrix to vector index in the tree       
        InputData* input;
        ValidCalculators* validCalculator;
-       SharedListVector* SharedList;
        SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
        string format, outputFile;