fixed bug in bootstrap command that was caused by globaldata's breakup, and made...

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 194aa33d457fd088e7f367c245e1a8b493a1de49..ee393f9eb3fecd8cac0ddfbea3c5e69863b8a621 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -12,44 +12,54 @@
  
 #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"
 #include "sharedutilities.h"
+#include "concensuscommand.h"
        
 class GlobalData;
 
 class BootSharedCommand : public Command {
        
 public:
-       BootSharedCommand();    
+       BootSharedCommand(string);      
        ~BootSharedCommand();
        int execute();  
+       void help();
        
 private:
-       void createTree(ostream*);
+       void createTree(ostream*, Tree*);
        void printSims();
+       void process(SharedOrderVector*);
+       
        
        GlobalData* globaldata;
        SharedUtil* util;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        TreeMap* tmap;
        Tree* t;
+       Tree* tempTree;
+       ConcensusCommand* concensus;
+       vector< vector<Tree*> > trees;  //a vector of trees for each calculator chosen
        vector<Calculator*> treeCalculators;
        vector<ofstream*> out;
        vector< vector<float> > simMatrix;
        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;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string outputFile, calc, groups, line, label;
        int numGroups, iters;
+       vector<string>  Estimators, Groups; //holds estimators to be used
 
 };