X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.h;h=be4a7648825ba541a253daa74817b120ed087f57;hb=44b464979e91c2a1f144ac45ca12c14fcf6579f0;hp=322cd28571d83ea08d080fb6c4098fbff1c67364;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 322cd28..be4a764 100644
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -12,7 +12,6 @@
  
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "readotu.h"
@@ -20,36 +19,46 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
+#include "consensuscommand.h"
 	
 class GlobalData;
 
 class BootSharedCommand : public Command {
 	
 public:
-	BootSharedCommand();	
+	BootSharedCommand(string);	
 	~BootSharedCommand();
 	int execute();	
+	void help();
 	
 private:
-	void createTree(ostream*);
+	int createTree(ostream*, Tree*);
 	void printSims();
+	int process(SharedOrderVector*);
+	
 	
 	GlobalData* globaldata;
 	SharedUtil* util;
 	ReadOTUFile* read;
 	TreeMap* tmap;
 	Tree* t;
+	Tree* tempTree;
+	ConcensusCommand* consensus;
+	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<string> labels; //holds labels to be used
+	string outputFile, calc, groups, label, outputDir;
 	int numGroups, iters;
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 
 };