X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.h;h=d5b48e8129ad2ebdacc5acff8f36bd82b92bea3b;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=194aa33d457fd088e7f367c245e1a8b493a1de49;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 194aa33..d5b48e8 100644
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -12,45 +12,57 @@
  
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-	
-class GlobalData;
+#include "consensuscommand.h"
 
 class BootSharedCommand : public Command {
 	
 public:
-	BootSharedCommand();	
+	BootSharedCommand(string);	
+	BootSharedCommand();
 	~BootSharedCommand();
-	int execute();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "bootstrap.shared";	}
+	string getCommandCategory()		{ return "Hidden";				}
+	string getHelpString();	
+	string getCitation() { return "no citation"; }
+	string getDescription()		{ return "bootstrap.shared"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void createTree(ostream*);
+	int createTree(ostream*, Tree*);
 	void printSims();
+	int process(SharedOrderVector*);
 	
-	GlobalData* globaldata;
 	SharedUtil* util;
-	ReadMatrix* 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;
-	int numGroups, iters;
 
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string outputFile, calc, groups, label, outputDir, sharedfile;
+	int numGroups, iters;
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 };