X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.h;h=d5b48e8129ad2ebdacc5acff8f36bd82b92bea3b;hb=e41b86a600fe30f5df9507d7e55027e7b8bd7dd6;hp=4d2ebe39fc3a3283ca2aa6ac844d6e2f5865f9e2;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 4d2ebe3..d5b48e8 100644
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -14,33 +14,41 @@
 #include "sharedordervector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-	
-class GlobalData;
+#include "consensuscommand.h"
 
 class BootSharedCommand : public Command {
 	
 public:
 	BootSharedCommand(string);	
+	BootSharedCommand();
 	~BootSharedCommand();
-	int execute();	
-	void help();
+	
+	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();
-	void process(SharedOrderVector*);
-	
+	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;
@@ -51,12 +59,10 @@ private:
 	vector<SharedRAbundVector*> lookup;
 
 	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;
+	string outputFile, calc, groups, label, outputDir, sharedfile;
 	int numGroups, iters;
-	vector<string>  Estimators, Groups; //holds estimators to be used
-
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 };