X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.h;h=53f6a26fd471d395a19d414af75640dc9bb0d62c;hb=1e0359c041eedc99670c93d824a2cf7fa72577cc;hp=ee393f9eb3fecd8cac0ddfbea3c5e69863b8a621;hpb=0bb069a445785a88a95e3f1427afba7df056a0b3;p=mothur.git

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index ee393f9..53f6a26 100644
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -19,7 +19,7 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-#include "concensuscommand.h"
+#include "consensuscommand.h"
 	
 class GlobalData;
 
@@ -27,14 +27,19 @@ class BootSharedCommand : public Command {
 	
 public:
 	BootSharedCommand(string);	
+	BootSharedCommand();
 	~BootSharedCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
 private:
-	void createTree(ostream*, Tree*);
+	int createTree(ostream*, Tree*);
 	void printSims();
-	void process(SharedOrderVector*);
+	int process(SharedOrderVector*);
 	
 	
 	GlobalData* globaldata;
@@ -43,7 +48,7 @@ private:
 	TreeMap* tmap;
 	Tree* t;
 	Tree* tempTree;
-	ConcensusCommand* concensus;
+	ConcensusCommand* consensus;
 	vector< vector<Tree*> > trees;  //a vector of trees for each calculator chosen
 	vector<Calculator*> treeCalculators;
 	vector<ofstream*> out;
@@ -55,11 +60,11 @@ 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;
 	int numGroups, iters;
-	vector<string>  Estimators, Groups; //holds estimators to be used
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+	map< string, vector<string> > outputTypes;
 
 };