X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.h;h=53f6a26fd471d395a19d414af75640dc9bb0d62c;hb=9f4c08cab5a7a9a0e156bd4a5a3a478b476162dc;hp=9ff44b377ab90472b8bb5867a9e5bb9a18208068;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 9ff44b3..53f6a26 100644
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -19,6 +19,7 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
+#include "consensuscommand.h"
 	
 class GlobalData;
 
@@ -26,14 +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*);
+	int createTree(ostream*, Tree*);
 	void printSims();
-	void process(SharedOrderVector*);
+	int process(SharedOrderVector*);
 	
 	
 	GlobalData* globaldata;
@@ -41,6 +47,9 @@ private:
 	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;
@@ -49,15 +58,13 @@ private:
 	ValidCalculators* validCalculator;
 	SharedOrderVector* order;
 	vector<SharedRAbundVector*> lookup;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+
 	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;
 
 };