added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 53f6a26fd471d395a19d414af75640dc9bb0d62c..d5b48e8129ad2ebdacc5acff8f36bd82b92bea3b 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -14,14 +14,11 @@
 #include "sharedordervector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
 #include "consensuscommand.h"
-       
-class GlobalData;
 
 class BootSharedCommand : public Command {
        
@@ -29,22 +26,24 @@ 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();
+       
+       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:
        int createTree(ostream*, Tree*);
        void printSims();
        int process(SharedOrderVector*);
        
-       
-       GlobalData* globaldata;
        SharedUtil* util;
-       ReadOTUFile* read;
        TreeMap* tmap;
        Tree* t;
        Tree* tempTree;
@@ -61,11 +60,9 @@ private:
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string outputFile, calc, groups, label, outputDir;
+       string outputFile, calc, groups, label, outputDir, sharedfile;
        int numGroups, iters;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
-       map< string, vector<string> > outputTypes;
-
 };