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

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 194aa33d457fd088e7f367c245e1a8b493a1de49..d5b48e8129ad2ebdacc5acff8f36bd82b92bea3b 100644 (file)
--- 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
 };