merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 194aa33d457fd088e7f367c245e1a8b493a1de49..4d2ebe39fc3a3283ca2aa6ac844d6e2f5865f9e2 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -12,10 +12,9 @@
  
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
@@ -26,17 +25,20 @@ class GlobalData;
 class BootSharedCommand : public Command {
        
 public:
-       BootSharedCommand();    
+       BootSharedCommand(string);      
        ~BootSharedCommand();
        int execute();  
+       void help();
        
 private:
        void createTree(ostream*);
        void printSims();
+       void process(SharedOrderVector*);
+       
        
        GlobalData* globaldata;
        SharedUtil* util;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        TreeMap* tmap;
        Tree* t;
        vector<Calculator*> treeCalculators;
@@ -45,11 +47,15 @@ private:
        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;
+
+       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;
        int numGroups, iters;
+       vector<string>  Estimators, Groups; //holds estimators to be used
 
 };