added pairwise.seqs

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index b632acede61e9f06c576ea236e7eac4b7c896153..53f6a26fd471d395a19d414af75640dc9bb0d62c 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -19,20 +19,27 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
+#include "consensuscommand.h"
        
 class GlobalData;
 
 class BootSharedCommand : public Command {
        
 public:
-       BootSharedCommand();    
+       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;
@@ -40,6 +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;
@@ -48,8 +58,13 @@ private:
        ValidCalculators* validCalculator;
        SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
-       string format, outputFile;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string outputFile, calc, groups, label, outputDir;
        int numGroups, iters;
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+       map< string, vector<string> > outputTypes;
 
 };