added pairwise.seqs

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 794da84001135d9b1ab365fc9014ed021a467d38..53f6a26fd471d395a19d414af75640dc9bb0d62c 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -27,14 +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*, Tree*);
+       int createTree(ostream*, Tree*);
        void printSims();
-       void process(SharedOrderVector*);
+       int process(SharedOrderVector*);
        
        
        GlobalData* globaldata;
@@ -56,9 +61,10 @@ private:
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string outputFile, calc, groups, 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;
 
 };