added pipeline commands which involved change to command factory and command class...

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index e23dc777689f80806a8d81e458c9acda7f3ba4aa..c61c9fbfa63bf84a2482955ca20aa914f89b9400 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -35,15 +35,20 @@ class TreeGroupCommand : public Command {
        
 public:
        TreeGroupCommand(string);       
+       TreeGroupCommand();
        ~TreeGroupCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
 private:
-       void createTree();
+       int createTree();
        void printSims(ostream&);
-       void makeSimsShared();
-       void makeSimsDist();
+       int makeSimsShared();
+       int makeSimsDist();
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -64,14 +69,15 @@ private:
        int numGroups;
        ofstream out;
        float precision, cutoff;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
        string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
-       vector<string>  Estimators, Groups; //holds estimators to be used
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
        
        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);