pat's changes to seq.error command

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 989c699c877ead1e27ea20a1c59a53a901bfa71a..c61c9fbfa63bf84a2482955ca20aa914f89b9400 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -34,15 +34,21 @@ typedef list<PCell>::iterator MatData;
 class TreeGroupCommand : public Command {
        
 public:
-       TreeGroupCommand();     
+       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;
@@ -58,13 +64,22 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       vector<SharedRAbundVector*> lastLookup;
+       string lastLabel;
        string format, outputFile, groupNames, filename;
        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, 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*>);
+       
+       
 
 };