added shhh.seqs command

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 7317c8a43092a5712a06dda00589d1eb4528c649..5bb690a854ed5c13f62a18fedc51cd39eee93f3a 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -24,7 +24,12 @@ class UnifracWeightedCommand : public Command {
        
        public:
                UnifracWeightedCommand(string);
+               UnifracWeightedCommand();
                ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();  
                void help();
        
@@ -56,8 +61,9 @@ class UnifracWeightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                
                bool abort, phylip, random;
-               string groups, itersString;
+               string groups, itersString, outputForm;
                vector<string> Groups, outputNames; //holds groups to be used
+               map<string, vector<string> > outputTypes;
                int processors;
 
                
@@ -69,8 +75,8 @@ class UnifracWeightedCommand : public Command {
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void calculateFreqsCumuls();
-               int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-               int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+               int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+               int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
                
 };