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

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index bd26173bfd5a2780ca745173dab40b53167b508c..f6c3bbe1d06495717310a464d423c884fb1ac717 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -18,19 +18,31 @@ class PhyloDiversityCommand : public Command {
        
        public:
                PhyloDiversityCommand(string);
+               PhyloDiversityCommand();
                ~PhyloDiversityCommand();
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();  
                void help();
        
        private:
                GlobalData* globaldata;
-       
-               int iters, freq;  
-               bool abort, rarefy;
+               
+               float freq;
+               int iters, processors;  
+               bool abort, rarefy, summary, collect, scale;
                string groups, outputDir;
                vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
+               map<string, vector<string> > outputTypes;
                
-               void printData(vector<int>&, vector< vector<float> >&, string);
+               void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
+               void printSumData(map< string, vector<float> >&, ofstream&, int);
+               float calcBranchLength(Tree*, int, map< string, set<int> >&);
+               int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
+               int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);
+
 };
 
 #endif