removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index f5e205c4e40ce010239c0cc8beba6798e1a17aa4..df04b35d66f1c0dc36893074f6c840711395c49b 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -12,31 +12,35 @@
 
 #include "command.hpp"
 #include "treemap.h"
-#include "globaldata.hpp"
+#include "readtree.h"
+#include "sharedutilities.h"
+
 
 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();
+               ~PhyloDiversityCommand(){}
        
-       private:
-               GlobalData* globaldata;
-               
+               vector<string> setParameters();
+               string getCommandName()                 { return "phylo.diversity";                     }
+               string getCommandCategory()             { return "Hypothesis Testing";          }
+               string getHelpString(); 
+       
+               int execute();
+               void help() { m->mothurOut(getHelpString()); }
+private:
+               ReadTree* read;
+               TreeMap* tmap;
                float freq;
-               int iters, processors;  
+               int iters, processors, numUniquesInName;  
                bool abort, rarefy, summary, collect, scale;
-               string groups, outputDir;
+               string groups, outputDir, treefile, groupfile, namefile;
                vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
-               map<string, vector<string> > outputTypes;
+               map<string, string> nameMap;
                
+               int readNamesFile();
                void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
                void printSumData(map< string, vector<float> >&, ofstream&, int);
                vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);