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

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 2eee7c44e674073420c217f1b4d49aa4dc769497..612b64abcfad0804c6981100dc6bdb12ebb5d219 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -16,22 +16,22 @@
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-class GlobalData;
+#include "readtree.h"
 
 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();
+               ~UnifracWeightedCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "unifrac.weighted";            }
+               string getCommandCategory()             { return "Hypothesis Testing";          }
+               string getHelpString(); 
+       
+               int execute();
+               void help() { m->mothurOut(getHelpString()); }
        
        private:
                struct linePair {
@@ -41,7 +41,7 @@ class UnifracWeightedCommand : public Command {
                };
                vector<linePair> lines;
                
-               GlobalData* globaldata;
+               ReadTree* read;
                SharedUtil* util;
                FileOutput* output;
                vector<Tree*> T;           //user trees
@@ -61,13 +61,11 @@ class UnifracWeightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                
                bool abort, phylip, random, includeRoot;
-               string groups, itersString, outputForm;
+               string groups, itersString, outputForm, treefile, groupfile, namefile;
                vector<string> Groups, outputNames; //holds groups to be used
-               map<string, vector<string> > outputTypes;
-               int processors;
-
-               
+               int processors, numUniquesInName;
                ofstream outSum;
+               map<string, string> nameMap;
                
                void printWSummaryFile();
                void printWeightedFile();  
@@ -77,6 +75,7 @@ class UnifracWeightedCommand : public Command {
                void calculateFreqsCumuls();
                int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
                int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
+               int readNamesFile();
                
 };