working on citations

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index fa87d8fa2a705287045489f9cdfef7f3bf51901c..fe5d76c700a130848c9f5f3eef657a3094cda177 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -16,22 +16,23 @@
 #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(); 
+               string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
+       
+               int execute();
+               void help() { m->mothurOut(getHelpString()); }
        
        private:
                struct linePair {
@@ -41,7 +42,7 @@ class UnifracWeightedCommand : public Command {
                };
                vector<linePair> lines;
                
-               GlobalData* globaldata;
+               ReadTree* read;
                SharedUtil* util;
                FileOutput* output;
                vector<Tree*> T;           //user trees
@@ -60,14 +61,12 @@ class UnifracWeightedCommand : public Command {
                vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c                                                                
                map<float, float>  validScores;  //map contains scores from random
                
-               bool abort, phylip, random;
-               string groups, itersString;
+               bool abort, phylip, random, includeRoot;
+               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();  
@@ -75,8 +74,9 @@ 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> >&);
+               int readNamesFile();
                
 };