removing extra file output from pintail

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 5cd93a94c0dcf96547ee409d4ca641092309d2bc..5f55deea98379b5813bed720fe9fad3bd76ac23f 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -17,16 +17,16 @@
 #include "sharedutilities.h"
 #include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; delete util; }
+               UnifracWeightedCommand(string); 
+               ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
                int execute();  
+               void help();
        
        private:
                GlobalData* globaldata;
@@ -48,11 +48,13 @@ class UnifracWeightedCommand : public Command {
                vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
                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
-               map<float, float>::iterator it2;
-               map<float, float>::iterator it;
                
-               ofstream outSum, out;
-               ifstream inFile;
+               bool abort;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
+               
+               ofstream outSum;
                
                void printWSummaryFile();
                void printWeightedFile();