version working on mac with .tellg changed to unget for windows

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index d9991e81ce3ddee08a4afc8fae19d78ce89f794e..7707df4126172061cef898db12a2a10352dee7a8 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -17,16 +17,15 @@
 #include "fileoutput.h"
 
 
-using namespace std;
-
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
        
        public:
-               UnifracUnweightedCommand();     
+               UnifracUnweightedCommand(string);       
                ~UnifracUnweightedCommand() { delete unweighted; delete util; }
-               int execute();  
+               int execute();
+               void help();    
        
        private:
                GlobalData* globaldata;
@@ -45,13 +44,15 @@ class UnifracUnweightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
                vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
-               map<float, float>::iterator it2;
-               map<float, float>::iterator it;
                
+               bool abort;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
                ofstream outSum, out;
                ifstream inFile;
                
-               void printUWSummaryFile();
+               void printUWSummaryFile(int);
                void printUnweightedFile();