worked on chimeras

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e900af4f8b0cc434bf16fae2f15535779032f901..2fca41a8388e7d3a6f20bbe79536cae9246eb2fb 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;
@@ -45,9 +44,11 @@ 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;
                
@@ -57,6 +58,4 @@ class UnifracUnweightedCommand : public Command {
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif