fixed read.tree so that it can read trees generated by fasttree

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 3c031c66c1da524e5b7f3177cfca7d0743573a7a..f6f867877620e7e6e69e4e446bdbe8da3815861a 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -23,7 +23,7 @@ class UnifracUnweightedCommand : public Command {
        
        public:
                UnifracUnweightedCommand(string);       
-               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
+               ~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
                int execute();
                void help();    
        
@@ -44,25 +44,19 @@ 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;
                
-               OptionParser* parser;
-               map<string, string> parameters;
-               map<string, string>::iterator it4;
-               bool abort;
-               string groups, itersString;
-               vector<string> Groups; //holds groups to be used
+               bool abort, phylip, random;
+               string groups, itersString, outputDir;
+               vector<string> Groups, outputNames; //holds groups to be used
 
                ofstream outSum, out;
                ifstream inFile;
                
                void printUWSummaryFile(int);
                void printUnweightedFile();
+               void createPhylipFile(int);
                 
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif