added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 7707df4126172061cef898db12a2a10352dee7a8..c98abc48d748be4dcbb8928283d808b118db29b8 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -45,8 +45,8 @@ class UnifracUnweightedCommand : public Command {
                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.
                
-               bool abort;
-               string groups, itersString;
+               bool abort, phylip, random;
+               string groups, itersString, outputDir;
                vector<string> Groups; //holds groups to be used
 
                ofstream outSum, out;
@@ -54,10 +54,9 @@ class UnifracUnweightedCommand : public Command {
                
                void printUWSummaryFile(int);
                void printUnweightedFile();
+               void createPhylipFile(int);
                 
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif