added distance search method to classify.seqs

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 5f55deea98379b5813bed720fe9fad3bd76ac23f..c36152d107d894c4e26c857ce3508e4780ae06ef 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -39,7 +39,7 @@ class UnifracWeightedCommand : public Command {
                Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
-               string sumFile;
+               string sumFile, outputDir;
                int iters, numGroups, numComp, counter;
                EstOutput userData;                     //weighted score info for user tree
                EstOutput randomData;           //weighted score info for random trees
@@ -49,7 +49,7 @@ class UnifracWeightedCommand : public Command {
                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
                
-               bool abort;
+               bool abort, phylip, random;
                string groups, itersString;
                vector<string> Groups; //holds groups to be used
 
@@ -58,6 +58,7 @@ class UnifracWeightedCommand : public Command {
                
                void printWSummaryFile();
                void printWeightedFile();  
+               void createPhylipFile();
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void calculateFreqsCumuls();