added countgaps parameter to chop.seqs command

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index bd26173bfd5a2780ca745173dab40b53167b508c..0aafb8dbc53305a327f7a2b825a2b9c74df8bdb9 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -24,13 +24,15 @@ class PhyloDiversityCommand : public Command {
        
        private:
                GlobalData* globaldata;
-       
-               int iters, freq;  
+               
+               float freq;
+               int iters;  
                bool abort, rarefy;
                string groups, outputDir;
                vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
                
-               void printData(vector<int>&, vector< vector<float> >&, string);
+               void printData(set<int>&, map< string, vector<float> >&, string);
+               float calcBranchLength(Tree*, int);
 };
 
 #endif