cleaned up code2

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 5d0cccf249099ac51d86b58e41e5098793ef3f3c..95276921149b5237a923928bc9f23a5e8e7aed1b 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -25,7 +25,8 @@ class PhyloDiversityCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "phylo.diversity";                     }
                string getCommandCategory()             { return "Hypothesis Testing";          }
-               string getHelpString(); 
+               string getOutputFileNameTag(string, string);
+       string getHelpString(); 
                string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
                string getDescription()         { return "phylo.diversity"; }
 
@@ -39,10 +40,11 @@ private:
                string groups, outputDir, treefile, groupfile, namefile;
                vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
                
+        map<string, int> getRootForGroups(Tree* t);
                int readNamesFile();
                void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
                void printSumData(map< string, vector<float> >&, ofstream&, int);
-               vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
+        vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
                int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
                int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);