added modify names parameter to set.dir

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 15c3b9684b01fa58403276b80864684f99e8d189..3961e53cb68c96e70dd5bcd55449ed5d72346cd9 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -12,7 +12,7 @@
 
 #include "command.hpp"
 #include "unweighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
 #include "readtree.h"
@@ -27,8 +27,9 @@ class UnifracUnweightedCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "unifrac.unweighted";          }
                string getCommandCategory()             { return "Hypothesis Testing";          }
-               string getOutputFileNameTag(string, string);
+               
        string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
                string getDescription()         { return "generic tests that describes whether two or more communities have the same structure"; }
 
@@ -39,7 +40,7 @@ class UnifracUnweightedCommand : public Command {
        private:
                FileOutput* output;
                vector<Tree*> T;           //user trees
-               TreeMap* tmap;
+               CountTable* ct;
                string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
                int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
@@ -50,7 +51,7 @@ class UnifracUnweightedCommand : public Command {
                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, phylip, random, includeRoot, consensus, subsample;
-               string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
+               string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
                vector<string> Groups, outputNames; //holds groups to be used
 
                ofstream outSum, out;
@@ -60,7 +61,7 @@ class UnifracUnweightedCommand : public Command {
                void printUWSummaryFile(int);
                void printUnweightedFile();
                void createPhylipFile(int);
-        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
         int getConsensusTrees(vector< vector<double> >&, int);
         int getAverageSTDMatrices(vector< vector<double> >&, int);