sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index ddbdc8548dad7e0545d75f8e98cd92fdb76a3419..1c67c32f81afb2535943934ab82d66629bbc05b2 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -12,7 +12,7 @@
 
 #include "command.hpp"
 #include "weighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
@@ -28,7 +28,9 @@ class UnifracWeightedCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "unifrac.weighted";            }
                string getCommandCategory()             { return "Hypothesis Testing";          }
-               string getHelpString(); 
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
                string getDescription()         { return "generic tests that describes whether two or more communities have the same structure"; }
 
@@ -42,7 +44,7 @@ class UnifracWeightedCommand : public Command {
                        linePair(int i, int j) : start(i), num(j) {}
                };
                vector<linePair> lines;
-        TreeMap* tmap;
+        CountTable* ct;
                FileOutput* output;
                vector<Tree*> T;           //user trees
                vector<double> utreeScores;  //user tree unweighted scores
@@ -57,9 +59,9 @@ class UnifracWeightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                
                bool abort, phylip, random, includeRoot, subsample, consensus;
-               string groups, itersString, outputForm, treefile, groupfile, namefile;
+               string groups, itersString, outputForm, treefile, groupfile, namefile, countfile;
                vector<string> Groups, outputNames; //holds groups to be used
-               int processors, numUniquesInName, subsampleSize, subsampleIters;
+               int processors, subsampleSize, subsampleIters;
                ofstream outSum;
                map<string, string> nameMap;
                
@@ -72,7 +74,7 @@ class UnifracWeightedCommand : public Command {
                int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
                int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
         int runRandomCalcs(Tree*, vector<double>);
-        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);