fixed phylo.diversity

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index ea2c41814ac1940a61bd8c48995ecebcff30f324..77dd10d3490999def3789b91d405ac76e470f360 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -14,20 +14,24 @@
 #include "weighted.h"
 #include "treemap.h"
 #include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; }
+               UnifracWeightedCommand(string);
+               ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
                int execute();  
+               void help();
        
        private:
                GlobalData* globaldata;
+               SharedUtil* util;
+               FileOutput* output;
                vector<Tree*> T;           //user trees
                vector<double> utreeScores;  //user tree unweighted scores
                vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
@@ -35,7 +39,7 @@ class UnifracWeightedCommand : public Command {
                Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
-               string weightedFile, weightedFileout, 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
@@ -44,22 +48,21 @@ class UnifracWeightedCommand : public Command {
                vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
                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
-               map<float, float>::iterator it2;
-               map<float, float>::iterator it;
                
-               ofstream outSum, out;
-               ifstream inFile;
+               bool abort, phylip, random;
+               string groups, itersString;
+               vector<string> Groups, outputNames; //holds groups to be used
+
+               
+               ofstream outSum;
                
                void printWSummaryFile();
                void printWeightedFile();  
+               void createPhylipFile();
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
-               void setGroups(); 
                void calculateFreqsCumuls();
-               void initFile(string);
-               void output(vector<double>);
-               void resetFile();
-
+               
 };