finished work on classify.seqs bayesian method and various bug fixes

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 351e05212437174a9efeb09ecbecc9a7da53f449..2fca41a8388e7d3a6f20bbe79536cae9246eb2fb 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,24 +13,28 @@
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
        
        public:
-               UnifracUnweightedCommand();     
-               ~UnifracUnweightedCommand() { delete unweighted; }
-               int execute();  
+               UnifracUnweightedCommand(string);       
+               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
+               int execute();
+               void help();    
        
        private:
                GlobalData* globaldata;
+               SharedUtil* util;
+               FileOutput* output;
                vector<Tree*> T;           //user trees
                TreeMap* tmap;
                Unweighted* unweighted;
-               string sumFile, unweightedFile, unweightedFileout;
+               string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
                int iters, numGroups, numComp, counter;
                EstOutput userData;                     //unweighted score info for user tree
@@ -40,22 +44,18 @@ class UnifracUnweightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
                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.
-               map<float, float>::iterator it2;
-               map<float, float>::iterator it;
                
+               bool abort;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
                ofstream outSum, out;
                ifstream inFile;
                
-               void printUWSummaryFile();
+               void printUWSummaryFile(int);
                void printUnweightedFile();
-               void setGroups();  
-               void initFile(string);
-               void output(vector<double>);
-               void resetFile();
- 
+                
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif