working on parallelizing unifrac.unweighted.

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index b572e4679845e63674bcecfb23710876504af90b..3e6d8354af5eda2c21f85c632a09b886962afb37 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,49 +13,50 @@
 #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() { globaldata->Groups.clear();  if (abort == false) { 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;
+               int iters, numGroups, numComp, counter, processors;
                EstOutput userData;                     //unweighted score info for user tree
                EstOutput randomData;           //unweighted score info for random trees
                vector< vector<float> > utreeScores; //scores for users trees for each comb.
                vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
-               vector< map<float, float> > validScores;  //map contains scores from both user and random
+               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, phylip, random;
+               string groups, itersString, outputDir;
+               vector<string> Groups, outputNames; //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();
- 
+               void createPhylipFile(int);
+                
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif