added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index ecf78f58a981e1f95602ed4e10973bcf7695cf14..c98abc48d748be4dcbb8928283d808b118db29b8 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -10,55 +10,53 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #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
-               vector<float> utreeScores;  //user tree unweighted scores
-               vector<float> UWScoreSig;  //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
-               Tree* randT;  //random tree
                TreeMap* tmap;
                Unweighted* unweighted;
-               string sumFile, distFile, unweightedFile;
-               int iters;
+               string sumFile, allGroups;
+               vector<string> groupComb; // AB. AC, BC...
+               int iters, numGroups, numComp, counter;
                EstOutput userData;                     //unweighted score info for user tree
                EstOutput randomData;           //unweighted score info for random trees
-               map<float, float> validScores;  //contains scores from both user and random
-               map<float, float> rscoreFreq;  //unweighted score, number of random trees with that score.
-               map<float, float> uscoreFreq;  //unweighted, number of user trees with that score.
-               map<float, float> totalrscoreFreq;  //unweighted score, number of random trees with that score.
-               map<float, float> rCumul;               //unweighted score, cumulative percentage of number of random trees with that score or higher.
-               map<float, float> uCumul;  //unweighted, cumulative percentage of number of user trees with that score or higher .
-               map<float, float>::iterator it;
-               map<float, float>::iterator it2;
+               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.
+               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.
                
-               ofstream outSum, outDist, out;
+               bool abort, phylip, random;
+               string groups, itersString, outputDir;
+               vector<string> Groups; //holds groups to be used
+
+               ofstream outSum, out;
+               ifstream inFile;
                
-               void printUWSummaryFile();
+               void printUWSummaryFile(int);
                void printUnweightedFile();
-               void saveRandomScores();    
+               void createPhylipFile(int);
+                
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif