added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 9fe164298b0c9191674a01b4a4fd72fc4fed37ae..d9991e81ce3ddee08a4afc8fae19d78ce89f794e 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,6 +13,9 @@
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+
 
 using namespace std;
 
@@ -22,35 +25,35 @@ class UnifracUnweightedCommand : public Command {
        
        public:
                UnifracUnweightedCommand();     
-               ~UnifracUnweightedCommand() { delete unweighted; }
+               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
                int execute();  
        
        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;
+               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.
                map<float, float>::iterator it2;
+               map<float, float>::iterator it;
                
-               ofstream outSum, outDist, out;
+               ofstream outSum, out;
+               ifstream inFile;
                
                void printUWSummaryFile();
                void printUnweightedFile();
-               void saveRandomScores();    
+                
                
 };