fix weighted unifrac bug in findIndex and randomize labels

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 047c92b2574515e20c439931808dce8dc5a34705..e8daaefccbead969b54f2996f83ae378fc407a1c 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -10,11 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
@@ -39,24 +34,21 @@ class UnifracWeightedCommand : public Command {
                Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
-               string weightedFile, sumFile, distFile;
+               string weightedFile, sumFile;
                int iters, numGroups, numComp;
                EstOutput userData;                     //weighted score info for user tree
                EstOutput randomData;           //weighted score info for random trees
-               vector< map<float, float> > validScores;  //vector<contains scores from both user and random> each group comb has an entry
-               vector< map<float, float> > rscoreFreq;  //vector<weighted score, number of random trees with that score.> each group comb has an entry
-               vector< map<float, float> > uscoreFreq;  //vector<weighted, number of user trees with that score.> each group comb has an entry
-               vector< map<float, float> > totalrscoreFreq;  //vector<weighted score, number of random trees with that score.> each group comb has an entry
-               vector< map<float, float> > rCumul;  //vector<weighted score, number of random trees with that score.> each group comb has an entry
-               vector< map<float, float> > uCumul;  //vector<weighted, cumulative percentage of number of user trees with that score or lower.> each group comb has an entry
-               map<float, float>::iterator it;
-               map<float, float>::iterator it2;
-               
-               ofstream outSum, outDist, out;
+               vector< vector<float> > validScores;  //vector<contains scores from both user and random> each group comb has an entry
+               vector< vector<float> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
+               vector< vector<float> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
+                                                               
+               ofstream outSum, out;
                
                void printWSummaryFile();
-               void printWeightedFile();  
-               void saveRandomScores(); 
+       //      void printWeightedFile();  
+               void removeValidScoresDuplicates();
+               int findIndex(float, int);
+               void setGroups(); 
 };