libshuff and updated help to include libshuff and modifications to read.dist.

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index e8daaefccbead969b54f2996f83ae378fc407a1c..e10aa44e8462d4690e095e4ab1ef37ea8542e9cd 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -28,27 +28,37 @@ class UnifracWeightedCommand : public Command {
        private:
                GlobalData* globaldata;
                vector<Tree*> T;           //user trees
-               vector<float> utreeScores;  //user tree unweighted scores
-               vector<float> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
+               vector<double> utreeScores;  //user tree unweighted scores
+               vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
                vector<string> groupComb; // AB. AC, BC...
                Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
-               string weightedFile, sumFile;
-               int iters, numGroups, numComp;
+               string weightedFile, weightedFileout, sumFile;
+               int iters, numGroups, numComp, counter;
                EstOutput userData;                     //weighted score info for user tree
                EstOutput randomData;           //weighted score info for random trees
-               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
-                                                               
+               vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
+               vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
+               vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
+               vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c                                                                
+               map<float, float>  validScores;  //map contains scores from random
+               map<float, float>::iterator it2;
+               map<float, float>::iterator it;
+               
                ofstream outSum, out;
+               ifstream inFile;
                
                void printWSummaryFile();
-       //      void printWeightedFile();  
-               void removeValidScoresDuplicates();
+               void printWeightedFile();  
+               //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void setGroups(); 
+               void calculateFreqsCumuls();
+               void initFile(string);
+               void output(vector<double>);
+               void resetFile();
+
 };