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

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 047c92b2574515e20c439931808dce8dc5a34705..c36152d107d894c4e26c857ce3508e4780ae06ef 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -10,53 +10,59 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; }
+               UnifracWeightedCommand(string); 
+               ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; 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> 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, distFile;
-               int iters, numGroups, numComp;
+               string sumFile, outputDir;
+               int iters, numGroups, numComp, counter;
                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;
+               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
                
-               ofstream outSum, outDist, out;
+               bool abort, phylip, random;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
+               
+               ofstream outSum;
                
                void printWSummaryFile();
                void printWeightedFile();  
-               void saveRandomScores(); 
+               void createPhylipFile();
+               //void removeValidScoresDuplicates();
+               int findIndex(float, int);
+               void calculateFreqsCumuls();
+               
 };