sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index d309566e45b0d58fb2631eeb1a0ad1816907f437..1c67c32f81afb2535943934ab82d66629bbc05b2 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -12,43 +12,72 @@
 
 #include "command.hpp"
 #include "weighted.h"
-#include "treemap.h"
-
-using namespace std;
-
-class GlobalData;
+#include "counttable.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
 
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; }
-               int execute();  
+               UnifracWeightedCommand(string);
+               UnifracWeightedCommand();
+               ~UnifracWeightedCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "unifrac.weighted";            }
+               string getCommandCategory()             { return "Hypothesis Testing";          }
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
+               string getDescription()         { return "generic tests that describes whether two or more communities have the same structure"; }
+
+               int execute();
+               void help() { m->mothurOut(getHelpString()); }
        
        private:
-               GlobalData* globaldata;
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+        CountTable* ct;
+               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;
-               int iters, numGroups, numComp;
-               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
-                                                               
-               ofstream outSum, out;
+               string sumFile, outputDir;
+               int iters, numGroups, numComp, counter;
+               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
+               
+               bool abort, phylip, random, includeRoot, subsample, consensus;
+               string groups, itersString, outputForm, treefile, groupfile, namefile, countfile;
+               vector<string> Groups, outputNames; //holds groups to be used
+               int processors, subsampleSize, subsampleIters;
+               ofstream outSum;
+               map<string, string> nameMap;
                
                void printWSummaryFile();
-       //      void printWeightedFile();  
-               void removeValidScoresDuplicates();
-               int findIndex(float);
-               void setGroups(); 
+               void printWeightedFile();  
+               void createPhylipFile();
+               //void removeValidScoresDuplicates();
+               int findIndex(float, int);
+               void calculateFreqsCumuls();
+               int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+               int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
+        int runRandomCalcs(Tree*, vector<double>);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
+               
 };