added root parameter to the unifrac commands so you can choose to include the entire...

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 751343b3f641d29799c8704d71f6684c04d504ac..2eee7c44e674073420c217f1b4d49aa4dc769497 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -17,18 +17,30 @@
 #include "sharedutilities.h"
 #include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; delete util; }
+               UnifracWeightedCommand(string);
+               UnifracWeightedCommand();
+               ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();  
+               void help();
        
        private:
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+               
                GlobalData* globaldata;
                SharedUtil* util;
                FileOutput* output;
@@ -36,10 +48,9 @@ class UnifracWeightedCommand : public Command {
                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, weightedFileout, sumFile;
+               string sumFile, outputDir;
                int iters, numGroups, numComp, counter;
                EstOutput userData;                     //weighted score info for user tree
                EstOutput randomData;           //weighted score info for random trees
@@ -48,21 +59,25 @@ class UnifracWeightedCommand : public Command {
                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;
+               bool abort, phylip, random, includeRoot;
+               string groups, itersString, outputForm;
+               vector<string> Groups, outputNames; //holds groups to be used
+               map<string, vector<string> > outputTypes;
+               int processors;
+
+               
+               ofstream outSum;
                
                void printWSummaryFile();
                void printWeightedFile();  
+               void createPhylipFile();
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void calculateFreqsCumuls();
-               //void initFile(string);
-               //void output(vector<double>);
-               //void resetFile();
-
+               int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+               int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
+               
 };