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 b6aea7dad9215a131691019445c2f911c77084a4..2eee7c44e674073420c217f1b4d49aa4dc769497 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -24,7 +24,12 @@ class UnifracWeightedCommand : public Command {
        
        public:
                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();
        
@@ -34,7 +39,7 @@ class UnifracWeightedCommand : public Command {
                        int num;
                        linePair(int i, int j) : start(i), num(j) {}
                };
-               vector<linePair*> lines;
+               vector<linePair> lines;
                
                GlobalData* globaldata;
                SharedUtil* util;
@@ -43,7 +48,6 @@ 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 sumFile, outputDir;
@@ -56,9 +60,10 @@ class UnifracWeightedCommand : public Command {
                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;
-               string groups, itersString;
+               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;
 
                
@@ -70,8 +75,8 @@ class UnifracWeightedCommand : public Command {
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void calculateFreqsCumuls();
-               int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-               int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+               int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+               int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
                
 };