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

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e900af4f8b0cc434bf16fae2f15535779032f901..cd46b62b3462a4db2baa57865743d4bb37c198a7 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -17,16 +17,20 @@
 #include "fileoutput.h"
 
 
-using namespace std;
-
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
        
        public:
-               UnifracUnweightedCommand();     
-               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
-               int execute();  
+               UnifracUnweightedCommand(string);       
+               UnifracUnweightedCommand();
+               ~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
+               int execute();
+               void help();    
        
        private:
                GlobalData* globaldata;
@@ -37,7 +41,7 @@ class UnifracUnweightedCommand : public Command {
                Unweighted* unweighted;
                string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
-               int iters, numGroups, numComp, counter;
+               int iters, numGroups, numComp, counter, processors;
                EstOutput userData;                     //unweighted score info for user tree
                EstOutput randomData;           //unweighted score info for random trees
                vector< vector<float> > utreeScores; //scores for users trees for each comb.
@@ -45,18 +49,20 @@ class UnifracUnweightedCommand : public Command {
                map<float, float>  validScores;  //map contains scores from random
                vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
                vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
-               map<float, float>::iterator it2;
-               map<float, float>::iterator it;
                
+               bool abort, phylip, random, includeRoot;
+               string groups, itersString, outputDir, outputForm;
+               vector<string> Groups, outputNames; //holds groups to be used
+               map<string, vector<string> > outputTypes;
+
                ofstream outSum, out;
                ifstream inFile;
                
                void printUWSummaryFile(int);
                void printUnweightedFile();
+               void createPhylipFile(int);
                 
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif