working on citations

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index d9991e81ce3ddee08a4afc8fae19d78ce89f794e..415279c9b2adad30f95a11eeef309d9d3fd3b802 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -15,21 +15,27 @@
 #include "treemap.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-using namespace std;
-
-class GlobalData;
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
        
        public:
-               UnifracUnweightedCommand();     
-               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
-               int execute();  
+               UnifracUnweightedCommand(string);       
+               UnifracUnweightedCommand();
+               ~UnifracUnweightedCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "unifrac.unweighted";          }
+               string getCommandCategory()             { return "Hypothesis Testing";          }
+               string getHelpString(); 
+               string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
+       
+               int execute();
+               void help() { m->mothurOut(getHelpString()); }
+       
        
        private:
-               GlobalData* globaldata;
+               ReadTree* read;
                SharedUtil* util;
                FileOutput* output;
                vector<Tree*> T;           //user trees
@@ -37,7 +43,7 @@ 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, numUniquesInName;
                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 +51,21 @@ 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, treefile, groupfile, namefile;
+               vector<string> Groups, outputNames; //holds groups to be used
+
                ofstream outSum, out;
                ifstream inFile;
+               map<string, string> nameMap;
                
-               void printUWSummaryFile();
+               void printUWSummaryFile(int);
                void printUnweightedFile();
+               void createPhylipFile(int);
+               int readNamesFile();
                 
                
 };
 
-
-
-#endif
\ No newline at end of file
+#endif