fixed bug with realigner for chimera slayer

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 1c8fbc4da656bf5c4240c1be8cb4a7843b3ac72c..97fcd1cce71290949fde06e96086ab0cc48db70b 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -13,36 +13,42 @@
 #include "command.hpp"
 #include "fullmatrix.h"
 #include "libshuff.h"
+#include "groupmap.h"
 
 
-class GlobalData;
-
 class LibShuffCommand : public Command {
        
 public:
-       LibShuffCommand(string);        
+       LibShuffCommand(string);
+       LibShuffCommand();      
        ~LibShuffCommand(){};
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "libshuff";                            }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       
        int execute();
-       void help();    
-
+       void help() { m->mothurOut(getHelpString()); }  
+       
 private:
        vector<string> groupNames;
        
        void setGroups();
        int printCoverageFile();
        int printSummaryFile();
-
-       GlobalData* globaldata;
+       
+       GroupMap* groupMap;
        FullMatrix* matrix;
        Libshuff* form;
        float cutOff, step;
        int numGroups, numComp, iters;
-       string coverageFile, summaryFile;
+       string coverageFile, summaryFile, phylipfile, groupfile;
        vector<vector<int> > pValueCounts;
        vector<vector<double> > savedDXYValues;
        vector<vector<vector<double> > > savedMinValues;
 
-       bool abort;
+       bool abort, sim;
        string outputFile, groups, userform, savegroups, outputDir;
        vector<string> Groups, outputNames; //holds groups to be used
 };