changes while testing

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 490f23eaf1e89e1047b4f0336decde5344e6e2e8..9148576b9135826ffe33b084d833525af182bb5a 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,21 +11,50 @@
  */
 
 #include "command.hpp"
+#include "fullmatrix.h"
+#include "libshuff.h"
+#include "groupmap.h"
 
-using namespace std;
-
-class GlobalData;
 
 class LibShuffCommand : public Command {
        
-       public:
-               LibShuffCommand();      
-               ~LibShuffCommand();
-               int execute();  
+public:
+       LibShuffCommand(string);
+       LibShuffCommand();      
+       ~LibShuffCommand(){};
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "libshuff";                            }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
+       string getDescription()         { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
        
-       private:
-               GlobalData* globaldata;
-               
+private:
+       vector<string> groupNames;
+       
+       void setGroups();
+       int printCoverageFile();
+       int printSummaryFile();
+       
+       GroupMap* groupMap;
+       FullMatrix* matrix;
+       Libshuff* form;
+       float cutOff, step;
+       int numGroups, numComp, iters;
+       string coverageFile, summaryFile, phylipfile, groupfile;
+       vector<vector<int> > pValueCounts;
+       vector<vector<double> > savedDXYValues;
+       vector<vector<vector<double> > > savedMinValues;
+
+       bool abort, sim;
+       string outputFile, groups, userform, savegroups, outputDir;
+       vector<string> Groups, outputNames; //holds groups to be used
 };
 
 #endif