added trim.seqs command

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 490f23eaf1e89e1047b4f0336decde5344e6e2e8..07c1ba5ceb732c52ce825419c8173f1746e10435 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,8 +11,9 @@
  */
 
 #include "command.hpp"
+#include "fullmatrix.h"
+#include "libshuff.h"
 
-using namespace std;
 
 class GlobalData;
 
@@ -20,12 +21,25 @@ class LibShuffCommand : public Command {
        
        public:
                LibShuffCommand();      
-               ~LibShuffCommand();
+               ~LibShuffCommand(){};
                int execute();  
        
        private:
-               GlobalData* globaldata;
+               vector<string> groupNames;
                
+               void setGroups();
+               void printCoverageFile();
+               void printSummaryFile();
+
+               GlobalData* globaldata;
+               FullMatrix* matrix;
+               Libshuff* form;
+               float cutOff, step;
+               int numGroups, numComp, iters;
+               string coverageFile, summaryFile;
+               vector<vector<int> > pValueCounts;
+               vector<vector<double> > savedDXYValues;
+               vector<vector<vector<double> > > savedMinValues;
 };
 
 #endif