added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 18bfadef5497316b27721a4d740c526cc3eec83a..da5f9e8c1d3d06cd7ad3812578ec83bf6bff5774 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -14,33 +14,37 @@
 #include "fullmatrix.h"
 #include "libshuff.h"
 
-using namespace std;
 
 class GlobalData;
 
 class LibShuffCommand : public Command {
        
-       public:
-               LibShuffCommand();      
-               ~LibShuffCommand(){};
-               int execute();  
+public:
+       LibShuffCommand(string);        
+       ~LibShuffCommand(){};
+       int execute();
+       void help();    
+
+private:
+       vector<string> groupNames;
        
-       private:
-               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;
+       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;
+
+       bool abort;
+       string outputFile, groups, userform, savegroups, outputDir;
+       vector<string> Groups; //holds groups to be used
 };
 
 #endif