line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index fdaa7eee6525ab15ff45407df12544a42e0ae949..07c1ba5ceb732c52ce825419c8173f1746e10435 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,10 +11,9 @@
  */
 
 #include "command.hpp"
-#include "coverage.h"
 #include "fullmatrix.h"
+#include "libshuff.h"
 
-using namespace std;
 
 class GlobalData;
 
@@ -22,32 +21,25 @@ class LibShuffCommand : public Command {
        
        public:
                LibShuffCommand();      
-               ~LibShuffCommand();
+               ~LibShuffCommand(){};
                int execute();  
        
        private:
-               vector< vector<float> > cValues; // vector of coverage scores, one for each comparison.
-               vector<float> deltaValues; // vector of delta scores, one for each comparison.
-               vector<float> sumDelta; //sum of delta scores, one for each comparison.
-               vector<float> sumDeltaSig; //number of random  matrixes with that delta value or ??
-               vector< vector<float> > rsumDelta; //vector< vector<sumdelta scores for a given comparison> >
-               vector<string> groupComb;
-               
+               vector<string> groupNames;
                
                void setGroups();
-               int findIndex(float, int);
-               void printCoverageFile(float);
+               void printCoverageFile();
                void printSummaryFile();
 
                GlobalData* globaldata;
-               Coverage* coverage;
                FullMatrix* matrix;
+               Libshuff* form;
                float cutOff, step;
                int numGroups, numComp, iters;
-               string coverageFile, summaryFile, form;
-               ofstream out, outSum;
-                               
-               
+               string coverageFile, summaryFile;
+               vector<vector<int> > pValueCounts;
+               vector<vector<double> > savedDXYValues;
+               vector<vector<vector<double> > > savedMinValues;
 };
 
 #endif