working on libshuff

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 490f23eaf1e89e1047b4f0336decde5344e6e2e8..b2474c52e4ea1188c042550033f6e27581a6f4a3 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,6 +11,8 @@
  */
 
 #include "command.hpp"
+#include "coverage.h"
+#include "fullmatrix.h"
 
 using namespace std;
 
@@ -24,7 +26,27 @@ class LibShuffCommand : public Command {
                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;
+               
+               
+               void setGroups();
+               int findIndex(float, int);
+               void printCoverageFile(float);
+               void printSummaryFile();
+
                GlobalData* globaldata;
+               Coverage* coverage;
+               FullMatrix* matrix;
+               float cutOff;
+               int numGroups, numComp, iters;
+               string coverageFile, summaryFile;
+               ofstream out, outSum;
+                               
                
 };