fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 490f23eaf1e89e1047b4f0336decde5344e6e2e8..950bb00809a6ba0371906269f9c4804b02c9a0fa 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 +26,28 @@ class LibShuffCommand : public Command {
                int execute();  
        
        private:
+               vector< vector< vector<float> > > cValues; // vector<vector of coverage scores, one for each comparison.> -one for each distance level.
+               vector< vector<float> > deltaValues; // vector< vector of delta scores, one for each comparison.> -one at each distance
+               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<float> dist;
+               
+               
+               void setGroups();
+               int findIndex(float, int);
+               void printCoverageFile();
+               void printSummaryFile();
+
                GlobalData* globaldata;
+               Coverage* coverage;
+               FullMatrix* matrix;
+               float cutOff, step;
+               int numGroups, numComp, iters;
+               string coverageFile, summaryFile, form;
+               ofstream out, outSum;
+                               
                
 };