libshuff and updated help to include libshuff and modifications to read.dist.

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index fdaa7eee6525ab15ff45407df12544a42e0ae949..950bb00809a6ba0371906269f9c4804b02c9a0fa 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -26,17 +26,18 @@ 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< 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(float);
+               void printCoverageFile();
                void printSummaryFile();
 
                GlobalData* globaldata;