removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index fdaa7eee6525ab15ff45407df12544a42e0ae949..97fcd1cce71290949fde06e96086ab0cc48db70b 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,43 +11,46 @@
  */
 
 #include "command.hpp"
-#include "coverage.h"
 #include "fullmatrix.h"
+#include "libshuff.h"
+#include "groupmap.h"
 
-using namespace std;
-
-class GlobalData;
 
 class LibShuffCommand : public Command {
        
-       public:
-               LibShuffCommand();      
-               ~LibShuffCommand();
-               int execute();  
+public:
+       LibShuffCommand(string);
+       LibShuffCommand();      
+       ~LibShuffCommand(){};
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "libshuff";                            }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       vector<string> groupNames;
+       
+       void setGroups();
+       int printCoverageFile();
+       int printSummaryFile();
        
-       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();
+       GroupMap* groupMap;
+       FullMatrix* matrix;
+       Libshuff* form;
+       float cutOff, step;
+       int numGroups, numComp, iters;
+       string coverageFile, summaryFile, phylipfile, groupfile;
+       vector<vector<int> > pValueCounts;
+       vector<vector<double> > savedDXYValues;
+       vector<vector<vector<double> > > savedMinValues;
 
-               GlobalData* globaldata;
-               Coverage* coverage;
-               FullMatrix* matrix;
-               float cutOff, step;
-               int numGroups, numComp, iters;
-               string coverageFile, summaryFile, form;
-               ofstream out, outSum;
-                               
-               
+       bool abort, sim;
+       string outputFile, groups, userform, savegroups, outputDir;
+       vector<string> Groups, outputNames; //holds groups to be used
 };
 
 #endif