merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 150bdb4aecdfeeae4b91b6e0152eb812dca846ea..1e5726dd770f928b62ca8ef07fa3c24150c0a8b5 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -19,34 +19,32 @@ class GlobalData;
 
 class LibShuffCommand : public Command {
        
-       public:
-               LibShuffCommand(string);        
-               ~LibShuffCommand(){};
-               int execute();
-               void help();    
+public:
+       LibShuffCommand(string);        
+       ~LibShuffCommand(){};
+       int execute();
+       void help();    
+
+private:
+       vector<string> groupNames;
        
-       private:
-               vector<string> groupNames;
-               
-               void setGroups();
-               void printCoverageFile();
-               void printSummaryFile();
-
-               GlobalData* globaldata;
-               FullMatrix* matrix;
-               Libshuff* form;
-               float cutOff, step;
-               int numGroups, numComp, iters;
-               string coverageFile, summaryFile;
-               vector<vector<int> > pValueCounts;
-               vector<vector<double> > savedDXYValues;
-               vector<vector<vector<double> > > savedMinValues;
-               OptionParser* parser;
-               map<string, string> parameters;
-               map<string, string>::iterator it;
-               bool abort;
-               string outputFile, groups, userform, savegroups;
-               vector<string> Groups; //holds groups to be used
+       void setGroups();
+       void printCoverageFile();
+       void printSummaryFile();
+
+       GlobalData* globaldata;
+       FullMatrix* matrix;
+       Libshuff* form;
+       float cutOff, step;
+       int numGroups, numComp, iters;
+       string coverageFile, summaryFile;
+       vector<vector<int> > pValueCounts;
+       vector<vector<double> > savedDXYValues;
+       vector<vector<vector<double> > > savedMinValues;
+
+       bool abort;
+       string outputFile, groups, userform, savegroups;
+       vector<string> Groups; //holds groups to be used
 };
 
 #endif