fixed sub.sample groups bug

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
index ac9f115a6a3205cd95d94000a4a88555a14e821e..a1c9d0e2e8b1d6806a7c84c45419f297110f5320 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
 /* 
@@ -26,21 +25,28 @@ class CatchAllCommand : public Command {
 public:
 
        CatchAllCommand(string);
-       ~CatchAllCommand() {};
-       int execute();
-       void help();    
+       CatchAllCommand();
+       ~CatchAllCommand() {}
        
-private:
-
-       GlobalData* globaldata;
-       ReadOTUFile* read;
-       InputData* input;
+       vector<string> setParameters();
+       string getCommandName()                 { return "catchall";                    }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
        
-       string outputDir, sabundfile, rabundfile, listfile, format;
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
        bool abort, allLines;
        set<string> labels;
+       vector<string> outputNames;
+       vector<string> groups;
        
-       string process(SAbundVector*);
+       string process(SAbundVector*, string);
+       int createSummaryFile(string, string, ofstream&); 
+       vector<string> parseSharedFile(string);
+       string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/