fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
index ac9f115a6a3205cd95d94000a4a88555a14e821e..44bde029e382a382fcc0b407da5d789a1f302cb7 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -26,21 +26,30 @@ class CatchAllCommand : public Command {
 public:
 
        CatchAllCommand(string);
-       ~CatchAllCommand() {};
+       CatchAllCommand();
+       ~CatchAllCommand() {}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map< string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
 private:
 
        GlobalData* globaldata;
-       ReadOTUFile* read;
-       InputData* input;
        
-       string outputDir, sabundfile, rabundfile, listfile, format;
+       string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path, savedOutputDir;
        bool abort, allLines;
        set<string> labels;
+       vector<string> outputNames;
+       map< string, vector<string> > outputTypes;
+       vector<string> groups;
        
-       string process(SAbundVector*);
+       string process(SAbundVector*, string);
+       int createSummaryFile(string, string, ofstream&); 
+       vector<string> parseSharedFile(string);
+       string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/