finished wrapper for catchall

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
index ac9f115a6a3205cd95d94000a4a88555a14e821e..d59855b240442d541699970cd0d75a9ef5cde452 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -26,7 +26,12 @@ 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();    
        
@@ -36,9 +41,11 @@ private:
        ReadOTUFile* read;
        InputData* input;
        
-       string outputDir, sabundfile, rabundfile, listfile, format;
+       string outputDir, sabundfile, rabundfile, listfile, format, path;
        bool abort, allLines;
        set<string> labels;
+       vector<string> outputNames;
+       map< string, vector<string> > outputTypes;
        
        string process(SAbundVector*);
 };