added cluster.classic command

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 4b2c37f11340e8dfc940f549b2c97a7c8c339b38..e853ac5f913a1d758e7a633510478ad30449feec 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -21,7 +21,12 @@ class GlobalData;
 class GetRAbundCommand : public Command {
 public:
        GetRAbundCommand(string);
+       GetRAbundCommand();
        ~GetRAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -33,13 +38,12 @@ private:
        InputData* input;
        ListVector* list;
        RAbundVector* rabund;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort, allLines;
-       set<int> lines; //hold lines to be used
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+
+       bool abort, allLines, sorted;
        set<string> labels; //holds labels to be used
-       string line, label;
+       string label;
 
        
 };