added [ERROR] flag if command aborts

[mothur.git] / getrelabundcommand.h

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
index aa123a4f24e73c8b9a1dc94449e2acccbfc003cb..90d5f9a2ceb9c3164640d8482e88599324557495 100644 (file)
--- a/getrelabundcommand.h
+++ b/getrelabundcommand.h
@@ -21,7 +21,12 @@ class GetRelAbundCommand : public Command {
 
 public:
        GetRelAbundCommand(string);
+       GetRelAbundCommand();
        ~GetRelAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -31,12 +36,13 @@ private:
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        
-       bool abort, allLines;
+       bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir, scale;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
        
-       int getRelAbundance(vector<SharedRAbundVector*>, ofstream&);
+       int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
 
 };