X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=eb0ca8f7832e5f1877a172fa0449a3ae29e5416f;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=dd0cf3adab7798c71e9e853ff1e5b33c8f53a690;hpb=f37a59b81c339f574d97042ff6e364146feb457a;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index dd0cf3a..eb0ca8f 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -20,7 +20,12 @@ class GlobalData;
 class ReadOtuCommand : public Command {
 public:
 	ReadOtuCommand(string);
+	ReadOtuCommand();
 	~ReadOtuCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
@@ -29,7 +34,9 @@ private:
 	InputData* input;
 	Command* shared;
 	GroupMap* groupMap;
-	string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format;
+	string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+	vector<string> Groups, outputNames;
+	map<string, vector<string> > outputTypes;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used