X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setcurrentcommand.h;h=effc266fc0dfaccd13d5d1e1fdbe6c348d4428d6;hp=98033b7b8d8bb4f1e68c5b62df4ddd97e239a35e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index 98033b7..effc266 100644
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -18,25 +18,30 @@ class SetCurrentCommand : public Command {
 public:
 	SetCurrentCommand(string);
 	SetCurrentCommand();
-	~SetCurrentCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~SetCurrentCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "set.current";	}
+	string getCommandCategory()		{ return "General";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string){ return ""; }	
+	string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
+	string getDescription()		{ return "set current files for mothur"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	bool abort;
 	
 	string clearTypes;
 	vector<string> types;
 	
-	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile;
+	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 	
 };