X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removerarecommand.h;h=6a9f2699c6d0a404403372e8ab081d11c9fa85d1;hp=388ec2d762e763ef1623d573eb90fa4074dbb039;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=99254b7a399bb635a4acfe8d9c8a586601db5a11

diff --git a/removerarecommand.h b/removerarecommand.h
index 388ec2d..6a9f269 100644
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -13,7 +13,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
-#include "globaldata.hpp"
+
 
 class RemoveRareCommand : public Command {
 	
@@ -22,27 +22,32 @@ public:
 	RemoveRareCommand(string);	
 	RemoveRareCommand();
 	~RemoveRareCommand(){}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "remove.rare";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
+	string getDescription()		{ return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
-	string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+	string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
 	int nseqs, allLines;
 	bool abort, byGroup;
 	vector<string> outputNames, Groups;
 	set<string> labels;
-	map<string, vector<string> > outputTypes;
 	
 	int processSabund();
 	int processRabund();
 	int processList();
 	int processShared();
-	int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+	int processLookup(vector<SharedRAbundVector*>&);
 	
 };