X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.h;h=2cab7be6fa870d763de76a559b4dfbb72823cfb6;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=7db54b409672af8937c456d731fffecf91cbe6c2;hpb=259b6adf51ef0639cafd88cf862e4ffd5e0c7576;p=mothur.git

diff --git a/removerarecommand.h b/removerarecommand.h
index 7db54b4..2cab7be 100644
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -14,6 +14,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 
+
 class RemoveRareCommand : public Command {
 	
 public:
@@ -21,25 +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:
-	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&);
 	
 };