X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=catchallcommand.h;h=32be8b63d2ce751391ae5ebbc6154be221b77c9d;hp=49e0d542374eea94228ca7fa7fb2932d511989e0;hb=615301e57c25e241356a9c2380648d117709458d;hpb=e99751591aa21705e58edda87383457b9738dd9e

diff --git a/catchallcommand.h b/catchallcommand.h
index 49e0d54..32be8b6 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
 /* 
@@ -28,22 +27,24 @@ public:
 	CatchAllCommand(string);
 	CatchAllCommand();
 	~CatchAllCommand() {}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map< string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
 	
-private:
-
-	GlobalData* globaldata;
+	vector<string> setParameters();
+	string getCommandName()			{ return "catchall";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics  28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
+	string getDescription()		{ return "estimate number of species"; }
 	
-	string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
 	bool abort, allLines;
 	set<string> labels;
 	vector<string> outputNames;
-	map< string, vector<string> > outputTypes;
 	vector<string> groups;
 	
 	string process(SAbundVector*, string);