X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;h=44ed3ef162b0a82465c1662f2f19e73d43468f86;hb=90708fe9701e3827e477c82fb3652539c3bf2a0d;hp=ac9f115a6a3205cd95d94000a4a88555a14e821e;hpb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
index ac9f115..44ed3ef 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
 /* 
@@ -26,21 +25,31 @@ class CatchAllCommand : public Command {
 public:
 
 	CatchAllCommand(string);
-	~CatchAllCommand() {};
-	int execute();
-	void help();	
+	CatchAllCommand();
+	~CatchAllCommand() {}
 	
-private:
-
-	GlobalData* globaldata;
-	ReadOTUFile* read;
-	InputData* input;
+	vector<string> setParameters();
+	string getCommandName()			{ return "catchall";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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, sabundfile, rabundfile, listfile, format;
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
 	bool abort, allLines;
 	set<string> labels;
+	vector<string> outputNames;
+	vector<string> groups;
 	
-	string process(SAbundVector*);
+	string process(SAbundVector*, string);
+	int createSummaryFile(string, string, ofstream&); 
+	vector<string> parseSharedFile(string);
+	string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/