X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=catchallcommand.h;h=32be8b63d2ce751391ae5ebbc6154be221b77c9d;hp=4406361a37230aced27bbaa4ca62c3f42bcd4db3;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=af27acb766f6947c45e1eb65438d878c7ea48ef3

diff --git a/catchallcommand.h b/catchallcommand.h
index 4406361..32be8b6 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
 /* 
@@ -28,27 +27,30 @@ 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;
-	ReadOTUFile* read;
-	InputData* input;
+	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, 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 process(SAbundVector*, string);
 	int createSummaryFile(string, string, ofstream&); 
+	vector<string> parseSharedFile(string);
+	string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/