X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;fp=catchallcommand.h;h=238dfb608bb412a311f184d8df2f5dd4d4db9ab9;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
new file mode 100644
index 0000000..238dfb6
--- /dev/null
+++ b/catchallcommand.h
@@ -0,0 +1,58 @@
+#ifndef CATCHALLCOMMAND_H
+#define CATCHALLCOMMAND_H
+
+/*
+ *  catchallcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/11/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sabundvector.hpp"
+
+/* 
+ citation goes here
+ */ 
+
+/****************************************************************************/
+
+class CatchAllCommand : public Command {
+
+public:
+
+	CatchAllCommand(string);
+	CatchAllCommand();
+	~CatchAllCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "catchall";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
+	string getDescription()		{ return "estimate number of species"; }
+	
+	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);
+	int createSummaryFile(string, string, ofstream&); 
+	vector<string> parseSharedFile(string);
+	string combineSummmary(vector<string>&);
+};
+
+/****************************************************************************/
+
+#endif
+
+