X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;h=a1c9d0e2e8b1d6806a7c84c45419f297110f5320;hb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;hp=8795cd7512284c32b96100d814e2febfecec9504;hpb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
index 8795cd7..a1c9d0e 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 +27,26 @@ 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 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 createSummaryFile(string, string); 
+	string process(SAbundVector*, string);
+	int createSummaryFile(string, string, ofstream&); 
+	vector<string> parseSharedFile(string);
+	string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/