X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;h=49e0d542374eea94228ca7fa7fb2932d511989e0;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=8795cd7512284c32b96100d814e2febfecec9504;hpb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
index 8795cd7..49e0d54 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -38,17 +38,18 @@ public:
 private:
 
 	GlobalData* globaldata;
-	ReadOTUFile* read;
-	InputData* input;
 	
-	string outputDir, sabundfile, rabundfile, listfile, format, path;
+	string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
 	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>&);
 };
 
 /****************************************************************************/