X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;h=44bde029e382a382fcc0b407da5d789a1f302cb7;hb=264c8a3c759d9a999c485236e98dac98d4f0db5f;hp=d59855b240442d541699970cd0d75a9ef5cde452;hpb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
index d59855b..44bde02 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -38,16 +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, 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>&);
 };
 
 /****************************************************************************/